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.

Non-recursive augmented Lagrangian algorithms for the forward and inverse dynamics of constrained flexible multibodies

NASA Technical Reports Server (NTRS)

Bayo, Eduardo; Ledesma, Ragnar

1993-01-01

A technique is presented for solving the inverse dynamics of flexible planar multibody systems. This technique yields the non-causal joint efforts (inverse dynamics) as well as the internal states (inverse kinematics) that produce a prescribed nominal trajectory of the end effector. A non-recursive global Lagrangian approach is used in formulating the equations for motion as well as in solving the inverse dynamics equations. Contrary to the recursive method previously presented, the proposed method solves the inverse problem in a systematic and direct manner for both open-chain as well as closed-chain configurations. Numerical simulation shows that the proposed procedure provides an excellent tracking of the desired end effector trajectory.

Probing Protein-Protein Interactions by Dynamic Force Correlation Spectroscopy

NASA Astrophysics Data System (ADS)

Barsegov, V.; Thirumalai, D.

2005-10-01

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

Oscillatory Dynamics of One-Dimensional Homogeneous Granular Chains

NASA Astrophysics Data System (ADS)

Starosvetsky, Yuli; Jayaprakash, K. R.; Hasan, Md. Arif; Vakakis, Alexander F.

The acoustics of the homogeneous granular chains has been studied extensively both numerically and experimentally in the references cited in the previous chapters. This chapter focuses on the oscillatory behavior of finite dimensional homogeneous granular chains. It is well known that normal vibration modes are the building blocks of the vibrations of linear systems due to the applicability of the principle of superposition. One the other hand, nonlinear theory is deprived of such a general superposition principle (although special cases of nonlinear superpositions do exist), but nonlinear normal modes ‒ NNMs still play an important role in the forced and resonance dynamics of these systems. In their basic definition [1], NNMs were defined as time-periodic nonlinear oscillations of discrete or continuous dynamical systems where all coordinates (degrees-of-freedom) oscillate in-unison with the same frequency; further extensions of this definition have been considered to account for NNMs of systems with internal resonances [2]...

Langevin Equation for DNA Dynamics

NASA Astrophysics Data System (ADS)

Grych, David; Copperman, Jeremy; Guenza, Marina

Under physiological conditions, DNA oligomers can contain well-ordered helical regions and also flexible single-stranded regions. We describe the site-specific motion of DNA with a modified Rouse-Zimm Langevin equation formalism that describes DNA as a coarse-grained polymeric chain with global structure and local flexibility. The approach has successfully described the protein dynamics in solution and has been extended to nucleic acids. Our approach provides diffusive mode analytical solutions for the dynamics of global rotational diffusion and internal motion. The internal DNA dynamics present a rich energy landscape that accounts for an interior where hydrogen bonds and base-stacking determine structure and experience limited solvent exposure. We have implemented several models incorporating different coarse-grained sites with anisotropic rotation, energy barrier crossing, and local friction coefficients that include a unique internal viscosity and our models reproduce dynamics predicted by atomistic simulations. The models reproduce bond autocorrelation along the sequence as compared to that directly calculated from atomistic molecular dynamics simulations. The Langevin equation approach captures the essence of DNA dynamics without a cumbersome atomistic representation.

Elastin: a representative ideal protein elastomer.

PubMed Central

Urry, D W; Hugel, T; Seitz, M; Gaub, H E; Sheiba, L; Dea, J; Xu, J; Parker, T

2002-01-01

During the last half century, identification of an ideal (predominantly entropic) protein elastomer was generally thought to require that the ideal protein elastomer be a random chain network. Here, we report two new sets of data and review previous data. The first set of new data utilizes atomic force microscopy to report single-chain force-extension curves for (GVGVP)(251) and (GVGIP)(260), and provides evidence for single-chain ideal elasticity. The second class of new data provides a direct contrast between low-frequency sound absorption (0.1-10 kHz) exhibited by random-chain network elastomers and by elastin protein-based polymers. Earlier composition, dielectric relaxation (1-1000 MHz), thermoelasticity, molecular mechanics and dynamics calculations and thermodynamic and statistical mechanical analyses are presented, that combine with the new data to contrast with random-chain network rubbers and to detail the presence of regular non-random structural elements of the elastin-based systems that lose entropic elastomeric force upon thermal denaturation. The data and analyses affirm an earlier contrary argument that components of elastin, the elastic protein of the mammalian elastic fibre, and purified elastin fibre itself contain dynamic, non-random, regularly repeating structures that exhibit dominantly entropic elasticity by means of a damping of internal chain dynamics on extension. PMID:11911774

Langevin Dynamics Simulations of Genome Packing in Bacteriophage

PubMed Central

Forrey, Christopher; Muthukumar, M.

2006-01-01

We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general. PMID:16617089

Langevin dynamics simulations of genome packing in bacteriophage.

PubMed

Forrey, Christopher; Muthukumar, M

2006-07-01

We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general.

Fast internal dynamics in alcohol dehydrogenase

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

Monkenbusch, M.; Stadler, A., E-mail: a.stadler@fz-juelich.de; Biehl, R.

2015-08-21

Large-scale domain motions in alcohol dehydrogenase (ADH) have been observed previously by neutron spin-echo spectroscopy (NSE). We have extended the investigation on the dynamics of ADH in solution by using high-resolution neutron time-of-flight (TOF) and neutron backscattering (BS) spectroscopy in the incoherent scattering range. The observed hydrogen dynamics were interpreted in terms of three mobility classes, which allowed a simultaneous description of the measured TOF and BS spectra. In addition to the slow global protein diffusion and domain motions observed by NSE, a fast internal process could be identified. Around one third of the protons in ADH participate in themore » fast localized diffusive motion. The diffusion coefficient of the fast internal motions is around two third of the value of the surrounding D{sub 2}O solvent. It is tempting to associate the fast internal process with solvent exposed amino acid residues with dangling side chains.« less

Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins.

PubMed

Avdoshenko, Stanislav M; Das, Atanu; Satija, Rohit; Papoian, Garegin A; Makarov, Dmitrii E

2017-03-21

A long time ago, Kuhn predicted that long polymers should approach a limit where their global motion is controlled by solvent friction alone, with ruggedness of their energy landscapes having no consequences for their dynamics. In contrast, internal friction effects are important for polymers of modest length. Internal friction in proteins, in particular, affects how fast they fold or find their binding targets and, as such, has attracted much recent attention. Here we explore the molecular origins of internal friction in unfolded proteins using atomistic simulations, coarse-grained models and analytic theory. We show that the characteristic internal friction timescale is directly proportional to the timescale of hindered dihedral rotations within the polypeptide chain, with a proportionality coefficient b that is independent of the chain length. Such chain length independence of b provides experimentally testable evidence that internal friction arises from concerted, crankshaft-like dihedral rearrangements. In accord with phenomenological models of internal friction, we find the global reconfiguration timescale of a polypeptide to be the sum of solvent friction and internal friction timescales. At the same time, the time evolution of inter-monomer distances within polypeptides deviates both from the predictions of those models and from a simple, one-dimensional diffusion model.

Feasibility analysis of system dynamics for inland maritime logistics.

DOT National Transportation Integrated Search

2014-02-01

In the last decades, a number of factors have re-shaped the shipping industry, including the growth of international trade, the emergence of new markets, and the development of multimodal supply chains. This has led maritime transportation system, wh...

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

PubMed Central

Soranno, Andrea; Buchli, Brigitte; Nettels, Daniel; Cheng, Ryan R.; Müller-Späth, Sonja; Pfeil, Shawn H.; Hoffmann, Armin; Lipman, Everett A.; Makarov, Dmitrii E.; Schuler, Benjamin

2012-01-01

Internal friction, which reflects the “roughness” of the energy landscape, plays an important role for proteins by modulating the dynamics of their folding and other conformational changes. However, the experimental quantification of internal friction and its contribution to folding dynamics has remained challenging. Here we use the combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and microfluidic mixing to determine the reconfiguration times of unfolded proteins and investigate the mechanisms of internal friction contributing to their dynamics. Using concepts from polymer dynamics, we determine internal friction with three complementary, largely independent, and consistent approaches as an additive contribution to the reconfiguration time of the unfolded state. We find that the magnitude of internal friction correlates with the compactness of the unfolded protein: its contribution dominates the reconfiguration time of approximately 100 ns of the compact unfolded state of a small cold shock protein under native conditions, but decreases for more expanded chains, and approaches zero both at high denaturant concentrations and in intrinsically disordered proteins that are expanded due to intramolecular charge repulsion. Our results suggest that internal friction in the unfolded state will be particularly relevant for the kinetics of proteins that fold in the microsecond range or faster. The low internal friction in expanded intrinsically disordered proteins may have implications for the dynamics of their interactions with cellular binding partners. PMID:22492978

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy.

PubMed

Soranno, Andrea; Buchli, Brigitte; Nettels, Daniel; Cheng, Ryan R; Müller-Späth, Sonja; Pfeil, Shawn H; Hoffmann, Armin; Lipman, Everett A; Makarov, Dmitrii E; Schuler, Benjamin

2012-10-30

Internal friction, which reflects the "roughness" of the energy landscape, plays an important role for proteins by modulating the dynamics of their folding and other conformational changes. However, the experimental quantification of internal friction and its contribution to folding dynamics has remained challenging. Here we use the combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and microfluidic mixing to determine the reconfiguration times of unfolded proteins and investigate the mechanisms of internal friction contributing to their dynamics. Using concepts from polymer dynamics, we determine internal friction with three complementary, largely independent, and consistent approaches as an additive contribution to the reconfiguration time of the unfolded state. We find that the magnitude of internal friction correlates with the compactness of the unfolded protein: its contribution dominates the reconfiguration time of approximately 100 ns of the compact unfolded state of a small cold shock protein under native conditions, but decreases for more expanded chains, and approaches zero both at high denaturant concentrations and in intrinsically disordered proteins that are expanded due to intramolecular charge repulsion. Our results suggest that internal friction in the unfolded state will be particularly relevant for the kinetics of proteins that fold in the microsecond range or faster. The low internal friction in expanded intrinsically disordered proteins may have implications for the dynamics of their interactions with cellular binding partners.

Load balancing and closed chain multiple arm control

NASA Technical Reports Server (NTRS)

Kreutz, Kenneth; Lokshin, Anatole

1988-01-01

The authors give the general dynamical equations for several rigid link manipulators rigidly grasping a commonly held rigid object. It is shown that the number of arm-configuration degrees of freedom lost due to imposing the closed-loop kinematic constraints is the same as the number of degrees of freedom gained for controlling the internal forces of the closed-chain system. This number is equal to the dimension of the kernel of the Jacobian operator which transforms contact forces to the net forces acting on the held object, and it is shown that this kernel can be identified with the subspace of controllable internal forces of the closed-chain system. Control of these forces makes it possible to regulate the grasping forces imparted to the held object or to control the load taken by each arm. It is shown that the internal forces can be influenced without affecting the control of the configuration degrees of freedom. Control laws of the feedback linearization type are shown to be useful for controlling the location and attitude of a frame fixed with respect to the held object, while simultaneously controlling the internal forces of the closed-chain system. Force feedback can be used to linearize and control the system even when the held object has unknown mass properties. If saturation effects are ignored, an unconstrained quadratic optimization can be performed to distribute the load optimally among the joint actuators.

Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations

PubMed Central

Soranno, Andrea; Holla, Andrea; Dingfelder, Fabian; Nettels, Daniel; Makarov, Dmitrii E.; Schuler, Benjamin

2017-01-01

Internal friction is an important contribution to protein dynamics at all stages along the folding reaction. Even in unfolded and intrinsically disordered proteins, internal friction has a large influence, as demonstrated with several experimental techniques and in simulations. However, these methods probe different facets of internal friction and have been applied to disparate molecular systems, raising questions regarding the compatibility of the results. To obtain an integrated view, we apply here the combination of two complementary experimental techniques, simulations, and theory to the same system: unfolded protein L. We use single-molecule Förster resonance energy transfer (FRET) to measure the global reconfiguration dynamics of the chain, and photoinduced electron transfer (PET), a contact-based method, to quantify the rate of loop formation between two residues. This combination enables us to probe unfolded-state dynamics on different length scales, corresponding to different parts of the intramolecular distance distribution. Both FRET and PET measurements show that internal friction dominates unfolded-state dynamics at low denaturant concentration, and the results are in remarkable agreement with recent large-scale molecular dynamics simulations using a new water model. The simulations indicate that intrachain interactions and dihedral angle rotation correlate with the presence of internal friction, and theoretical models of polymer dynamics provide a framework for interrelating the contribution of internal friction observed in the two types of experiments and in the simulations. The combined results thus provide a coherent and quantitative picture of internal friction in unfolded proteins that could not be attained from the individual techniques. PMID:28223518

Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations.

PubMed

Soranno, Andrea; Holla, Andrea; Dingfelder, Fabian; Nettels, Daniel; Makarov, Dmitrii E; Schuler, Benjamin

2017-03-07

Internal friction is an important contribution to protein dynamics at all stages along the folding reaction. Even in unfolded and intrinsically disordered proteins, internal friction has a large influence, as demonstrated with several experimental techniques and in simulations. However, these methods probe different facets of internal friction and have been applied to disparate molecular systems, raising questions regarding the compatibility of the results. To obtain an integrated view, we apply here the combination of two complementary experimental techniques, simulations, and theory to the same system: unfolded protein L. We use single-molecule Förster resonance energy transfer (FRET) to measure the global reconfiguration dynamics of the chain, and photoinduced electron transfer (PET), a contact-based method, to quantify the rate of loop formation between two residues. This combination enables us to probe unfolded-state dynamics on different length scales, corresponding to different parts of the intramolecular distance distribution. Both FRET and PET measurements show that internal friction dominates unfolded-state dynamics at low denaturant concentration, and the results are in remarkable agreement with recent large-scale molecular dynamics simulations using a new water model. The simulations indicate that intrachain interactions and dihedral angle rotation correlate with the presence of internal friction, and theoretical models of polymer dynamics provide a framework for interrelating the contribution of internal friction observed in the two types of experiments and in the simulations. The combined results thus provide a coherent and quantitative picture of internal friction in unfolded proteins that could not be attained from the individual techniques.

Myosin light chain kinase and Src control membrane dynamics in volume recovery from cell swelling

PubMed Central

Barfod, Elisabeth T.; Moore, Ann L.; Van de Graaf, Benjamin G.; Lidofsky, Steven D.

2011-01-01

 The expansion of the plasma membrane, which occurs during osmotic swelling of epithelia, must be retrieved for volume recovery, but the mechanisms are unknown. Here we have identified myosin light chain kinase (MLCK) as a regulator of membrane internalization in response to osmotic swelling in a model liver cell line. On hypotonic exposure, we found that there was time-dependent phosphorylation of the MLCK substrate myosin II regulatory light chain. At the sides of the cell, MLCK and myosin II localized to swelling-induced membrane blebs with actin just before retraction, and MLCK inhibition led to persistent blebbing and attenuated cell volume recovery. At the base of the cell, MLCK also localized to dynamic actin-coated rings and patches upon swelling, which were associated with uptake of the membrane marker FM4-64X, consistent with sites of membrane internalization. Hypotonic exposure evoked increased biochemical association of the cell volume regulator Src with MLCK and with the endocytosis regulators cortactin and dynamin, which colocalized within these structures. Inhibition of either Src or MLCK led to altered patch and ring lifetimes, consistent with the concept that Src and MLCK form a swelling-induced protein complex that regulates volume recovery through membrane turnover and compensatory endocytosis under osmotic stress. PMID:21209319

Subsampled Numerical Experiments as a Guide for Field Deployment of Thermistor Chains

NASA Astrophysics Data System (ADS)

Shaw, Justin; Stastna, Marek

2017-11-01

Thermistor chains are a standard tool for recording temperature profiles in geophysical flows. Density values can be inferred from readings and the resulting density field analyzed for the passage of internal waves, Kelvin-Helmholtz billows, and other dynamic events. The number and spacing of the thermistors, both on and between chains, determines which events can be identified in the dataset. We examine the effect of changing these variables by subsampling a set of numerical experiments to simulate thermistor chain locations. A pseudo spectral method was used to solve the incompressible Navier-Stokes equations under the Boussinesq approximation. The resulting flows are a set of high resolution seiches where the depth was held constant across experiments, and the length was varied. Sampling a known, commonly occurring flow with relatively simple geometry allows for a clear analysis of the effects of thermistor placement in the capture of dynamic events. We will discuss three dimensional deployment strategies, as well as EOF and DMD analyses if there is time. Funded by a Grant from the National Sciences and Engineering Research Council of Canada.

Granular dynamics during impact.

PubMed

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

2014-06-06

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

Improving Markov Chain Models for Road Profiles Simulation via Definition of States

DTIC Science & Technology

2012-04-01

wavelet transform in pavement profile analysis," Vehicle System Dynamics: International Journal of Vehicle Mechanics and Mobility, vol. 47, no. 4...34Estimating Markov Transition Probabilities from Micro -Unit Data," Journal of the Royal Statistical Society. Series C (Applied Statistics), pp. 355-371

Forced unfolding of single-chain polymeric nanoparticles.

PubMed

Hosono, Nobuhiko; Kushner, Aaron M; Chung, Jaeyoon; Palmans, Anja R A; Guan, Zhibin; Meijer, E W

2015-06-03

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is applied to single-chain polymeric nanoparticles (SCPNs) to acquire information about the internal folding structure of SCPNs and inherent kinetic parameters of supramolecular self-assembling motifs embedded into the SCPNs. The SCPNs used here are polyacrylate-based polymers carrying 2-ureido-4-[1H]-pyrimidinone (UPy) or benzene-1,3,5-tricarboxamide (BTA) pendants that induce an intramolecular chain collapse into nanoparticles consisting of one polymer chain only via internal supramolecular cross-linking. The SCPN is stretched by an AFM cantilever to unfold mechanically, which allows measuring of force-extension profiles of the SCPNs. Consecutive peaks observed in the force profiles are attributed to rupture events of self-assembled UPy/BTA units in the SCPNs. The force profiles have been analyzed statistically for a series of polymers with different UPy/BTA incorporation densities. The results provide insights into the internal conformation of SCPNs, where the folding structure can be changed with the incorporation density of UPy/BTA. In addition, dynamic loading rate analysis allows the determination of kinetic parameters of BTA self-assembly, which has not been accessible by any other method. This study offers a rational tool for understanding the folding structure, kinetics, and pathway of two series of SCPNs.

International ring trial for the validation of an event-specific Golden Rice 2 quantitative real-time polymerase chain reaction method.

PubMed

Jacchia, Sara; Nardini, Elena; Bassani, Niccolò; Savini, Christian; Shim, Jung-Hyun; Trijatmiko, Kurniawan; Kreysa, Joachim; Mazzara, Marco

2015-05-27

This article describes the international validation of the quantitative real-time polymerase chain reaction (PCR) detection method for Golden Rice 2. The method consists of a taxon-specific assay amplifying a fragment of rice Phospholipase D α2 gene, and an event-specific assay designed on the 3' junction between transgenic insert and plant DNA. We validated the two assays independently, with absolute quantification, and in combination, with relative quantification, on DNA samples prepared in haploid genome equivalents. We assessed trueness, precision, efficiency, and linearity of the two assays, and the results demonstrate that both the assays independently assessed and the entire method fulfill European and international requirements for methods for genetically modified organism (GMO) testing, within the dynamic range tested. The homogeneity of the results of the collaborative trial between Europe and Asia is a good indicator of the robustness of the method.

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

PubMed

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

2013-02-21

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

Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins.

PubMed

Mercadante, Davide; Wagner, Johannes A; Aramburu, Iker V; Lemke, Edward A; Gräter, Frauke

2017-09-12

Molecular dynamics (MD) simulations have valuably complemented experiments describing the dynamics of intrinsically disordered proteins (IDPs), particularly since the proposal of models to solve the artificial collapse of IDPs in silico. Such models suggest redefining nonbonded interactions, by either increasing water dispersion forces or adopting the Kirkwood-Buff force field. These approaches yield extended conformers that better comply with experiments, but it is unclear if they all sample the same intrachain dynamics of IDPs. We have tested this by employing MD simulations and single-molecule Förster resonance energy transfer spectroscopy to sample the dimensions of systems with different sequence compositions, namely strong and weak polyelectrolytes. For strong polyelectrolytes in which charge effects dominate, all the proposed solutions equally reproduce the expected ensemble's dimensions. For weak polyelectrolytes, at lower cutoffs, force fields abnormally alter intrachain dynamics, overestimating excluded volume over chain flexibility or reporting no difference between the dynamics of different chains. The TIP4PD water model alone can reproduce experimentally observed changes in extensions (dimensions), but not quantitatively and with only weak statistical significance. Force field limitations are reversed with increased interaction cutoffs, showing that chain dynamics are critically defined by the presence of long-range interactions. Force field analysis aside, our study provides the first insights into how long-range interactions critically define IDP dimensions and raises the question of which length range is crucial to correctly sample the overall dimensions and internal dynamics of the large group of weakly charged yet highly polar IDPs.

Interaction of arginine, lysine, and guanidine with surface residues of lysozyme: implication to protein stability.

PubMed

Shah, Dhawal; Shaikh, Abdul Rajjak

2016-01-01

Additives are widely used to suppress aggregation of therapeutic proteins. However, the molecular mechanisms of effect of additives to stabilize proteins are still unclear. To understand this, we herein perform molecular dynamics simulations of lysozyme in the presence of three commonly used additives: arginine, lysine, and guanidine. These additives have different effects on stability of proteins and have different structures with some similarities; arginine and lysine have aliphatic side chain, while arginine has a guanidinium group. We analyze atomic contact frequencies to study the interactions of the additives with individual residues of lysozyme. Contact coefficient, quantified from contact frequencies, is helpful in analyzing the interactions with the guanidine groups as well as aliphatic side chains of arginine and lysine. Strong preference for contacts to the additives (over water) is seen for the acidic followed by polar and the aromatic residues. Further analysis suggests that the hydration layer around the protein surface is depleted more in the presence of arginine, followed by lysine and guanidine. Molecular dynamics simulations also reveal that the internal dynamics of protein, as indicated by the lifetimes of the hydrogen bonds within the protein, changes depending on the additives. Particularly, we note that the side-chain hydrogen-bonding patterns within the protein differ with the additives, with several side-chain hydrogen bonds missing in the presence of guanidine. These results collectively indicate that the aliphatic chain of arginine and lysine plays a critical role in the stabilization of the protein.

Dynamics of Single Chains of Suspended Ferrofluid Particles

NASA Technical Reports Server (NTRS)

Cutillas, S.; Liu, J.

1999-01-01

We present an experimental study of the dynamics of isolated chains made of super-paramagnetic particles under the influence of a magnetic field. The motivation of this work is to understand if the chain fluctuations exist and, if it does, how does the fluctuation affect chain aggregation. We find that single chains strongly fluctuate and that the characteristic frequency of their fluctuations is inversely proportional to the magnetic field strength. The higher the field the lower the characteristic frequency of the chain fluctuations. In the high magnetic field limit, chains behave like rigid rods without any internal motions. In this work, we used ferrofluid particles suspended in water. These particles do not have any intrinsic magnetization. Once a magnetic field is applied, a dipole moment is induced in each particle, proportional to the magnetic field. A dipolar magnetic interaction then occurs between particles. If dipole-dipole magnetic energy is higher than the thermal energy, the result is a structure change inside the dipolar fluid. The ratio of these two energies is expressed by a coupling constant lambda as: lambda = (pi(a(exp 3))(chi(exp 2))(mu(sub 0))(H(sub 0))(exp 2))/18kT Where a is the particle radius, mu(sub 0) is the vacuum magnetic permeability, H(sub 0) the applied magnetic field, k the Boltzmann constant and T the absolute temperature. If lambda > 1, magnetic particles form chains along the field direction. The lateral coalescence of several chains may form bigger aggregates especially if the particle volume fraction is high. While many studies and applications deal with the rheological properties and the structural changes of these dipolar fluids, this work focuses on the understanding of the chain dynamics. In order to probe the chain dynamics, we used dynamic light scattering (DLS) in self-beating mode as our experimental technique. The experimental geometry is such that the scattering plane is perpendicular to the magnetic field. Therefore, only motions in this plane are probed. A very dilute sample of a ferrofluid emulsion with a particle volume fraction of 10(exp -5) is used in this experiment. We chose such a low volume fraction to avoid multiple light scattering as well as lateral chain-chain aggregation. DLS measures the dynamic structure factor S(q,t) of the sample (q is the scattering wave vector, t is the time). In the absence of the magnetic field, identical particles of ferrofluid droplets are randomly distributed and S(q,t) reduces to exp(-q(exp 2)2D(sub 0)t). D(sub 0)=(kT/(6(pi)(eta)(a)) is the diffusion coefficient of Brownian particles (where Xi = (6(pi)(eta)(a)) is the Stokes frictional coefficient of a spherical particle in a fluid of viscosity eta). If interactions or polydispersity can not be ignored, an effective diffusion coefficient is introduced. Formally, D(sub eff) is defined as: D(sub eff) = - q(exp -2) partial derivative of (ln(S(q,t)) with respect to time, as t goes to 0. D(sub eff) reduces to D(sub 0) if no interactions and only a few particles size are present. Therefore, we can use DLS to measure particle size. The particle radius was found to be a=0.23 mu m with 7% of polydispersity. In this case, if we vary the scattering angle theta (and so q) we do not have any change in the measured diffusion coefficient: it is q-independent. When a magnetic field is applied, particles aggregate into chains if lambda > 1. We first studied the kinetics of the chain formation when lambda = 406. At a fixed scattering angle, we measured diffusion coefficient D(sub eff) as a function of time. Experimentally, we find that D(sub eff) decreases monotonously with time. Physically, this means that chains are becoming longer and longer. Since we are only sensitive to motions in the scattering plane and since chains have their main axis perpendicular to this plane, the measured diffusion coefficient is the trans-verse diffusion coefficient. We can relate D(sub eff) to the mean number of particles per chain N(t) at a given time and to the diffusion coefficient of an isolated particle D(sub 0) as D(sub eff)=f(N(t))D(sub 0). Since f(N) is known from other recent work, N can be expressed as a function of the time. We found a square root dependency: N(t) proportional to the square root of t. As expected for very low volume fraction, this behavior is characteristic of a diffusion-limited aggregation as suggested by several authors and by our previous work. In this study, we focus on the dependence of the effective diffusion coefficient on the scattering angle and the magnetic field strength. After the magnetic field is applied (lambda = 406) for a long time, typically 6 hours, kinetics of chain formation becomes very slow. Chain size does not vary much over the next hour period. Thus, we can perform different interesting experiments. First, at a fixed magnetic field, we measure the effective diffusion coefficient as a function of the scattering angle (from 5 to 130 deg). Our results show that the measured diffusion coefficient increases linearly with the scattering angle: D(sub eff) proportional to q. If we do the same experiment for different lambda values, D(sub eff) depends on lambda as D(sub eff) proportional to lambda(exp -1/2). We also find for different lambda values that the same asymptotic D(sub eff) value is obtained when q approaches zero. The angle dependency of D(sub eff) suggests that an additional motion exists besides chain drifting. Chain size is constant during experiment, which was verified by measuring the same diffusion coefficient at the beginning and at the end of the angle switching. If chains are rigid, D(sub eff) is independent of q. Therefore, we found that D(sub eff) not only measures the motion of the entire chain but also its internal fluctuations. These internal motions are the fluctuations of the particles in the chain. To understand the q dependency of D(sub eff), let us look at the probing length used. In our study, the characteristic length scale probed is l=2pi/q which is in the range of 0.9

Unit and internal chain profiles of maca amylopectin.

PubMed

Zhang, Ling; Li, Guantian; Yao, Weirong; Zhu, Fan

2018-03-01

Unit chain length distributions of amylopectin and its φ, β-limit dextrins, which reflect amylopectin internal structure from three maca starches, were determined by high-performance anion-exchange chromatography with pulsed amperometric detection after debranching, and the samples were compared with maize starch. The amylopectins exhibited average chain lengths ranging from 16.72 to 17.16, with ranges of total internal chain length, external chain length, and internal chain length of the maca amylopectins at 12.49 to 13.68, 11.24 to 11.89, and 4.27 to 4.48. The average chain length, external chain length, internal chain length, and total internal chain length were comparable in three maca amylopectins. Amylopectins of the three maca genotypes studied here presented no significant differences in their unit chain length profiles, but did show significant differences in their internal chain profiles. Additional genetic variations between different maca genotypes need to be studied to provide unit- and internal chain profiles of maca amylopectin. Copyright © 2017. Published by Elsevier Ltd.

Conformational Dynamics of Insulin

PubMed Central

Hua, Qing-Xin; Jia, Wenhua; Weiss, Michael A.

2011-01-01

We have exploited a prandial insulin analog to elucidate the underlying structure and dynamics of insulin as a monomer in solution. A model was provided by insulin lispro (the active component of Humalog®; Eli Lilly and Co.). Whereas NMR-based modeling recapitulated structural relationships of insulin crystals (T-state protomers), dynamic anomalies were revealed by amide-proton exchange kinetics in D2O. Surprisingly, the majority of hydrogen bonds observed in crystal structures are only transiently maintained in solution, including key T-state-specific inter-chain contacts. Long-lived hydrogen bonds (as defined by global exchange kinetics) exist only at a subset of four α-helical sites (two per chain) flanking an internal disulfide bridge (cystine A20–B19); these sites map within the proposed folding nucleus of proinsulin. The anomalous flexibility of insulin otherwise spans its active surface and may facilitate receptor binding. Because conformational fluctuations promote the degradation of pharmaceutical formulations, we envisage that “dynamic re-engineering” of insulin may enable design of ultra-stable formulations for humanitarian use in the developing world. PMID:22649374

Phase sensitive molecular dynamics of self-assembly glycolipid thin films: A dielectric spectroscopy investigation

NASA Astrophysics Data System (ADS)

Velayutham, T. S.; Ng, B. K.; Gan, W. C.; Majid, W. H. Abd.; Hashim, R.; Zahid, N. I.; Chaiprapa, Jitrin

2014-08-01

Glycolipid, found commonly in membranes, is also a liquid crystal material which can self-assemble without the presence of a solvent. Here, the dielectric and conductivity properties of three synthetic glycolipid thin films in different thermotropic liquid crystal phases were investigated over a frequency and temperature range of (10-2-106 Hz) and (303-463 K), respectively. The observed relaxation processes distinguish between the different phases (smectic A, columnar/hexagonal, and bicontinuous cubic Q) and the glycolipid molecular structures. Large dielectric responses were observed in the columnar and bicontinuous cubic phases of the longer branched alkyl chain glycolipids. Glycolipids with the shortest branched alkyl chain experience the most restricted self-assembly dynamic process over the broad temperature range studied compared to the longer ones. A high frequency dielectric absorption (Process I) was observed in all samples. This is related to the dynamics of the hydrogen bond network from the sugar group. An additional low-frequency mechanism (Process II) with a large dielectric strength was observed due to the internal dynamics of the self-assembly organization. Phase sensitive domain heterogeneity in the bicontinuous cubic phase was related to the diffusion of charge carriers. The microscopic features of charge hopping were modelled using the random walk scheme, and two charge carrier hopping lengths were estimated for two glycolipid systems. For Process I, the hopping length is comparable to the hydrogen bond and is related to the dynamics of the hydrogen bond network. Additionally, that for Process II is comparable to the bilayer spacing, hence confirming that this low-frequency mechanism is associated with the internal dynamics within the phase.

Transportation and dynamic networks: Models, theory, and applications to supply chains, electric power, and financial networks

NASA Astrophysics Data System (ADS)

Liu, Zugang

Network systems, including transportation and logistic systems, electric power generation and distribution networks as well as financial networks, provide the critical infrastructure for the functioning of our societies and economies. The understanding of the dynamic behavior of such systems is also crucial to national security and prosperity. The identification of new connections between distinct network systems is the inspiration for the research in this dissertation. In particular, I answer two questions raised by Beckmann, McGuire, and Winsten (1956) and Copeland (1952) over half a century ago, which are, respectively, how are electric power flows related to transportation flows and does money flow like water or electricity? In addition, in this dissertation, I achieve the following: (1) I establish the relationships between transportation networks and three other classes of complex network systems: supply chain networks, electric power generation and transmission networks, and financial networks with intermediation. The establishment of such connections provides novel theoretical insights as well as new pricing mechanisms, and efficient computational methods. (2) I develop new modeling frameworks based on evolutionary variational inequality theory that capture the dynamics of such network systems in terms of the time-varying flows and incurred costs, prices, and, where applicable, profits. This dissertation studies the dynamics of such network systems by addressing both internal competition and/or cooperation, and external changes, such as varying costs and demands. (3) I focus, in depth, on electric power supply chains. By exploiting the relationships between transportation networks and electric power supply chains, I develop a large-scale network model that integrates electric power supply chains and fuel supply markets. The model captures both the economic transactions as well as the physical transmission constraints. The model is then applied to the New England electric power supply chain consisting of 6 states, 5 fuel types, 82 power generators, with a total of 573 generating units, and 10 demand markets. The empirical case study demonstrates that the regional electricity prices simulated by the model match very well the actual electricity prices in New England. I also utilize the model to study interactions between electric power supply chains and energy fuel markets.

Internalization and vacuolar targeting of the brassinosteroid hormone receptor BRI1 are regulated by ubiquitination.

PubMed

Martins, Sara; Dohmann, Esther M N; Cayrel, Anne; Johnson, Alexander; Fischer, Wolfgang; Pojer, Florence; Satiat-Jeunemaître, Béatrice; Jaillais, Yvon; Chory, Joanne; Geldner, Niko; Vert, Grégory

2015-01-21

Brassinosteroids are plant steroid hormones that control many aspects of plant growth and development, and are perceived at the cell surface by the plasma membrane-localized receptor kinase BRI1. Here we show that BRI1 is post-translationally modified by K63 polyubiquitin chains in vivo. Using both artificial ubiquitination of BRI1 and generation of an ubiquitination-defective BRI1 mutant form, we demonstrate that ubiquitination promotes BRI1 internalization from the cell surface and is essential for its recognition at the trans-Golgi network/early endosomes (TGN/EE) for vacuolar targeting. Finally, we demonstrate that the control of BRI1 protein dynamics by ubiquitination is an important control mechanism for brassinosteroid responses in plants. Altogether, our results identify ubiquitination and K63-linked polyubiquitin chain formation as a dual targeting signal for BRI1 internalization and sorting along the endocytic pathway, and highlight its role in hormonally controlled plant development.

Polymer scaling and dynamics in steady-state sedimentation at infinite Péclet number.

PubMed

Lehtola, V; Punkkinen, O; Ala-Nissila, T

2007-11-01

We consider the static and dynamical behavior of a flexible polymer chain under steady-state sedimentation using analytic arguments and computer simulations. The model system comprises a single coarse-grained polymer chain of N segments, which resides in a Newtonian fluid as described by the Navier-Stokes equations. The chain is driven into nonequilibrium steady state by gravity acting on each segment. The equations of motion for the segments and the Navier-Stokes equations are solved simultaneously using an immersed boundary method, where thermal fluctuations are neglected. To characterize the chain conformation, we consider its radius of gyration RG(N). We find that the presence of gravity explicitly breaks the spatial symmetry leading to anisotropic scaling of the components of RG with N along the direction of gravity RG, parallel and perpendicular to it RG, perpendicular, respectively. We numerically estimate the corresponding anisotropic scaling exponents nu parallel approximately 0.79 and nu perpendicular approximately 0.45, which differ significantly from the equilibrium scaling exponent nue=0.588 in three dimensions. This indicates that on the average, the chain becomes elongated along the sedimentation direction for large enough N. We present a generalization of the Flory scaling argument, which is in good agreement with the numerical results. It also reveals an explicit dependence of the scaling exponents on the Reynolds number. To study the dynamics of the chain, we compute its effective diffusion coefficient D(N), which does not contain Brownian motion. For the range of values of N used here, we find that both the parallel and perpendicular components of D increase with the chain length N, in contrast to the case of thermal diffusion in equilibrium. This is caused by the fluid-driven fluctuations in the internal configuration of the polymer that are magnified as polymer size becomes larger.

Topological structure and mechanics of glassy polymer networks.

PubMed

Elder, Robert M; Sirk, Timothy W

2017-11-22

The influence of chain-level network architecture (i.e., topology) on mechanics was explored for unentangled polymer networks using a blend of coarse-grained molecular simulations and graph-theoretic concepts. A simple extension of the Watts-Strogatz model is proposed to control the graph properties of the network such that the corresponding physical properties can be studied with simulations. The architecture of polymer networks assembled with a dynamic curing approach were compared with the extended Watts-Strogatz model, and found to agree surprisingly well. The final cured structures of the dynamically-assembled networks were nearly an intermediate between lattice and random connections due to restrictions imposed by the finite length of the chains. Further, the uni-axial stress response, character of the bond breaking, and non-affine displacements of fully-cured glassy networks were analyzed as a function of the degree of disorder in the network architecture. It is shown that the architecture strongly affects the network stability, flow stress, onset of bond breaking, and ultimate stress while leaving the modulus and yield point nearly unchanged. The results show that internal restrictions imposed by the network architecture alter the chain-level response through changes to the crosslink dynamics in the flow regime and through the degree of coordinated chain failure at the ultimate stress. The properties considered here are shown to be sensitive to even incremental changes to the architecture and, therefore, the overall network architecture, beyond simple defects, is predicted to be a meaningful physical parameter in the mechanics of glassy polymer networks.

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

Efficient dynamic simulation for multiple chain robotic mechanisms

NASA Technical Reports Server (NTRS)

Lilly, Kathryn W.; Orin, David E.

1989-01-01

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

Vulnerability of networks of interacting Markov chains.

PubMed

Kocarev, L; Zlatanov, N; Trajanov, D

2010-05-13

The concept of vulnerability is introduced for a model of random, dynamical interactions on networks. In this model, known as the influence model, the nodes are arranged in an arbitrary network, while the evolution of the status at a node is according to an internal Markov chain, but with transition probabilities that depend not only on the current status of that node but also on the statuses of the neighbouring nodes. Vulnerability is treated analytically and numerically for several networks with different topological structures, as well as for two real networks--the network of infrastructures and the EU power grid--identifying the most vulnerable nodes of these networks.

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.

Polymer Chain Conformation and Dynamical Confinement in a Model One-Component Nanocomposite

NASA Astrophysics Data System (ADS)

Mark, C.; Holderer, O.; Allgaier, J.; Hübner, E.; Pyckhout-Hintzen, W.; Zamponi, M.; Radulescu, A.; Feoktystov, A.; Monkenbusch, M.; Jalarvo, N.; Richter, D.

2017-07-01

We report a neutron-scattering investigation on the structure and dynamics of a single-component nanocomposite based on SiO2 particles that were grafted with polyisoprene chains at the entanglement limit. By skillful labeling, we access both the monomer density in the corona as well as the conformation of the grafted chains. While the corona profile follows a r-1 power law, the conformation of a grafted chain is identical to that of a chain in a reference melt, implying a high mutual penetration of the coronas from different particles. The brush crowding leads to topological confinement of the chain dynamics: (i) At local scales, the segmental dynamics is unchanged compared to the reference melt, while (ii) at the scale of the chain, the dynamics appears to be slowed down; (iii) by performing a mode analysis in terms of end-fixed Rouse chains, the slower dynamics is tracked to topological confinement within the cone spanned by the adjacent grafts; (iv) by adding 50% matrix chains, the topological confinement sensed by the grafted chain is lifted partially and the apparent chain motion is accelerated. We observe a crossover from pure Rouse motion at short times to topological confined motion beyond the time when the segmental mean squared displacement has reached the distance to the next graft.

Self-consistent Simulation of Microparticle and Ion Wakefield Configuration

NASA Astrophysics Data System (ADS)

Sanford, Dustin; Brooks, Beau; Ellis, Naoki; Matthews, Lorin; Hyde, Truell

2017-10-01

In a complex plasma, positively charged ions often have a directed flow with respect to the negatively charged dust grains. The resulting interaction between the dust and the flowing plasma creates an ion wakefield downstream from the dust particles, with the resulting positive space region modifying the interaction between the grains and contributing to the observed dynamics and equilibrium structure of the system. Here we present a proof of concept method that uses a molecular dynamics simulation to model the ion wakefield allowing the dynamics of the dust particles to be determined self-consistently. The trajectory of each ion is calculated including the forces from all other ions, which are treated as ``Yukawa particles'' and shielded from thermal electrons and the forces of the charged dust particles. Both the dust grain charge and the wakefield structure are also self-consistently determined for various particle configurations. The resultant wakefield potentials are then used to provide dynamic simulations of dust particle pairs. These results will be employed to analyze the formation and dynamics of field-aligned chains in CASPER's PK4 experiment onboard the International Space Station, allowing examination of extended dust chains without the masking force of gravity. This work was supported by the National Science Foundation under Grants PHY-1414523 and PHY-1740203.

Loschmidt echo as a robust decoherence quantifier for many-body systems

NASA Astrophysics Data System (ADS)

Zangara, Pablo R.; Dente, Axel D.; Levstein, Patricia R.; Pastawski, Horacio M.

2012-07-01

We employ the Loschmidt echo, i.e., the signal recovered after the reversal of an evolution, to identify and quantify the processes contributing to decoherence. This procedure, which has been extensively used in single-particle physics, is employed here in a spin ladder. The isolated chains have 1/2 spins with XY interaction and their excitations would sustain a one-body-like propagation. One of them constitutes the controlled system S whose reversible dynamics is degraded by the weak coupling with the uncontrolled second chain, i.e., the environment E. The perturbative SE coupling is swept through arbitrary combinations of XY and Ising-like interactions, that contain the standard Heisenberg and dipolar ones. Different time regimes are identified for the Loschmidt echo dynamics in this perturbative configuration. In particular, the exponential decay scales as a Fermi golden rule, where the contributions of the different SE terms are individually evaluated and analyzed. Comparisons with previous analytical and numerical evaluations of decoherence based on the attenuation of specific interferences show that the Loschmidt echo is an advantageous decoherence quantifier at any time, regardless of the S internal dynamics.

Antibody to ricin a chain hinders intracellular routing of toxin and protects cells even after toxin has been internalized.

PubMed

Song, Kejing; Mize, R Ranney; Marrero, Luis; Corti, Miriam; Kirk, Jason M; Pincus, Seth H

2013-01-01

Mechanisms of antibody-mediated neutralization are of much interest. For plant and bacterial A-B toxins, A chain mediates toxicity and B chain binds target cells. It is generally accepted and taught that antibody (Ab) neutralizes by preventing toxin binding to cells. Yet for some toxins, ricin included, anti-A chain Abs afford greater protection than anti-B. The mechanism(s) whereby Abs to the A chain neutralize toxins are not understood. We use quantitative confocal imaging, neutralization assays, and other techniques to study how anti-A chain Abs function to protect cells. Without Ab, ricin enters cells and penetrates to the endoplasmic reticulum within 15 min. Within 45-60 min, ricin entering and being expelled from cells reaches equilibrium. These results are consistent with previous observations, and support the validity of our novel methodology. The addition of neutralizing Ab causes ricin accumulation at the cell surface, delays internalization, and postpones retrograde transport of ricin. Ab binds ricin for >6hr as they traffic together through the cell. Ab protects cells even when administered hours after exposure. CONCLUSIONS/KEY FINDINGS: We demonstrate the dynamic nature of the interaction between the host cell and toxin, and how Ab can alter the balance in favor of the cell. Ab blocks ricin's entry into cells, hinders its intracellular routing, and can protect even after ricin is present in the target organelle, providing evidence that the major site of neutralization is intracellular. These data add toxins to the list of pathogenic agents that can be neutralized intracellularly and explain the in vivo efficacy of delayed administration of anti-toxin Abs. The results encourage the use of post-exposure passive Ab therapy, and show the importance of the A chain as a target of Abs.

System Dynamics Modeling for Supply Chain Information Sharing

NASA Astrophysics Data System (ADS)

Feng, Yang

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

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

Iodine binding to explore the conformational state of internal chains of amylopectin.

PubMed

Shen, Xinyu; Bertoft, Eric; Zhang, Genyi; Hamaker, Bruce R

2013-10-15

Previous studies have found that the proportion of long chains of amylopectin correlates to its functional and nutritional properties. As a possible explanation of this correlation, the iodine binding property of amylopectin internal chains was investigated as an indirect evidence of their ability to form helices for intra- or inter-molecular interactions. Waxy and amylose-extender waxy corn starches were hydrolyzed by β-amylase for varying periods of time to incrementally remove the external chains, and the absorbance and the wavelength of maximum absorbance of iodine binding were examined. Experimental results suggest that iodine can bind with both external and internal chains; a significant amount of absorption comes from the latter, as stepwise removal of external chains only somewhat reduced absorption. Internal amylopectin chains, thus, were concluded to likely pre-exist in helical form, as opposed to a conformational change into helices facilitating iodine binding in the absence of external chains. Such internal chain helical structures possibly drive intermolecular interactions that would explain why amylopectin with high proportion of internal chains form harder gels, create pastes less prone to shear breakdown, and are more slowly digesting. Copyright © 2013 Elsevier Ltd. All rights reserved.

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures

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

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003)] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here in this paper, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013)] tomore » obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S = 1/2, we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.« less

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures

DOE PAGES

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio; ...

2018-04-20

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003)] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here in this paper, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013)] tomore » obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S = 1/2, we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.« less

A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation

NASA Astrophysics Data System (ADS)

Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.

2016-02-01

Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics—like sequences of amino acids or even an entire protein—are poorly modelled by invariable particles. We develop a highly coarse grained polymorph patchy particle with the ultimate aim of simulating proteins as chains of particles at the secondary structure level. Conformational changes, e.g., a transition between disordered and β-sheet states, are accommodated by internal coordinates that determine the shape and interaction characteristics of the particles. The internal coordinates, as well as the particle positions and orientations, are propagated by Brownian Dynamics in response to their local environment. As an example of the potential offered by polymorph particles, we model the amyloidogenic intrinsically disordered protein α-synuclein, involved in Parkinson's disease, as a single particle with two internal states. The simulations yield oligomers of particles in the disordered state and fibrils of particles in the "misfolded" cross-β-sheet state. The aggregation dynamics is complex, as aggregates can form by a direct nucleation-and-growth mechanism and by two-step-nucleation through conversions between the two cluster types. The aggregation dynamics is complex, with fibrils formed by direct nucleation-and-growth, by two-step-nucleation through the conversion of an oligomer and by auto-catalysis of this conversion.

Using Adobe Flash animations of electron transport chain to teach and learn biochemistry.

PubMed

Teplá, Milada; Klímová, Helena

2015-01-01

Teaching the subject of the electron transport chain is one of the most challenging aspects of the chemistry curriculum at the high school level. This article presents an educational program called "Electron Transport Chain" which consists of 14 visual animations including a biochemistry quiz. The program was created in the Adobe Flash CS3 Professional animation program and is designed for high school chemistry students. Our goal is to develop educational materials that facilitate the comprehension of this complex subject through dynamic animations which show the course of the electron transport chain and simultaneously explain its nature. We record the process of the electron transport chain, including connections with oxidative phosphorylation, in such a way as to minimize the occurrence of discrepancies in interpretation. The educational program was evaluated in high schools through the administration of a questionnaire, which contained 12 opened-ended items and which required participants to evaluate the graphics of the animations, chemical content, student preferences, and its suitability for high school biochemistry teaching. © 2015 The International Union of Biochemistry and Molecular Biology.

How thermal stress alters the confinement of polymers vitrificated in nanopores

NASA Astrophysics Data System (ADS)

Teng, Chao; Li, Linling; Wang, Yong; Wang, Rong; Chen, Wei; Wang, Xiaoliang; Xue, Gi

2017-05-01

Understanding and controlling the glass transition temperature (Tg) and dynamics of polymers in confined geometries are of significance in both academia and industry. Here, we investigate how the thermal stress induced by a mismatch in the coefficient of thermal expansion affects the Tg behavior of polystyrene (PS) nanorods located inside cylindrical alumina nanopores. The size effects and molecular weight dependence of the Tg are also studied. A multi-step relaxation process was employed to study the relationship between thermal stress and cooling rate. At fast cooling rates, the imparted thermal stress would overcome the yield stress of PS and peel chains off the pore walls, while at slow cooling rates, chains are kept in contact with the pore walls due to timely dissipation of the produced thermal stress during vitrification. In smaller nanopores, more PS chains closely contact with pore walls, then stronger internal thermal stress would be generated between core and shell of PS nanorod, which results in a larger deviation between two Tgs. The core part of PS shows lower Tg than bulk value, which can induce faster dynamics in the center region. A complex and important role stress plays is supposed in complex confinement condition, e.g., in nanopores, during vitrification.

Measures of International Manufacturing and Trade of Clean Energy Technologies

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

Engel-Cox, Jill; Sandor, Debbie; Keyser, David

The technologies that produce clean energy, such as solar photovoltaic panels and lithium ion batteries for electric vehicles, are globally manufactured and traded. As demand and deployment of these technologies grows exponentially, the innovation to reach significant economies of scale and drive down energy production costs becomes less in the technology and more in the manufacturing of the technology. Manufacturing innovations and other manufacturing decisions can reduce costs of labor, materials, equipment, operating costs, and transportation, across all the links in the supply chain. To better understand the manufacturing aspect of the clean energy economy, we have developed key metricsmore » for systematically measuring and benchmarking international manufacturing of clean energy technologies. The metrics are: trade, market size, manufacturing value-added, and manufacturing capacity and production. These metrics were applied to twelve global economies and four representative technologies: wind turbine components, crystalline silicon solar photovoltaic modules, vehicle lithium ion battery cells, and light emitting diode packages for efficient lighting and other consumer products. The results indicated that clean energy technologies are being developed via complex, dynamic, and global supply chains, with individual economies benefiting from different technologies and links in the supply chain, through both domestic manufacturing and global trade.« less

Chain Conformation and Dynamics in Spin-Assisted Weak Polyelectrolyte Multilayers

DOE PAGES

Zhuk, Aliaksandr; Selin, Victor; Zhuk, Iryna; ...

2015-03-13

In this paper, we report on the effect of the deposition technique on film layering, stability, and chain mobility in weak polyelectrolyte layer-by-layer (LbL) films. Ellipsometry and neutron reflectometry (NR) showed that shear forces arising during spin-assisted assembly lead to smaller amounts of adsorbed polyelectrolytes within LbL films, result in a higher degree of internal film order, and dramatically improve stability of assemblies in salt solutions as compared to dip-assisted LbL assemblies. The underlying flattening of polyelectrolyte chains in spin-assisted LbL films was also revealed as an increase in ionization degree of the assembled weak polyelectrolytes. As demonstrated by fluorescencemore » recovery after photobleaching (FRAP), strong binding between spin-deposited polyelectrolytes results in a significant slowdown of chain diffusion in salt solutions as compared to dip-deposited films. Moreover, salt-induced chain intermixing in the direction perpendicular to the substrate is largely inhibited in spin-deposited films, resulting in only subdiffusional (<2 Å) chain displacements even after 200 h exposure to 1 M NaCl solutions. Finally, this persistence of polyelectrolyte layering has important ramifications for multistage drug delivery and optical applications of LbL assemblies.« 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.

Self Diffusion in Nano Filled Polymer Melts: a Molecular Dynamics Simulation Study

NASA Astrophysics Data System (ADS)

Desai, Tapan; Keblinski, Pawel

2003-03-01

SELF DIFFUSION IN NANO FILLED POLYMER MELTS: A MOLECULAR DYNAMICS SIMULATION STUDY* T. G. Desai,P. Keblinski, Material Science and Engineering Department, Rensselaer Polytechnic Institute, Troy, NY. Using molecular dynamics simulations, we studied the dynamics of the polymeric systems containing immobile and analytically smooth spherical nanoparticles. Each chain consisted of N monomers connected by an anharmonic springs described by the finite extendible nonlinear elastic, FENE potential. The system comprises of 3nanoparticles and the rest by freely rotating but not overlapping chains. The longest chain studied has a Radius of gyration equal to particle size radius and comparable to inter-particle distance. There is no effect on the structural characteristics such as Radius of gyration or end to end distance due to the nanoparticles. Diffusion of polymeric chains is not affected by the presence of either attractive or repulsive nanoparticles. In all cases Rouse dynamics is observed for short chains with a crossover to reptation dynamics for longer chains.

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.

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.

Simulation study of the initial crystallization processes of poly(3-hexylthiophene) in solution: ordering dynamics of main chains and side chains.

PubMed

Takizawa, Yuumi; Shimomura, Takeshi; Miura, Toshiaki

2013-05-23

We study the initial nucleation dynamics of poly(3-hexylthiophene) (P3HT) in solution, focusing on the relationship between the ordering process of main chains and that of side chains. We carried out Langevin dynamics simulation and found that the initial nucleation processes consist of three steps: the ordering of ring orientation, the ordering of main-chain vectors, and the ordering of side chains. At the start, the normal vectors of thiophene rings aligned in a very short time, followed by alignment of main-chain end-to-end vectors. The flexible side-chain ordering took almost 5 times longer than the rigid-main-chain ordering. The simulation results indicated that the ordering of side chains was induced after the formation of the regular stack structure of main chains. This slow ordering dynamics of flexible side chains is one of the factors that cause anisotropic nuclei growth, which would be closely related to the formation of nanofiber structures without external flow field. Our simulation results revealed how the combined structure of the planar and rigid-main-chain backbones and the sparse flexible side chains lead to specific ordering behaviors that are not observed in ordinary linear polymer crystallization processes.

Quantum decision-maker theory and simulation

NASA Astrophysics Data System (ADS)

Zak, Michail; Meyers, Ronald E.; Deacon, Keith S.

2000-07-01

A quantum device simulating the human decision making process is introduced. It consists of quantum recurrent nets generating stochastic processes which represent the motor dynamics, and of classical neural nets describing the evolution of probabilities of these processes which represent the mental dynamics. The autonomy of the decision making process is achieved by a feedback from the mental to motor dynamics which changes the stochastic matrix based upon the probability distribution. This feedback replaces unavailable external information by an internal knowledge- base stored in the mental model in the form of probability distributions. As a result, the coupled motor-mental dynamics is described by a nonlinear version of Markov chains which can decrease entropy without an external source of information. Applications to common sense based decisions as well as to evolutionary games are discussed. An example exhibiting self-organization is computed using quantum computer simulation. Force on force and mutual aircraft engagements using the quantum decision maker dynamics are considered.

Glycan-independent binding and internalization of human IgM to FCMR, its cognate cellular receptor

NASA Astrophysics Data System (ADS)

Lloyd, Katy A.; Wang, Jiabin; Urban, Britta C.; Czajkowsky, Daniel M.; Pleass, Richard J.

2017-02-01

IgM is the first antibody to be produced in immune responses and plays an important role in the neutralization of bacteria and viruses. Human IgM is heavily glycosylated, featuring five N-linked glycan sites on the μ chain and one on the J-chain. Glycosylation of IgG is known to modulate the effector functions of Fcγ receptors. In contrast, little is known about the effect of glycosylation on IgM binding to the human Fcμ receptor (hFCMR). In this study, we identify the Cμ4 domain of IgM as the target of hFCMR, and show that binding and internalization of IgM by hFCMR is glycan-independent. We generated a homology-based structure for hFCMR and used molecular dynamic simulations to show how this interaction with IgM may occur. Finally, we reveal an inhibitory function for IgM in the proliferation of T cells.

Supply chain dynamics in healthcare services.

PubMed

Samuel, Cherian; Gonapa, Kasiviswanadh; Chaudhary, P K; Mishra, Ananya

2010-01-01

The purpose of this paper is to analyse health service supply chain systems. A great deal of literature is available on supply chain management in finished goods inventory situations; however, little research exists on managing service capacity when finished goods inventories are absent. System dynamics models for a typical service-oriented supply chain such as healthcare processes are developed, wherein three service stages are presented sequentially. Just like supply chains with finished goods inventory, healthcare service supply chains also show dynamic behaviour. Comparing options, service reduction, and capacity adjustment delays showed that reducing capacity adjustment and service delays gives better results. The study is confined to health service-oriented supply chains. Further work includes extending the study to service-oriented supply chains with parallel processing, i.e. having more than one stage to perform a similar operation and also to study the behaviour in service-oriented supply chains that have re-entrant orders and applications. Specific case studies can also be developed to reveal factors relevant to particular service-oriented supply chains. The paper explains the bullwhip effect in healthcare service-oriented supply chains. Reducing stages and capacity adjustment are strategic options for service-oriented supply chains. The paper throws light on policy options for managing healthcare service-oriented supply chain dynamics.

Rouse mode analysis of chain relaxation in polymer nanocomposites

DOE PAGES

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

2015-04-20

Large-scale molecular dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, asmore » in the case of a polymer–solvent system. However, for NPs larger than half the entanglement mesh size, the effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Furthermore, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect.« less

Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks.

PubMed

Haidari, Leila A; Connor, Diana L; Wateska, Angela R; Brown, Shawn T; Mueller, Leslie E; Norman, Bryan A; Schmitz, Michelle M; Paul, Proma; Rajgopal, Jayant; Welling, Joel S; Leonard, Jim; Claypool, Erin G; Weng, Yu-Ting; Chen, Sheng-I; Lee, Bruce Y

2013-01-01

Although vaccine supply chains in many countries require additional stationary storage and transport capacity to meet current and future needs, international donors tend to donate stationary storage devices far more often than transport equipment. To investigate the impact of only adding stationary storage equipment on the capacity requirements of transport devices and vehicles, we used HERMES (Highly Extensible Resource for Modeling Supply Chains) to construct a discrete event simulation model of the Niger vaccine supply chain. We measured the transport capacity requirement for each mode of transport used in the Niger vaccine cold chain, both before and after adding cold rooms and refrigerators to relieve all stationary storage constraints in the system. With the addition of necessary stationary storage, the average transport capacity requirement increased from 88% to 144% for cold trucks, from 101% to 197% for pickup trucks, and from 366% to 420% for vaccine carriers. Therefore, adding stationary storage alone may worsen or create new transport bottlenecks as more vaccines flow through the system, preventing many vaccines from reaching their target populations. Dynamic modeling can reveal such relationships between stationary storage capacity and transport constraints.

Only Adding Stationary Storage to Vaccine Supply Chains May Create and Worsen Transport Bottlenecks

PubMed Central

Haidari, Leila A.; Connor, Diana L.; Wateska, Angela R.; Brown, Shawn T.; Mueller, Leslie E.; Norman, Bryan A.; Schmitz, Michelle M.; Paul, Proma; Rajgopal, Jayant; Welling, Joel S.; Leonard, Jim; Claypool, Erin G.; Weng, Yu-Ting; Chen, Sheng-I; Lee, Bruce Y.

2015-01-01

Although vaccine supply chains in many countries require additional stationary storage and transport capacity to meet current and future needs, international donors tend to donate stationary storage devices far more often than transport equipment. To investigate the impact of only adding stationary storage equipment on the capacity requirements of transport devices and vehicles, we used HERMES (Highly Extensible Resource for Modeling Supply Chains) to construct a discrete event simulation model of the Niger vaccine supply chain. We measured the transport capacity requirement for each mode of transport used in the Niger vaccine cold chain, both before and after adding cold rooms and refrigerators to relieve all stationary storage constraints in the system. With the addition of necessary stationary storage, the average transport capacity requirement increased from 88% to 144% for cold trucks, from 101% to 197% for pickup trucks, and from 366% to 420% for vaccine carriers. Therefore, adding stationary storage alone may worsen or create new transport bottlenecks as more vaccines flow through the system, preventing many vaccines from reaching their target populations. Dynamic modeling can reveal such relationships between stationary storage capacity and transport constraints. PMID:23903398

Entropic Elastic Processes in Protein Mechanisms. Part 1. Elastic Structure Due to an Inverse Temperature Transition and Elasticity Due to Internal Chain Dynamics,

DTIC Science & Technology

1986-01-01

Bungenberg de Jong , H . G . and Kruyt, H . R. (1930). Kolloid-Z 50, 39-48. Bungenberg de Jong , H . G . and Kruyt, H . R. (1929). Proc. Kon. Ned. Adak...Submitted). Bungenbery de Jong , H . G . (1949). In Colloid Science, Vol. 2 (Kruyt, H . R., ed.) Elsevier/North Holland Publishers, Amsterdam, pp. 232...Resonance Relaxation Studies g . Dielectric Relaxation Studies h . Temperature Dependence

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

PubMed

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

2016-09-01

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

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures.

PubMed

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio; Tohyama, Takami

2018-04-01

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003)PRBMDO0163-182910.1103/PhysRevB.68.235106] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013)PRLTAO0031-900710.1103/PhysRevLett.111.010401] to obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S=1/2, we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.

Accuracy of the microcanonical Lanczos method to compute real-frequency dynamical spectral functions of quantum models at finite temperatures

NASA Astrophysics Data System (ADS)

Okamoto, Satoshi; Alvarez, Gonzalo; Dagotto, Elbio; Tohyama, Takami

2018-04-01

We examine the accuracy of the microcanonical Lanczos method (MCLM) developed by Long et al. [Phys. Rev. B 68, 235106 (2003), 10.1103/PhysRevB.68.235106] to compute dynamical spectral functions of interacting quantum models at finite temperatures. The MCLM is based on the microcanonical ensemble, which becomes exact in the thermodynamic limit. To apply the microcanonical ensemble at a fixed temperature, one has to find energy eigenstates with the energy eigenvalue corresponding to the internal energy in the canonical ensemble. Here, we propose to use thermal pure quantum state methods by Sugiura and Shimizu [Phys. Rev. Lett. 111, 010401 (2013), 10.1103/PhysRevLett.111.010401] to obtain the internal energy. After obtaining the energy eigenstates using the Lanczos diagonalization method, dynamical quantities are computed via a continued fraction expansion, a standard procedure for Lanczos-based numerical methods. Using one-dimensional antiferromagnetic Heisenberg chains with S =1 /2 , we demonstrate that the proposed procedure is reasonably accurate, even for relatively small systems.

Antibody to Ricin A Chain Hinders Intracellular Routing of Toxin and Protects Cells Even after Toxin Has Been Internalized

PubMed Central

Song, Kejing; Mize, R. Ranney; Marrero, Luis; Corti, Miriam; Kirk, Jason M.; Pincus, Seth H.

2013-01-01

Background Mechanisms of antibody-mediated neutralization are of much interest. For plant and bacterial A-B toxins, A chain mediates toxicity and B chain binds target cells. It is generally accepted and taught that antibody (Ab) neutralizes by preventing toxin binding to cells. Yet for some toxins, ricin included, anti-A chain Abs afford greater protection than anti-B. The mechanism(s) whereby Abs to the A chain neutralize toxins are not understood. Methodology/Principal Findings We use quantitative confocal imaging, neutralization assays, and other techniques to study how anti-A chain Abs function to protect cells. Without Ab, ricin enters cells and penetrates to the endoplasmic reticulum within 15 min. Within 45–60 min, ricin entering and being expelled from cells reaches equilibrium. These results are consistent with previous observations, and support the validity of our novel methodology. The addition of neutralizing Ab causes ricin accumulation at the cell surface, delays internalization, and postpones retrograde transport of ricin. Ab binds ricin for >6hr as they traffic together through the cell. Ab protects cells even when administered hours after exposure. Conclusions/Key Findings We demonstrate the dynamic nature of the interaction between the host cell and toxin, and how Ab can alter the balance in favor of the cell. Ab blocks ricin’s entry into cells, hinders its intracellular routing, and can protect even after ricin is present in the target organelle, providing evidence that the major site of neutralization is intracellular. These data add toxins to the list of pathogenic agents that can be neutralized intracellularly and explain the in vivo efficacy of delayed administration of anti-toxin Abs. The results encourage the use of post-exposure passive Ab therapy, and show the importance of the A chain as a target of Abs. PMID:23638075

Dynamic Impact of Online Word-of-Mouth and Advertising on Supply Chain Performance.

PubMed

Feng, Jian; Liu, Bin

2018-01-04

Cooperative (co-op) advertising investments benefit brand goodwill and further improve supply chain performance. Meanwhile, online word-of-mouth (OWOM) can also play an important role in supply chain performance. On the basis of co-op advertising, this paper considers a single supply chain structure led by a manufacturer and examines a fundamental issue concerning the impact of OWOM on supply chain performance. Firstly, by the method of differential game, this paper analyzes the dynamic impact of OWOM and advertising on supply chain performance (i.e., brand goodwill, sales, and profits) under three different supply chain decisions (i.e., only advertising, and manufacturers with and without sharing cost of OWOM with retailers). We compare and analyze the optimal strategies of advertising and OWOM under the above different supply chain decisions. Secondly, the system dynamics model is established to reflect the dynamic impact of OWOM and advertising on supply chain performance. Finally, three supply chain decisions under two scenarios, strong brand and weak brand, are analyzed through the system dynamics simulation. The results show that the input of OWOM can enhance brand goodwill and improve earnings. It further promotes the OWOM reputation and improves the supply chain performance if manufacturers share the cost of OWOM with retailers. Then, in order to eliminate the retailers from word-of-mouth fraud and establish a fair competition mechanism, the third parties (i.e., regulators or e-commerce platforms) should take appropriate punitive measures against retailers. Furthermore, the effect of OWOM on supply chain performance under a strong brand differed from those under a weak brand. Last but not least, if OWOM is improved, there would be more remarkable performance for the weak brand than that for the strong brand in the supply chain.

Dynamic Impact of Online Word-of-Mouth and Advertising on Supply Chain Performance

PubMed Central

Feng, Jian

2018-01-01

Cooperative (co-op) advertising investments benefit brand goodwill and further improve supply chain performance. Meanwhile, online word-of-mouth (OWOM) can also play an important role in supply chain performance. On the basis of co-op advertising, this paper considers a single supply chain structure led by a manufacturer and examines a fundamental issue concerning the impact of OWOM on supply chain performance. Firstly, by the method of differential game, this paper analyzes the dynamic impact of OWOM and advertising on supply chain performance (i.e., brand goodwill, sales, and profits) under three different supply chain decisions (i.e., only advertising, and manufacturers with and without sharing cost of OWOM with retailers). We compare and analyze the optimal strategies of advertising and OWOM under the above different supply chain decisions. Secondly, the system dynamics model is established to reflect the dynamic impact of OWOM and advertising on supply chain performance. Finally, three supply chain decisions under two scenarios, strong brand and weak brand, are analyzed through the system dynamics simulation. The results show that the input of OWOM can enhance brand goodwill and improve earnings. It further promotes the OWOM reputation and improves the supply chain performance if manufacturers share the cost of OWOM with retailers. Then, in order to eliminate the retailers from word-of-mouth fraud and establish a fair competition mechanism, the third parties (i.e., regulators or e-commerce platforms) should take appropriate punitive measures against retailers. Furthermore, the effect of OWOM on supply chain performance under a strong brand differed from those under a weak brand. Last but not least, if OWOM is improved, there would be more remarkable performance for the weak brand than that for the strong brand in the supply chain. PMID:29300361

Mesoporous silica nanoparticles functionalized with hyaluronic acid. Effect of the biopolymer chain length on cell internalization.

PubMed

Nairi, Valentina; Magnolia, Silvia; Piludu, Marco; Nieddu, Mariella; Caria, Cristian Antonio; Sogos, Valeria; Vallet-Regì, Maria; Monduzzi, Maura; Salis, Andrea

2018-02-12

Mesoporous silica nanoparticles (MSNs) were functionalized with amino groups (MSN-NH 2 ) and then with hyaluronic acid, a biocompatible biopolymer which can be recognized by CD44 receptors in tumor cells, to obtain a targeting drug delivery system. To this purpose, three hyaluronic acid samples differing for the molecular weight, namely HA S (8-15 kDa), HA M (30-50 kDa) and HA L (90-130 kDa), were used. The MSN-HA S , MSN-HA M , and MSN-HA L materials were characterized through zeta potential and dynamic light scattering measurements at pH = 7.4 and T = 37 °C to simulate physiological conditions. While zeta potential showed an increasing negative value with the increase of the HA chain length, an anomalous value of the hydrodynamic diameter was observed for MSN-HA L , which was smaller than that of MSN-HA S and MSN-HA M samples. The cellular uptake of MSN-HA samples on HeLa cells at 37 °C was studied by optical and electron microscopy. HA chain length affected significantly the cellular uptake that occurred at a higher extent for MSN-NH 2 and MSN-HA S than for MSN-HA M and MSN-HA L samples. Cellular uptake experiments carried out at 4 °C showed that the internalization process was inhibited for MSN-HA samples but not for MSN-NH 2 . This suggests the occurrence of two different mechanisms of internalization. For MSN-NH 2 the uptake is mainly driven by the attractive electrostatic interaction with membrane phospholipids, while MSN-HA internalization involves CD44 receptors overexpressed in HeLa cells. Copyright © 2018 Elsevier B.V. All rights reserved.

Stochastic entangled chain dynamics of dense polymer solutions.

PubMed

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

2010-10-14

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

Manifestations of Dynamical Localization in the Disordered XXZ Spin Chain

NASA Astrophysics Data System (ADS)

Elgart, Alexander; Klein, Abel; Stolz, Günter

2018-04-01

We study disordered XXZ spin chains in the Ising phase exhibiting droplet localization, a single cluster localization property we previously proved for random XXZ spin chains. It holds in an energy interval I near the bottom of the spectrum, known as the droplet spectrum. We establish dynamical manifestations of localization in the energy window I, including non-spreading of information, zero-velocity Lieb-Robinson bounds, and general dynamical clustering. Our results do not rely on knowledge of the dynamical characteristics of the model outside the droplet spectrum. A byproduct of our analysis is that for random XXZ spin chains this droplet localization can happen only inside the droplet spectrum.

Unit and internal chain profile of African rice (Oryza glaberrima) amylopectin.

PubMed

Gayin, Joseph; Abdel-Aal, El-Sayed M; Manful, John; Bertoft, Eric

2016-02-10

High-performance anion-exchange chromatography was used to study the unit chain profiles of amylopectins and their φ,β-limit dextrins from two African rice (Oryza glaberrima) accessions-TOG 12440 and IRGC 103759. The samples were compared with two Asian rice (Oryza sativa) samples (cv Koshihikari and cv WITA 4) and one O. sativa × O. glaberrima cross (NERICA 4). The ratio of short:long chains ranged between 12.1 and 13.8, and the ratio of A:B-chains was ∼ 1.0 in all samples. A significant difference was observed in the distribution of internal chains with regards to the proportion of short "fingerprint" B-chains (Bfp-chains), which in the φ,β-limit dextrins have a degree of polymerization (DP) 3-7. The African rice starches and NERICA 4 had higher levels of Bfp-chains, but the major group of short B-chains (DP 8-25) was similar to that of the Asian rice samples. The average chain length (CL), internal chain length (ICL), and total internal chain length (TICL) were similar in all samples. However, the external chain length (ECL) was longer in the African rice samples and NERICA 4. ECL correlated positively and significantly (p<0.05) with gelatinization transition temperatures and enthalpy suggesting differences between the two rice types in cooking properties. Copyright © 2015 Elsevier Ltd. All rights reserved.

Event-chain algorithm for the Heisenberg model: Evidence for z≃1 dynamic scaling.

PubMed

Nishikawa, Yoshihiko; Michel, Manon; Krauth, Werner; Hukushima, Koji

2015-12-01

We apply the event-chain Monte Carlo algorithm to the three-dimensional ferromagnetic Heisenberg model. The algorithm is rejection-free and also realizes an irreversible Markov chain that satisfies global balance. The autocorrelation functions of the magnetic susceptibility and the energy indicate a dynamical critical exponent z≈1 at the critical temperature, while that of the magnetization does not measure the performance of the algorithm. We show that the event-chain Monte Carlo algorithm substantially reduces the dynamical critical exponent from the conventional value of z≃2.

Backbone hydration determines the folding signature of amino acid residues.

PubMed

Bignucolo, Olivier; Leung, Hoi Tik Alvin; Grzesiek, Stephan; Bernèche, Simon

2015-04-08

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.

Rheological properties in relation to molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2018-07-15

Quinoa starch granules are small (~0.5 - 3μm) with potentials for some food and other applications. To better exploit it as a new starch resource, this study investigates the steady shear and dynamic oscillatory properties of 9 quinoa starches varying in composition and structure. Steady shear analysis shows that the flow curves could be well described by 4 selected mathematic models. Temperature sweep analysis reveals that the quinoa starch encounters a 4-stage process including 2 phase transitions. Structure-function relationship analysis showed that composition as well as unit and internal chain length distribution of amylopectin have significant impact on the rheological properties (e.g., G' at 90°C) of quinoa starch. The roles of some individual unit chains and super-long unit chains of amylopectin in determining the rheological properties of quinoa starch were revealed. This study may stimulate further interest in understanding the structural basis of starch rheology. Copyright © 2018 Elsevier B.V. All rights reserved.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

A Framework of Multi Objectives Negotiation for Dynamic Supply Chain Model

NASA Astrophysics Data System (ADS)

Chai, Jia Yee; Sakaguchi, Tatsuhiko; Shirase, Keiichi

Trends of globalization and advances in Information Technology (IT) have created opportunity in collaborative manufacturing across national borders. A dynamic supply chain utilizes these advances to enable more flexibility in business cooperation. This research proposes a concurrent decision making framework for a three echelons dynamic supply chain model. The dynamic supply chain is formed by autonomous negotiation among agents based on multi agents approach. Instead of generating negotiation aspects (such as amount, price and due date) arbitrary, this framework proposes to utilize the information available at operational level of an organization in order to generate realistic negotiation aspect. The effectiveness of the proposed model is demonstrated by various case studies.

Hybrid Correlation Energy (HyCE): An Approach Based on Separate Evaluations of Internal and External Components.

PubMed

Ivanic, Joseph; Schmidt, Michael W

2018-06-04

A novel hybrid correlation energy (HyCE) approach is proposed that determines the total correlation energy via distinct computation of its internal and external components. This approach evolved from two related studies. First, rigorous assessment of the accuracies and size extensivities of a number of electron correlation methods, that include perturbation theory (PT2), coupled-cluster (CC), configuration interaction (CI), and coupled electron pair approximation (CEPA), shows that the CEPA(0) variant of the latter and triples-corrected CC methods consistently perform very similarly. These findings were obtained by comparison to near full CI results for four small molecules and by charting recovered correlation energies for six steadily growing chain systems. Second, by generating valence virtual orbitals (VVOs) and utilizing the CEPA(0) method, we were able to partition total correlation energies into internal (or nondynamic) and external (or dynamic) parts for the aforementioned six chain systems and a benchmark test bed of 36 molecules. When using triple-ζ basis sets it was found that per orbital internal correlation energies were appreciably larger than per orbital external energies and that the former showed far more chemical variation than the latter. Additionally, accumulations of external correlation energies were seen to proceed smoothly, and somewhat linearly, as the virtual space is gradually increased. Combination of these two studies led to development of the HyCE approach, whereby the internal and external correlation energies are determined separately by CEPA(0)/VVO and PT2/external calculations, respectively. When applied to the six chain systems and the 36-molecule benchmark test set it was found that HyCE energies followed closely those of triples-corrected CC and CEPA(0) while easily outperforming MP2 and CCSD. The success of the HyCE approach is more notable when considering that its cost is only slightly more than MP2 and significantly cheaper than the CC approaches.

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

Topological edge states and impurities: Manifestation in the local static and dynamical characteristics of dimerized quantum chains

NASA Astrophysics Data System (ADS)

Zvyagin, A. A.

2018-04-01

Based on the results of exact analytic calculations, we show that topological edge states and impurities in quantum dimerized chains manifest themselves in various local static and dynamical characteristics, which can be measured in experiments. In particular, topological edge states can be observed in the magnetic field behavior of the local magnetization or magnetic susceptibility of dimerized spin chains as jumps (for the magnetization) and features (for the static susceptibility) at zero field. In contrast, impurities reveal themselves in similar jumps and features, however, at nonzero values of the critical field. We also show that dynamical characteristics of dimerized quantum chains also manifest the features, related to the topological edge states and impurities. Those features, as a rule, can be seen more sharply than the manifestation of bulk extended states in, e.g., the dynamical local susceptibility. Such peculiarities can be observed in one-dimensional dimerized spin chains, e.g., in NMR experiments, or in various realizations of quantum dimerized chains in optical experiments.

The Ultrasensitivity of Living Polymers

NASA Astrophysics Data System (ADS)

O'Shaughnessy, Ben; Vavylonis, Dimitrios

2003-03-01

Synthetic and biological living polymers are self-assembling chains whose chain length distributions (CLDs) are dynamic. We show these dynamics are ultrasensitive: Even a small perturbation (e.g., temperature jump) nonlinearly distorts the CLD, eliminating or massively augmenting short chains. The origin is fast relaxation of mass variables (mean chain length, monomer concentration) which perturbs CLD shape variables before these can relax via slow chain growth rate fluctuations. Viscosity relaxation predictions agree with experiments on the best-studied synthetic system, α-methylstyrene.

Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

PubMed Central

Weidner, Tobias; Breen, Nicholas F.; Li, Kun; Drobny, Gary P.; Castner, David G.

2010-01-01

The power of combining sum frequency generation (SFG) vibrational spectroscopy and solid-state nuclear magnetic resonance (ssNMR) spectroscopy to quantify, with site specificity and atomic resolution, the orientation and dynamics of side chains in synthetic model peptides adsorbed onto polystyrene (PS) surfaces is demonstrated in this study. Although isotopic labeling has long been used in ssNMR studies to site-specifically probe the structure and dynamics of biomolecules, the potential of SFG to probe side chain orientation in isotopically labeled surface-adsorbed peptides and proteins remains largely unexplored. The 14 amino acid leucine-lysine peptide studied in this work is known to form an α-helical secondary structure at liquid-solid interfaces. Selective, individual deuteration of the isopropyl group in each leucine residue was used to probe the orientation and dynamics of each individual leucine side chain of LKα14 adsorbed onto PS. The selective isotopic labeling methods allowed SFG analysis to determine the orientations of individual side chains in adsorbed peptides. Side chain dynamics were obtained by fitting the deuterium ssNMR line shape to specific motional models. Through the combined use of SFG and ssNMR, the dynamic trends observed for individual side chains by ssNMR have been correlated with side chain orientation relative to the PS surface as determined by SFG. This combination provides a more complete and quantitative picture of the structure, orientation, and dynamics of these surface-adsorbed peptides than could be obtained if either technique were used separately. PMID:20628016

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

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.

Exact goodness-of-fit tests for Markov chains.

PubMed

Besag, J; Mondal, D

2013-06-01

Goodness-of-fit tests are useful in assessing whether a statistical model is consistent with available data. However, the usual χ² asymptotics often fail, either because of the paucity of the data or because a nonstandard test statistic is of interest. In this article, we describe exact goodness-of-fit tests for first- and higher order Markov chains, with particular attention given to time-reversible ones. The tests are obtained by conditioning on the sufficient statistics for the transition probabilities and are implemented by simple Monte Carlo sampling or by Markov chain Monte Carlo. They apply both to single and to multiple sequences and allow a free choice of test statistic. Three examples are given. The first concerns multiple sequences of dry and wet January days for the years 1948-1983 at Snoqualmie Falls, Washington State, and suggests that standard analysis may be misleading. The second one is for a four-state DNA sequence and lends support to the original conclusion that a second-order Markov chain provides an adequate fit to the data. The last one is six-state atomistic data arising in molecular conformational dynamics simulation of solvated alanine dipeptide and points to strong evidence against a first-order reversible Markov chain at 6 picosecond time steps. © 2013, The International Biometric Society.

Effect of Chain Conformation on the Single-Molecule Melting Force in Polymer Single Crystals: Steered Molecular Dynamics Simulations Study.

PubMed

Feng, Wei; Wang, Zhigang; Zhang, Wenke

2017-02-28

Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain. To do that, steered molecular dynamics simulations were performed on those polymer single crystals by pulling individual polymer chains out of the crystals. Our results show that the patterns of force-extension curve as well as the chain moving mode are closely related to the conformation of the polymer chain in the single crystal. In addition, hydrogen bonds can enhance greatly the force required to stretch the polymer chain out of the single crystal. The dynamic breaking and reformation of multivalent hydrogen bonds have been observed for the first time in PA66 at the single molecule level.

Dynamic Simulation Research on Chain Drive Mechanism of Corn Seeder Based on ADAMS

NASA Astrophysics Data System (ADS)

Wang, Y. B.; Jia, H. P.

2017-12-01

In order to reduce the damage to the chain and improve the seeding quality of the seeding machine, the corn seeder has the characteristics of the seeding quality and some technical indexes in the work of the corn seeding machine. The dynamic analysis of the chain drive mechanism is carried out by using the dynamic virtual prototype. In this paper, the speed of the corn planter is 5km/h, and the speed of the simulated knuckle is 0.1~0.9s. The velocity is 0.12m/s, which is equal to the chain speed when the seeder is running normally. Of the dynamic simulation of the movement and the actual situation is basically consistent with the apparent speed of the drive wheel has changed the acceleration and additional dynamic load, the chain drive has a very serious damage, and the maximum load value of 47.28N, in order to reduce the damage to the chain, As far as possible so that the sowing machine in the work to maintain a reasonable uniform speed, to avoid a greater acceleration, the corn sowing machine drive the design of a certain reference.

Entanglement spreading after a geometric quench in quantum spin chains

NASA Astrophysics Data System (ADS)

Alba, Vincenzo; Heidrich-Meisner, Fabian

2014-08-01

We investigate the entanglement spreading in the anisotropic spin-1/2 Heisenberg (XXZ) chain after a geometric quench. This corresponds to a sudden change of the geometry of the chain or, in the equivalent language of interacting fermions confined in a box trap, to a sudden increase of the trap size. The entanglement dynamics after the quench is associated with the ballistic propagation of a magnetization wave front. At the free fermion point (XX chain), the von Neumann entropy SA exhibits several intriguing dynamical regimes. Specifically, at short times a logarithmic increase is observed, similar to local quenches. This is accurately described by an analytic formula that we derive from heuristic arguments. At intermediate times partial revivals of the short-time dynamics are superposed with a power-law increase SA˜tα, with α <1. Finally, at very long times a steady state develops with constant entanglement entropy, apart from oscillations. As expected, since the model is integrable, we find that the steady state is nonthermal, although it exhibits extensive entanglement entropy. We also investigate the entanglement dynamics after the quench from a finite to the infinite chain (sudden expansion). While at long times the entanglement vanishes, we demonstrate that its relaxation dynamics exhibits a number of scaling properties. Finally, we discuss the short-time entanglement dynamics in the XXZ chain in the gapless phase. The same formula that describes the time dependence for the XX chain remains valid in the whole gapless phase.

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.

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.

Quantum spin chains with multiple dynamics

NASA Astrophysics Data System (ADS)

Chen, Xiao; Fradkin, Eduardo; Witczak-Krempa, William

2017-11-01

Many-body systems with multiple emergent time scales arise in various contexts, including classical critical systems, correlated quantum materials, and ultracold atoms. We investigate such nontrivial quantum dynamics in a different setting: a spin-1 bilinear-biquadratic chain. It has a solvable entangled ground state, but a gapless excitation spectrum that is poorly understood. By using large-scale density matrix renormalization group simulations, we find that the lowest excitations have a dynamical exponent z that varies from 2 to 3.2 as we vary a coupling in the Hamiltonian. We find an additional gapless mode with a continuously varying exponent 2 ≤z <2.7 , which establishes the presence of multiple dynamics. In order to explain these striking properties, we construct a continuum wave function for the ground state, which correctly describes the correlations and entanglement properties. We also give a continuum parent Hamiltonian, but show that additional ingredients are needed to capture the excitations of the chain. By using an exact mapping to the nonequilibrium dynamics of a classical spin chain, we find that the large dynamical exponent is due to subdiffusive spin motion. Finally, we discuss the connections to other spin chains and to a family of quantum critical models in two dimensions.

Dependence of Ion Dynamics on the Polymer Chain Length in Poly(ethylene oxide)-Based Polymer Electrolytes.

PubMed

Chattoraj, Joyjit; Knappe, Marisa; Heuer, Andreas

2015-06-04

It is known from experiments that in the polymer electrolyte system, which contains poly(ethylene oxide) chains (PEO), lithium-cations (Li(+)), and bis(trifluoromethanesulfonyl)imide-anions (TFSI(-)), the cation and the anion diffusion and the ionic conductivity exhibit a similar chain-length dependence: with increasing chain length, they start dropping steadily, and later, they saturate to constant values. These results are surprising because Li-cations are strongly correlated with the polymer chains, whereas TFSI-anions do not have such bonding. To understand this phenomenon, we perform molecular dynamics simulations of this system for four different polymer chain lengths. The diffusion results obtained from our simulations display excellent agreement with the experimental data. The cation transport model based on the Rouse dynamics can successfully quantify the Li-diffusion results, which correlates Li diffusion with the polymer center-of-mass motion and the polymer segmental motion. The ionic conductivity as a function of the chain length is then estimated based on the chain-length-dependent ion diffusion, which shows a temperature-dependent deviation for short chain lengths. We argue that in the first regime, counterion correlations modify the conductivity, whereas for the long chains, the system behaves as a strong electrolyte.

Heterogeneous chain dynamics and aggregate lifetimes in precise acid-containing polyethylenes: Experiments and simulations

DOE PAGES

Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph; ...

2016-11-10

Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less

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

Microscopic Chain Motion in Polymer Nanocomposites with Dynamically Asymmetric Interphases

PubMed Central

Senses, Erkan; Faraone, Antonio; Akcora, Pinar

2016-01-01

Dynamics of the interphase region between matrix and bound polymers on nanoparticles is important to understand the macroscopic rheological properties of nanocomposites. Here, we present neutron scattering investigations on nanocomposites with dynamically asymmetric interphases formed by a high-glass transition temperature polymer, poly(methyl methacrylate), adsorbed on nanoparticles and a low-glass transition temperature miscible matrix, poly(ethylene oxide). By taking advantage of selective isotope labeling of the chains, we studied the role of interfacial polymer on segmental and collective dynamics of the matrix chains from subnanoseconds to 100 nanoseconds. Our results show that the Rouse relaxation remains unchanged in a weakly attractive composite system while the dynamics significantly slows down in a strongly attractive composite. More importantly, the chains disentangle with a remarkable increase of the reptation tube size when the bound polymer is vitreous. The glassy and rubbery states of the bound polymer as temperature changes underpin the macroscopic stiffening of nanocomposites. PMID:27457056

Enhancing Electrophoretic Display Lifetime: Thiol-Polybutadiene Evaporation Barrier Property Response to Network Microstructure

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

Cook, Caitlyn Christian

An evaporation barrier is required to enhance the lifetime of electrophoretic deposition (EPD) displays. As EPD functions on the basis of reversible deposition and resuspension of colloids suspended in a solvent, evaporation of the solvent ultimately leads to device failure. Incorporation of a thiol-polybutadiene elastomer into EPD displays enabled display lifetime surpassing six months in counting and catalyzed rigid display transition into a flexible package. Final flexible display transition to mass production compels an electronic-ink approach to encapsulate display suspension within an elastomer shell. Final thiol-polybutadiene photosensitive resin network microstructure was idealized to be dense, homogeneous, and expose an elasticmore » response to deformation. Research at hand details an approach to understanding microstructural change within display elastomers. Polybutadiene-based resin properties are modified via polymer chain structure, with and without added aromatic urethane methacrylate difunctionality, and in measuring network response to variation in thiol and initiator concentration. Dynamic mechanical analysis results signify that cross-linked segments within a difunctionalized polybutadiene network were on average eight times more elastically active than that of linked segments within a non-functionalized polybutadiene network. Difunctionalized polybutadiene samples also showed a 2.5 times greater maximum elastic modulus than non-functionalized samples. Hybrid polymer composed of both polybutadiene chains encompassed TE-2000 stiffness and B-1000 elasticity for use in encapsulating display suspension. Later experiments measured kinetic and rheological response due to alteration in dithiol cross-linker chain length via real time Fourier transform infrared spectroscopy and real-time dynamic rheology. Distinct differences were discovered between dithiol resin systems, as maximum thiol conversion achieved in short and long chain length dithiols was 86% and 11%, respectively. Oscillatory real-time rheological experiments confirmed a more uniform network to better dissipate applied shear in short chain length dithiol systems, as long chain length dithiols relayed a steep internal stress build-up due to less cross-links and chain entanglements. Thorough understanding of network formation aids the production of a stronger and impermeable elastomeric barrier for preservation of EPD displays.« less

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.

Entanglement dynamics in critical random quantum Ising chain with perturbations

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

Huang, Yichen, E-mail: ychuang@caltech.edu

We simulate the entanglement dynamics in a critical random quantum Ising chain with generic perturbations using the time-evolving block decimation algorithm. Starting from a product state, we observe super-logarithmic growth of entanglement entropy with time. The numerical result is consistent with the analytical prediction of Vosk and Altman using a real-space renormalization group technique. - Highlights: • We study the dynamical quantum phase transition between many-body localized phases. • We simulate the dynamics of a very long random spin chain with matrix product states. • We observe numerically super-logarithmic growth of entanglement entropy with time.

Multiple dynamic regimes in colloid-polymer dispersions: New insight using X-ray photon correlation spectroscopy

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

Srivastava, Sunita; Kishore, Suhasini; Narayanan, Suresh

We present an X-ray photon correlation spectros- copy (XPCS) study of dynamic transitions in an anisotropic colloid-polymer dispersion with multiple arrested states. The results provide insight into the mechanism for formation of repulsive glasses, attractive glasses, and networked gels of col- loids with weakly adsorbing polymer chains. In the presence of adsorbing polymer chains, we observe three distinct regimes: a state with slow dynamics consisting of finite particles and clusters, for which interparticle interactions are predominantly repulsive; a second dynamic regime occurring above the satu- ration concentration of added polymer, in which small clusters of nanoparticles form via a short-rangemore » depletion attraction; and a third regime above the overlap concentration in which dynamics of clusters are independent of polymer chain length. The observed complex dynamic state diagram is primarily gov- erned by the structural reorganization of a nanoparticle cluster and polymer chains at the nanoparticle-polymer surface and in the concentrated medium, which in turn controls the dynamics of the dispersion« less

Impact of hydrogen bonding on dynamics of hydroxyl-terminated polydimethylsiloxane

DOE PAGES

Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori; ...

2016-04-06

Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

Constraints on food chain length arising from regional metacommunity dynamics

PubMed Central

Calcagno, Vincent; Massol, François; Mouquet, Nicolas; Jarne, Philippe; David, Patrice

2011-01-01

Classical ecological theory has proposed several determinants of food chain length, but the role of metacommunity dynamics has not yet been fully considered. By modelling patchy predator–prey metacommunities with extinction–colonization dynamics, we identify two distinct constraints on food chain length. First, finite colonization rates limit predator occupancy to a subset of prey-occupied sites. Second, intrinsic extinction rates accumulate along trophic chains. We show how both processes concur to decrease maximal and average food chain length in metacommunities. This decrease is mitigated if predators track their prey during colonization (habitat selection) and can be reinforced by top-down control of prey vital rates (especially extinction). Moreover, top-down control of colonization and habitat selection can interact to produce a counterintuitive positive relationship between perturbation rate and food chain length. Our results show how novel limits to food chain length emerge in spatially structured communities. We discuss the connections between these constraints and the ones commonly discussed, and suggest ways to test for metacommunity effects in food webs. PMID:21367786

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers

NASA Astrophysics Data System (ADS)

Pitman, Michael C.; Suits, Frank; Gawrisch, Klaus; Feller, Scott E.

2005-06-01

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of H2 spin-lattice relaxation rates, nuclear overhauser enhancement spectroscopy (NOESY) cross-relaxation rates, and lateral diffusion coefficients. Additionally, we describe the dynamics of hydrogen bonding through an analysis of hydrogen bond lifetimes and the time evolution of clusters of hydrogen bonded lipids. The simulated trajectory is shown to be consistent with experimental measures of internal, intermolecular, and diffusive motion. Consistent with our analysis of SOPE structure in the companion paper, we see hydrogen bonding dominating the dynamics of the interface region. Comparison of H2 T1 relaxation rates for chain methylene segments in phosphatidylcholine and phosphatidylethanolamine bilayers indicates that slower motion resulting from hydrogen bonding extends at least three carbons into the hydrophobic core. NOESY cross-relaxation rates compare well with experimental values, indicating the observed hydrogen bonding dynamics are realistic. Calculated lateral diffusion rates (4±1×10-8cm2/s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.

Rapid Production of Internally Structured Colloids by Flash Nanoprecipitation of Block Copolymer Blends.

PubMed

Grundy, Lorena S; Lee, Victoria E; Li, Nannan; Sosa, Chris; Mulhearn, William D; Liu, Rui; Register, Richard A; Nikoubashman, Arash; Prud'homme, Robert K; Panagiotopoulos, Athanassios Z; Priestley, Rodney D

2018-05-08

Colloids with internally structured geometries have shown great promise in applications ranging from biosensors to optics to drug delivery, where the internal particle structure is paramount to performance. The growing demand for such nanomaterials necessitates the development of a scalable processing platform for their production. Flash nanoprecipitation (FNP), a rapid and inherently scalable colloid precipitation technology, is used to prepare internally structured colloids from blends of block copolymers and homopolymers. As revealed by a combination of experiments and simulations, colloids prepared from different molecular weight diblock copolymers adopt either an ordered lamellar morphology consisting of concentric shells or a disordered lamellar morphology when chain dynamics are sufficiently slow to prevent defect annealing during solvent exchange. Blends of homopolymer and block copolymer in the feed stream generate more complex internally structured colloids, such as those with hierarchically structured Janus and patchy morphologies, due to additional phase separation and kinetic trapping effects. The ability of the FNP process to generate such a wide range of morphologies using a simple and scalable setup provides a pathway to manufacturing internally structured colloids on an industrial scale.

Polymer models of interphase chromosomes

PubMed Central

Vasquez, Paula A; Bloom, Kerry

2014-01-01

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

The surprising dynamics of a chain on a pulley: lift off and snapping

PubMed Central

Audoly, Basile

2016-01-01

The motion of weights attached to a chain or string moving on a frictionless pulley is a classic problem of introductory physics used to understand the relationship between force and acceleration. Here, we consider the dynamics of the chain when one of the weights is removed and, thus, one end is pulled with constant acceleration. This simple change has dramatic consequences for the ensuing motion: at a finite time, the chain ‘lifts off’ from the pulley, and the free end subsequently accelerates faster than the end that is pulled. Eventually, the chain undergoes a dramatic reversal of curvature reminiscent of the crack or snap, of a whip. We combine experiments, numerical simulations and theoretical arguments to explain key aspects of this dynamical problem. PMID:27436987

The surprising dynamics of a chain on a pulley: lift off and snapping.

PubMed

Brun, P-T; Audoly, Basile; Goriely, Alain; Vella, Dominic

2016-06-01

The motion of weights attached to a chain or string moving on a frictionless pulley is a classic problem of introductory physics used to understand the relationship between force and acceleration. Here, we consider the dynamics of the chain when one of the weights is removed and, thus, one end is pulled with constant acceleration. This simple change has dramatic consequences for the ensuing motion: at a finite time, the chain 'lifts off' from the pulley, and the free end subsequently accelerates faster than the end that is pulled. Eventually, the chain undergoes a dramatic reversal of curvature reminiscent of the crack or snap, of a whip. We combine experiments, numerical simulations and theoretical arguments to explain key aspects of this dynamical problem.

Conformational dynamics of a protein in the folded and the unfolded state

NASA Astrophysics Data System (ADS)

Fitter, Jörg

2003-08-01

In a quasielastic neutron scattering experiment, the picosecond dynamics of α-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D 2O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 Å; unfolded state, 1.8 Å). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

α - synuclein under the magnifying glass. Insights from atomistic and coarse-grain simulations

NASA Astrophysics Data System (ADS)

Ilie, Ioana M.; Nayar, Divya; den Otter, Wouter K.; van der Vegt, Nico F. A.; Briels, Wim J.; University of Twente Collaboration; University of Darmstadt Collaboration

Neurodegenerative diseases are linked to the accumulation of misfolded intrinsically disordered proteins in the brain. Here, we use both all-atom and coarse-grain simulations to explore the intricate dynamics and the aggregation of α-synuclein, the protein implicated in Parkinson's disease. We explore the free energy landscapes of α-synuclein by using Molecular Dynamics simulations and extract information on the structure of the protein as well as on its binding affinities. Next, to study the aggregation, we proceed with representing α-synuclein as a chain of deformable particles that can adapt their geometry, binding affinities and can rearrange into different disordered and ordered structures. We use Brownian Dynamics to simulate the translational and rotational motions of the particles, as well as their interaction properties. The simulations show valuable insight into the internal dynamics of α-synuclein and the formation of ordered and disordered aggregates. In addition, the study is extended to investigate the attachment and folding of a protein to a fiber.

Four-stranded mini microtubules formed by Prosthecobacter BtubAB show dynamic instability.

PubMed

Deng, Xian; Fink, Gero; Bharat, Tanmay A M; He, Shaoda; Kureisaite-Ciziene, Danguole; Löwe, Jan

2017-07-18

Microtubules, the dynamic, yet stiff hollow tubes built from αβ-tubulin protein heterodimers, are thought to be present only in eukaryotic cells. Here, we report a 3.6-Å helical reconstruction electron cryomicroscopy structure of four-stranded mini microtubules formed by bacterial tubulin-like Prosthecobacter dejongeii BtubAB proteins. Despite their much smaller diameter, mini microtubules share many key structural features with eukaryotic microtubules, such as an M-loop, alternating subunits, and a seam that breaks overall helical symmetry. Using in vitro total internal reflection fluorescence microscopy, we show that bacterial mini microtubules treadmill and display dynamic instability, another hallmark of eukaryotic microtubules. The third protein in the btub gene cluster, BtubC, previously known as "bacterial kinesin light chain," binds along protofilaments every 8 nm, inhibits BtubAB mini microtubule catastrophe, and increases rescue. Our work reveals that some bacteria contain regulated and dynamic cytomotive microtubule systems that were once thought to be only useful in much larger and sophisticated eukaryotic cells.

Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study.

PubMed

ManickamAchari, Vijayan; Bryce, Richard A; Hashim, Rauzah

2014-01-01

The rational design of a glycolipid application (e.g. drug delivery) with a tailored property depends on the detailed understanding of its structure and dynamics. Because of the complexity of sugar stereochemistry, we have undertaken a simulation study on the conformational dynamics of a set of synthetic glycosides with different sugar groups and chain design, namely dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside and a C12C10 branched β-maltoside under anhydrous conditions. We examined the chain structure in detail, including the chain packing, gauche/trans conformations and chain tilting. In addition, we also investigated the rotational dynamics of the headgroup and alkyl chains. Monoalkylated glycosides possess a small amount of gauche conformers (∼20%) in the hydrophobic region of the lamellar crystal (LC) phase. In contrast, the branched chain glycolipid in the fluid Lα phase has a high gauche population of up to ∼40%. Rotational diffusion analysis reveals that the carbons closest to the headgroup have the highest correlation times. Furthermore, its value depends on sugar type, where the rotational dynamics of an isomaltose was found to be 11-15% and more restrained near the sugar, possibly due to the chain disorder and partial inter-digitation compared to the other monoalkylated lipids. Intriguingly, the present simulation demonstrates the chain from the branched glycolipid bilayer has the ability to enter into the hydrophilic region. This interesting feature of the anhydrous glycolipid bilayer simulation appears to arise from a combination of lipid crowding and the amphoteric nature of the sugar headgroups.

Accessing the dynamics of end-grafted flexible polymer chains by atomic force-electrochemical microscopy. Theoretical modeling of the approach curves by the elastic bounded diffusion model and Monte Carlo simulations. Evidence for compression-induced lateral chain escape.

PubMed

Abbou, Jeremy; Anne, Agnès; Demaille, Christophe

2006-11-16

The dynamics of a molecular layer of linear poly(ethylene glycol) (PEG) chains of molecular weight 3400, bearing at one end a ferrocene (Fc) label and thiol end-grafted at a low surface coverage onto a gold substrate, is probed using combined atomic force-electrochemical microscopy (AFM-SECM), at the scale of approximately 100 molecules. Force and current approach curves are simultaneously recorded as a force-sensing microelectrode (tip) is inserted within the approximately 10 nm thick, redox labeled, PEG chain layer. Whereas the force approach curve gives access to the structure of the compressed PEG layer, the tip-current, resulting from tip-to-substrate redox cycling of the Fc head of the chain, is controlled by chain dynamics. The elastic bounded diffusion model, which considers the motion of the Fc head as diffusion in a conformational field, complemented by Monte Carlo (MC) simulations, from which the chain conformation can be derived for any degree of confinement, allows the theoretical tip-current approach curve to be calculated. The experimental current approach curve can then be very satisfyingly reproduced by theory, down to a tip-substrate separation of approximately 2 nm, using only one adjustable parameter characterizing the chain dynamics: the effective diffusion coefficient of the chain head. At closer tip-substrate separations, an unpredicted peak is observed in the experimental current approach curve, which is shown to find its origin in a compression-induced escape of the chain from within the narrowing tip-substrate gap. MC simulations provide quantitative support for lateral chain elongation as the escape mechanism.

Measuring Fission Chain Dynamics Through Inter-event Timing of Correlated Particles

NASA Astrophysics Data System (ADS)

Monterial, Mateusz

Neutrons born from fission may go on to induce subsequent fissions in self-propagating series of reactions resulting in a fission chain. Fissile materials comprise all isotopes capable of sustaining nuclear fission chain reactions, and are therefore a necessary prerequisite for the construction of a nuclear weapon. As a result the accountancy and characterization of fissile material is of great importance for national security and the international community. The rate at which neutrons "multiply" in a fissile material is a function of the composition, total mass, density, and shape of the object. These are key characteristics sought out in areas of nuclear non-proliferation, safeguards, treaty verification and emergency response. This thesis demonstrates a novel technique of measuring the underlying fission chain dynamics in fissile material through temporal correlation of neutrons and gamma rays emitted from fission. Fissile material exhibits key detectable signatures through the emission of correlated neutrons and gamma rays from fission. The Non-Destructive Assay (NDA) community has developed mature techniques of assaying fissile material that detect these signatures, such as neutron counting by thermal capture based detectors, and gamma-ray spectroscopy. An alternative use of fast organic scintillators provides three additional capabilities: (1) discrimination between neutrons and gamma-ray pulses (2) sub-nanosecond scale timing between correlated events (3) measurement of deposited neutron energy in the detector. This thesis leverages these capabilities into to measure a new signature, which is demonstrated to be sensitive to both fissile neutron multiplication and presence of neutronically coupled reflectors. In addition, a new 3D imaging method of sources of correlated gamma rays and neutrons is presented, which can improve estimation of total source volume and localization.

Dynamics of the metal binding domains and regulation of the human copper transporters ATP7B and ATP7A.

PubMed

Yu, Corey H; Dolgova, Natalia V; Dmitriev, Oleg Y

2017-04-01

Copper transporters ATP7A and ATP7B regulate copper levels in the human cells and deliver copper to the biosynthetic pathways. ATP7A and ATP7B belong to the P-type ATPases and share much of the domain architecture and the mechanism of ATP hydrolysis with the other, well-studied, enzymes of this type. A unique structural feature of the copper ATPases is the chain of six cytosolic metal-binding domains (MBDs), which are believed to be involved in copper-dependent regulation of the activity and intracellular localization of these enzymes. Although the structures of all the MBDs have been solved, the mechanism of copper-dependent regulation of ATP7B and ATP7A, the roles of individual MBDs, and the relationship between the regulatory and catalytic copper binding are still unknown. We describe the structure and dynamics of the MBDs, review the current knowledge about their functional roles and propose a mechanism of regulation of ATP7B by copper-dependent changes in the dynamics and conformation of the MBD chain. Transient interactions between the MBDs, rather than transitions between distinct static conformations are likely to form the structural basis of regulation of the ATP-dependent copper transporters in human cells. © 2016 IUBMB Life, 69(4):226-235, 2017. © 2017 International Union of Biochemistry and Molecular Biology.

Dynamic Models and Coordination Analysis of Reverse Supply Chain with Remanufacturing

NASA Astrophysics Data System (ADS)

Yan, Nina

In this paper, we establish a reverse chain system with one manufacturer and one retailer under demand uncertainties. Distinguishing between the recycling process of the retailer and the remanufacturing process of the manufacturer, we formulate a two-stage dynamic model for reverse supply chain based on remanufacturing. Using buyback contract as coordination mechanism and applying dynamic programming the optimal decision problems for each stage are analyzed. It concluded that the reverse supply chain system could be coordinated under the given condition. Finally, we carry out numerical calculations to analyze the expected profits for the manufacturer and the retailer under different recovery rates and recovery prices and the outcomes validate the theoretical analyses.

Crossover transition in flowing granular chains

NASA Astrophysics Data System (ADS)

Ulrich, Xialing; Fried, Eliot; Shen, Amy Q.

2009-09-01

We report on the dynamical and statistical behavior of flowing collections of granular chains confined two-dimensionally (2D) within a rotating tumbler. Experiments are conducted with systems of chains of fixed length, but various lengths are considered. The dynamics are punctuated by cascades of chains along a free-surface cascades, which drive the development of mixed porous/laminar packing arrangements in bulk. We investigate the conformation of the system, as characterized by the porosity of the flow region occupied by the chains and the mean-square end-to-end distance of the chains during flow. Both of these measures show crossover transitions from a 2D self-avoiding walk to a 2D random walk when the chain length becomes long enough to allow self-contact.

Adsorption and Exchange Dynamics in Aging Hydroxyethylcellulose Layers on Silica.

PubMed

Mubarekyan; Santore

2000-07-15

The adsorption kinetics of hydroxyethylcellulose (HEC) on silica and relaxations in adsorbed HEC layers were probed using total internal reflectance fluorescence and near-Brewster reflectivity. Like many random-coil polymers, HEC was found to adsorb at the transport-limited rate. Relaxations occurred at nearly constant interfacial mass when HEC layers were exposed to aqueous solvent, causing the subsequent exchange of chains between the layer and the free solution to become increasingly hindered. Eventually, on the time scale of a day, layers became immobilized and unable to accommodate chains from free solution. A continued fluorescence decay, beyond time scales that could be probed with self exchange, suggested further relaxations of the adsorbed HEC. The polydisperse HEC system (with an average molecular weight near 450,000) behaved qualitatively similar to molecular weight standard polyethylene oxide (PEO) layers on silica. For instance, relaxations in PEO layers occurred on a time scale of 10-20 h, like the HEC layers. Young layers of the latter, however, exhibited self-exchange kinetics that were an order of magnitude slower than PEO layers of similar age. This difference in adsorbed layer dynamics was attributed to HEC's stiffer backbone, compared with flexible PEO. Copyright 2000 Academic Press.

Exact solutions for discrete breathers in a forced-damped chain.

PubMed

Gendelman, O V

2013-06-01

Exact solutions for symmetric on-site discrete breathers (DBs) are obtained in a forced-damped linear chain with on-site vibro-impact constraints. The damping in the system is caused by inelastic impacts; the forcing functions should satisfy conditions of periodicity and antisymmetry. Global conditions for existence and stability of the DBs are established by a combination of analytic and numeric methods. The DB can lose its stability through either pitchfork, or Neimark-Sacker bifurcations. The pitchfork bifurcation is related to the internal dynamics of each individual oscillator. It is revealed that the coupling can suppress this type of instability. To the contrary, the Neimark-Sacker bifurcation occurs for relatively large values of the coupling, presumably due to closeness of the excitation frequency to a boundary of the propagation zone of the chain. Both bifurcation mechanisms seem to be generic for the considered type of forced-damped lattices. Some unusual phenomena, like nonmonotonous dependence of the stability boundary on the forcing amplitude, are revealed analytically for the initial system and illustrated numerically for small periodic lattices.

Chain Dynamics in Magnetorheological Suspensions

NASA Technical Reports Server (NTRS)

Gast, A. P.; Furst, E. M.

1999-01-01

Magnetorheological (MR) suspensions are composed of colloidal particles which acquire dipole moments when subjected to an external magnetic field. At sufficient field strengths and concentrations, the dipolar particles rapidly aggregate to form long chains. Subsequent lateral cross-linking of the dipolar chains is responsible for a rapid liquid-to-solid-like rheological transition. The unique, magnetically-activated rheological properties of MR suspensions make them ideal for interfacing mechanical systems to electronic controls. Additionally, the ability to experimentally probe colloidal suspensions interacting through tunable anisotropic potentials is of fundamental interest. Our current experimental work has focused on understanding the fluctuations of dipolar chains. It has been proposed by Halsey and Toor (HT) that the strong Landau-Peierls thermal fluctuations of dipolar chains could be responsible for long-range attractions between chains. Such interactions will govern the long-time relaxation of MR suspensions. We have synthesized monodisperse neutrally buoyant MR suspensions by density matching stabilized ferrofluid emulsion droplets with D2O. This allows us to probe the dynamics of the dipolar chains using light scattering without gravitational, interfacial, and polydispersity effects to resolve the short-wavelength dynamics of the dipolar chains. We used diffusing wave spectroscopy to measure these dynamics. The particle displacements at short times that show an independence to the field strength, but at long times exhibit a constrained, sub-diffusive motion that slows as the dipole strength is increased. The experiments are in good qualitative agreement with Brownian dynamics simulations of dipolar chains. Although there have been several important and detailed studies of the structure and interactions in MR suspensions, there has not been conclusive evidence that supports or contradicts the HT model prediction that long-range interactions exist between fluctuating chains of dipolar particles. Resolving this issue would contribute greatly to the understanding of these interesting and important materials. We have begun to test the predictions of the HT model by both examining the dynamics of individual chains and by measuring the forces between dipolar chains directly to accurately and quantitatively assess the interactions that they experience. To do so, we employ optical trapping techniques and video-microscopy to manipulate and observe our samples on the microscopic level. With these techniques, it is possible to observe chains that are fluctuating freely in three-dimensions, independent of interfacial effects. More importantly, we are able to controllably observe the interactions of two chains at various separations to measure the force-distance profile. The techniques also allow us to study the mechanical properties of individual chains and chain clusters. Our work to this point has focused on reversibly-formed dipolar chains due to field induced dipoles where the combination of this chaining, the dipolar forces, and the hydrodynamic interactions that dictate the rheology of the suspensions. One can envision, however, many situations where optical, electronic, or rheological behavior may be optimized with magneto-responsive anisotropic particles. Chains of polarizable particles may have the best properties as they can coil and flex in the absence of a field and stiffen and orient when a field is applied. We have recently demonstrated a synthesis of stable, permanent paramagnetic chains by both covalently and physically linking paramagnetic colloidal particles. The method employed allows us to create monodisperse chains of controlled length. We observed the stability, field-alignment, and rigidity of this new class of materials. The chains may exhibit unique rheological properties in an applied magnetic field over isotropic suspensions of paramagnetic particles. They are also useful rheological models as bead-spring systems. These chains form the basis for our current experiments with optical traps.

From powder to solution: hydration dependence of human hemoglobin dynamics correlated to body temperature.

PubMed

Stadler, A M; Digel, I; Embs, J P; Unruh, T; Tehei, M; Zaccai, G; Büldt, G; Artmann, G M

2009-06-17

A transition in hemoglobin (Hb), involving partial unfolding and aggregation, has been shown previously by various biophysical methods. The correlation between the transition temperature and body temperature for Hb from different species, suggested that it might be significant for biological function. To focus on such biologically relevant human Hb dynamics, we studied the protein internal picosecond motions as a response to hydration, by elastic and quasielastic neutron scattering. Rates of fast diffusive motions were found to be significantly enhanced with increasing hydration from fully hydrated powder to concentrated Hb solution. In concentrated protein solution, the data showed that amino acid side chains can explore larger volumes above body temperature than expected from normal temperature dependence. The body temperature transition in protein dynamics was absent in fully hydrated powder, indicating that picosecond protein dynamics responsible for the transition is activated only at a sufficient level of hydration. A collateral result from the study is that fully hydrated protein powder samples do not accurately describe all aspects of protein picosecond dynamics that might be necessary for biological function.

Structure and dynamics of solvated polyethylenimine chains

NASA Astrophysics Data System (ADS)

Beu, Titus A.; Farcaş, Alexandra

2017-12-01

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

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

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

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

DOE PAGES

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

2017-03-11

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

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.

ChainMail based neural dynamics modeling of soft tissue deformation for surgical simulation.

PubMed

Zhang, Jinao; Zhong, Yongmin; Smith, Julian; Gu, Chengfan

2017-07-20

Realistic and real-time modeling and simulation of soft tissue deformation is a fundamental research issue in the field of surgical simulation. In this paper, a novel cellular neural network approach is presented for modeling and simulation of soft tissue deformation by combining neural dynamics of cellular neural network with ChainMail mechanism. The proposed method formulates the problem of elastic deformation into cellular neural network activities to avoid the complex computation of elasticity. The local position adjustments of ChainMail are incorporated into the cellular neural network as the local connectivity of cells, through which the dynamic behaviors of soft tissue deformation are transformed into the neural dynamics of cellular neural network. Experiments demonstrate that the proposed neural network approach is capable of modeling the soft tissues' nonlinear deformation and typical mechanical behaviors. The proposed method not only improves ChainMail's linear deformation with the nonlinear characteristics of neural dynamics but also enables the cellular neural network to follow the principle of continuum mechanics to simulate soft tissue deformation.

Forced reptation revealed by chain pull-out simulations.

PubMed

Bulacu, Monica; van der Giessen, Erik

2009-08-14

We report computation results obtained from extensive molecular dynamics simulations of tensile disentanglement of connector chains placed at the interface between two polymer bulks. Each polymer chain (either belonging to the bulks or being a connector) is treated as a sequence of beads interconnected by springs, using a coarse-grained representation based on the Kremer-Grest model, extended to account for stiffness along the chain backbone. Forced reptation of the connectors was observed during their disentanglement from the bulk chains. The extracted chains are clearly seen following an imaginary "tube" inside the bulks as they are pulled out. The entropic and energetic responses to the external deformation are investigated by monitoring the connector conformation tensor and the modifications of the internal parameters (bonds, bending, and torsion angles along the connectors). The work needed to separate the two bulks is computed from the tensile force induced during debonding in the connector chains. The value of the work reached at total separation is considered as the debonding energy G. The most important parameters controlling G are the length (n) of the chains placed at the interface and their areal density. Our in silico experiments are performed at relatively low areal density and are disregarded if chain scission occurs during disentanglement. As predicted by the reptation theory, for this pure pull-out regime, the power exponent from the scaling G proportional, variant n(a) is a approximately 2, irrespective of chain stiffness. Small variations are found when the connectors form different number of stitches at the interface, or when their length is randomly distributed in between the two bulks. Our results show that the effects of the number of stitches and of the randomness of the block lengths have to be considered together, especially when comparing with experiments where they cannot be controlled rigorously. These results may be significant for industrial applications, such reinforcement of polymer-polymer adhesion by connector chains, when incorporated as constitutive laws at higher time/length scales in finite element calculations.

Stabilizing coherence with nested environments: a numerical study using kicked Ising models

NASA Astrophysics Data System (ADS)

González-Gutiérrez, C.; Villaseñor, E.; Pineda, C.; Seligman, T. H.

2016-08-01

We study a tripartite system of coupled spins, where a first set of one or two spins is our central system which is coupled to another set considered, the near environment, in turn coupled to the third set, the far environment. The dynamics considered are those of a generalized kicked spin chain in the regime of quantum chaotic dynamics. This allows us to test recent results that suggest that the presence of a far environment, coupled to the near environment, slows decoherence of the central system. After an extensive numerical study, we confirm previous results for extreme values and special cases. In particular, under a wide variety of circumstances an increasing coupling between near and far environment, slows decoherence, as measured by purity, and protects internal entanglement.

Convergent mechanisms favor fast amyloid formation in two lambda 6a Ig light chain mutants.

PubMed

Valdés-García, Gilberto; Millán-Pacheco, César; Pastor, Nina

2017-08-01

Extracellular deposition as amyloids of immunoglobulin light chains causes light chain amyloidosis. Among the light chain families, lambda 6a is one of the most frequent in light chain amyloidosis patients. Its germline protein, 6aJL2, and point mutants, R24G and P7S, are good models to study fibrillogenesis, because their stability and fibril formation characteristics have been described. Both mutations make the germline protein unstable and speed up its ability to aggregate. To date, there is no molecular mechanism that explains how these differences in amyloidogenesis can arise from a single mutation. To look into the structural and dynamical differences in the native state of these proteins, we carried out molecular dynamics simulations at room temperature. Despite the structural similarity of the germline protein and the mutants, we found differences in their dynamical signatures that explain the mutants' increased tendency to form amyloids. The contact network alterations caused by the mutations, though different, converge in affecting two anti-aggregation motifs present in light chain variable domains, suggesting a different starting point for aggregation in lambda chains compared to kappa chains. © 2017 Wiley Periodicals, Inc.

Deuteration as a Means to Tune Crystallinity of Conducting Polymers

DOE PAGES

Jakowski, Jacek; Huang, Jingsong; Garashchuk, Sophya; ...

2017-08-25

The effects of deuterium isotope substitution on conjugated polymer chain stacking of poly(3-hexylthiophene) is studied in this paper experimentally by X-ray diffraction (XRD) in combination with gel permeation chromatography and theoretically using density functional theory and quantum molecular dynamics. For four P3HT materials with different levels of deuteration (pristine, main-chain deuterated, side-chain deuterated, and fully deuterated), the XRD measurements show that main-chain thiophene deuteration significantly reduces crystallinity, regardless of the side-chain deuteration. The reduction of crystallinity due to the main-chain deuteration is a quantum nuclear effect resulting from a static zero-point vibrational energy combined with a dynamic correlation of themore » dipole fluctuations. The quantum molecular dynamics simulations confirm the interchain correlation of the proton–proton and deuteron–deuteron motions but not of the proton–deuteron motion. Thus and finally, isotopic purity is an important factor affecting stability and properties of conjugated polymer crystals, which should be considered in the design of electronic and spintronic devices.« less

Deuteration as a Means to Tune Crystallinity of Conducting Polymers

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

Jakowski, Jacek; Huang, Jingsong; Garashchuk, Sophya

The effects of deuterium isotope substitution on conjugated polymer chain stacking of poly(3-hexylthiophene) is studied in this paper experimentally by X-ray diffraction (XRD) in combination with gel permeation chromatography and theoretically using density functional theory and quantum molecular dynamics. For four P3HT materials with different levels of deuteration (pristine, main-chain deuterated, side-chain deuterated, and fully deuterated), the XRD measurements show that main-chain thiophene deuteration significantly reduces crystallinity, regardless of the side-chain deuteration. The reduction of crystallinity due to the main-chain deuteration is a quantum nuclear effect resulting from a static zero-point vibrational energy combined with a dynamic correlation of themore » dipole fluctuations. The quantum molecular dynamics simulations confirm the interchain correlation of the proton–proton and deuteron–deuteron motions but not of the proton–deuteron motion. Thus and finally, isotopic purity is an important factor affecting stability and properties of conjugated polymer crystals, which should be considered in the design of electronic and spintronic devices.« less

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins.

PubMed

Damjanović, Ana; Brooks, Bernard R; García-Moreno, Bertrand

2011-04-28

Molecular dynamics simulations were used to examine the effects of ionization of internal groups on the structures of eighteen variants of staphylococcal nuclease (SNase) with internal Lys, Asp, or Glu. In most cases the RMSD values of internal ionizable side chains were larger when the ionizable moieties were charged than when they were neutral. Calculations of solvent-accessible surface area showed that the internal ionizable side chains were buried in the protein interior when they were neutral and moved toward crevices and toward the protein-water interface when they were charged. The only exceptions are Lys-36, Lys-62, and Lys-103, which remained buried even after charging. With the exception of Lys-38, the number of internal water molecules surrounding the ionizable group increased upon charging: the average number of water oxygen atoms within the first hydration shell increased by 1.7 for Lys residues, by 5.2 for Asp residues, and by 3.2 for Glu residues. The polarity of the microenvironment of the ionizable group also increased when the groups were charged: the average number of polar atoms of any kind within the first hydration shell increased by 2.7 for Lys residues, by 4.8 for Asp residues, and by 4.0 for Glu residues. An unexpected correlation was observed between the absolute value of the shifts in pK(a) values measured experimentally, and several parameters of structural relaxation: the net difference in the polarity of the microenvironment of the charged and neutral forms of the ionizable groups, the net difference in hydration of the charged and neutral forms of the ionizable groups, and the difference in RMSD values of the charged and neutral forms of the ionizable groups. The effects of ionization of internal groups on the conformation of the backbone were noticeable but mostly small and localized to the area immediately next to the internal ionizable moiety. Some variants did exhibit local unfolding.

The nexus between OSH and subcontracting.

PubMed

Nunes, Isabel L

2012-01-01

Subcontracting of specialized functions to external companies (e.g. cleaning or maintenance) is actually very common within several industries. These external companies' are called contractors and their contracting is often designated as outsourcing. Frequently contractors involve other companies (the sub-contractors) to assist them in fulfilling the contract, resulting in a complex chain of organizations focused on interchange of work - the contracting chain. Therefore in the same work site can coexist workers form the client-company and workers from the contractors and/or subcontractors. Since contractors perform their job in client's facilities, they can be exposed to hazards that are unknown to them. On other hand, workers of the client company can also be exposed to hazardous situations derived from the work performed by the contractors. The paper discusses how adequate occupational safety and health conditions can be assured when dealing with this kind of dynamic labor networks. Two case-studies and several examples coming from international literature will be presented.

Structure and Entanglement Factors on Dynamics of Polymer-Grafted Nanoparticles

DOE PAGES

Liu, Siqi; Senses, Erkan; Jiao, Yang; ...

2016-04-15

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Dynamic and thermodynamic response of the Ras protein Cdc42Hs upon association with the effector domain of PAK3

PubMed Central

Moorman, Veronica R.; Valentine, Kathleen G.; Bédard, Sabrina; Kasinath, Vignesh; Dogan, Jakob; Love, Fiona M.; Wand, A. Joshua

2014-01-01

Human cell division cycle protein 42 (Cdc42Hs) is a small, Rho-type GTPase involved in multiple cellular processes through its interactions with downstream effectors. The binding domain of one such effector, the actin cytoskeleton-regulating p21 activated kinase 3 (PAK3) is known as PBD46. Nitrogen-15 backbone and carbon-13 methyl NMR relaxation were measured to investigate the dynamical changes in activated GMPPCP•Cdc42Hs upon PBD46 binding. Changes in internal motion of the Cdc42Hs, as revealed by methyl axis order parameters, were observed not only near the Cdc42Hs–PBD46 interface but also in remote sites on the Cdc42Hs molecule. The binding-induced changes in side chain dynamics propagate along the long axis of Cdc42Hs away from the site of PBD46 binding with a sharp distance dependence. Overall, the binding of the PBD46 effector domain on the dynamics of methyl bearing side chains of Cdc42Hs results in a modest rigidification, which is estimated to correspond to an unfavorable change in conformational entropy of approximately −10 kcal mol−1 at 298 K. A cluster of methyl probes closest to the nucleotide-binding pocket of Cdc42Hs become more rigid upon binding of PBD46 and is proposed to slow the catalytic hydrolysis of the γ phosphate moiety. An additional cluster of methyl probes surrounding the guanine ring become more flexible on binding of PBD46, presumably facilitating nucleotide exchange mediated by a guanosine exchange factor. In addition, the Rho insert helix, which is located at a site remote from the PBD46 binding interface, shows a significant dynamic response to PBD46 binding. PMID:25109462

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

PubMed

Lietzow, Michael A; Hubbell, Wayne L

2004-03-23

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

Dissipative Quantum Control of a Spin Chain

NASA Astrophysics Data System (ADS)

Morigi, Giovanna; Eschner, Jürgen; Cormick, Cecilia; Lin, Yiheng; Leibfried, Dietrich; Wineland, David J.

2015-11-01

A protocol is discussed for preparing a spin chain in a generic many-body state in the asymptotic limit of tailored nonunitary dynamics. The dynamics require the spectral resolution of the target state, optimized coherent pulses, engineered dissipation, and feedback. As an example, we discuss the preparation of an entangled antiferromagnetic state, and argue that the procedure can be applied to chains of trapped ions or Rydberg atoms.

Value-Chain Dynamics of the West Point Foundry, 1817-1911: A Historical Case Analysis in Marketing

ERIC Educational Resources Information Center

Petkus, Ed, Jr.

2013-01-01

This case provides the opportunity for students to explore marketing and value/supply-chain dynamics in a unique historical context. The West Point Foundry (WPF), located in Cold Spring, New York, was one of the most important manufacturing ventures in the United States from 1817 to 1911. The case outlines the supply-chain details of the WPF as…

Dynamical phase transition in the simplest molecular chain model

NASA Astrophysics Data System (ADS)

Malyshev, V. A.; Muzychka, S. A.

2014-04-01

We consider the dynamics of the simplest chain of a large number N of particles. In the double scaling limit, we find the partition of the parameter space into two domains: for one domain, the supremum over the time interval ( 0,∞) of the relative extension of the chain tends to 1 as N → ∞, and for the other domain, to infinity.

Determining rotational dynamics of the guanidino group of arginine side chains in proteins by carbon-detected NMR.

PubMed

Gerecht, Karola; Figueiredo, Angelo Miguel; Hansen, D Flemming

2017-09-16

Arginine residues are imperative for many active sites and protein-interaction interfaces. A new NMR-based method is presented to determine the rotational dynamics around the N ε -C ζ bond of arginine side chains. An application to a 19 kDa protein shows that the strengths of interactions involving arginine side chains can be characterised.

Finite-size effects on the dynamic susceptibility of CoPhOMe single-chain molecular magnets in presence of a static magnetic field

NASA Astrophysics Data System (ADS)

Pini, M. G.; Rettori, A.; Bogani, L.; Lascialfari, A.; Mariani, M.; Caneschi, A.; Sessoli, R.

2011-09-01

The static and dynamic properties of the single-chain molecular magnet Co(hfac)2NITPhOMe (CoPhOMe) (hfac = hexafluoroacetylacetonate, NITPhOMe = 4'-methoxy-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) are investigated in the framework of the Ising model with Glauber dynamics, in order to take into account both the effect of an applied magnetic field and a finite size of the chains. For static fields of moderate intensity and short chain lengths, the approximation of a monoexponential decay of the magnetization fluctuations is found to be valid at low temperatures; for strong fields and long chains, a multiexponential decay should rather be assumed. The effect of an oscillating magnetic field, with intensity much smaller than that of the static one, is included in the theory in order to obtain the dynamic susceptibility χ(ω). We find that, for an open chain with N spins, χ(ω) can be written as a weighted sum of N frequency contributions, with a sum rule relating the frequency weights to the static susceptibility of the chain. Very good agreement is found between the theoretical dynamic susceptibility and the ac susceptibility measured in moderate static fields (Hdc≤2 kOe), where the approximation of a single dominating frequency for each segment length turns out to be valid. For static fields in this range, data for the relaxation time, τ versus Hdc, of the magnetization of CoPhOMe at low temperature are also qualitatively reproduced by theory, provided that finite-size effects are included.

Coulomb repulsion in short polypeptides.

PubMed

Norouzy, Amir; Assaf, Khaleel I; Zhang, Shuai; Jacob, Maik H; Nau, Werner M

2015-01-08

Coulomb repulsion between like-charged side chains is presently viewed as a major force that impacts the biological activity of intrinsically disordered polypeptides (IDPs) by determining their spatial dimensions. We investigated short synthetic models of IDPs, purely composed of ionizable amino acid residues and therefore expected to display an extreme structural and dynamic response to pH variation. Two synergistic, custom-made, time-resolved fluorescence methods were applied in tandem to study the structure and dynamics of the acidic and basic hexapeptides Asp6, Glu6, Arg6, Lys6, and His6 between pH 1 and 12. (i) End-to-end distances were obtained from the short-distance Förster resonance energy transfer (sdFRET) from N-terminal 5-fluoro-l-tryptophan (FTrp) to C-terminal Dbo. (ii) End-to-end collision rates were obtained for the same peptides from the collision-induced fluorescence quenching (CIFQ) of Dbo by FTrp. Unexpectedly, the very high increase of charge density at elevated pH had no dynamical or conformational consequence in the anionic chains, neither in the absence nor in the presence of salt, in conflict with the common view and in partial conflict with accompanying molecular dynamics simulations. In contrast, the cationic peptides responded to ionization but with surprising patterns that mirrored the rich individual characteristics of each side chain type. The contrasting results had to be interpreted, by considering salt screening experiments, N-terminal acetylation, and simulations, in terms of an interplay of local dielectric constant and peptide-length dependent side chain charge-charge repulsion, side chain functional group solvation, N-terminal and side chain charge-charge repulsion, and side chain-side chain as well as side chain-backbone interactions. The common picture that emerged is that Coulomb repulsion between water-solvated side chains is efficiently quenched in short peptides as long as side chains are not in direct contact with each other or the main chain.

Decomposition of total solvation energy into core, side-chains and water contributions: Role of cross correlations and protein conformational fluctuations in dynamics of hydration layer

NASA Astrophysics Data System (ADS)

Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

2017-09-01

Dynamical coupling between water and amino acid side-chain residues in solvation dynamics is investigated by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain and (iii) water. Significant anti cross-correlation among these contributions are observed. When the motion of the protein side-chains is quenched, solvation either becomes faster or slower depending on the location of the probe.

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

Equilibrium and Dynamics Properties of Poly(oxyethylene) Melts and Related Poly(alkylethers) from Simulations and Ab Initio Calculations

NASA Technical Reports Server (NTRS)

Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)

1994-01-01

Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.

Design and analysis of the Gemini chain system in dual clutch transmission of automobile

NASA Astrophysics Data System (ADS)

Cheng, Yabing; Guo, Haitao; Fu, Zhenming; Wan, Nen; Li, Lei; Wang, Yang

2015-01-01

Chain drive system is widely used in the conditions of high-speed, overload, variable speed and load. Many studies are focused on the meshing theory and wear characteristics of chain drive system, but system design, analysis, and noise characteristics of the chain drive system are weak. System design and noise characteristic are studied for a new type Gemini chain of dual-clutch automatic transmission. Based on the meshing theory of silent chain, the design parameters of the Gemini chain system are calculated and the mathematical models and dynamic analysis models of the Gemini chain system are established. Dynamic characteristics of the Gemini chain system is simulated and the contact force of plate and pin, plate and sprockets, the chain tension forces, the transmission error and the stress of plates and pins are analyzed. According to the simulation results of the Gemini chain system, the noise experiment about system is carried out. The noise values are tested at different speed and load and spectral characteristics are analyzed. The results of simulation and experimental show that the contact forces of plate and pin, plate and sprockets are smaller than the allowable stress values, the chain tension force is less than ultimate tension and transmission error is limited in 1.2%. The noise values can meet the requirements of industrial design, and it is proved that the design and analysis method of the Gemini chain system is scientific and feasible. The design and test system is built from analysis to test of Gemini chain system. This research presented will provide a corresponding theoretical guidance for the design and dynamic characteristics and noise characteristics of chain drive system.

Hidden chiral symmetries in BDI multichannel Kitaev chains

NASA Astrophysics Data System (ADS)

Manesco, Antônio L. R.; Weber, Gabriel; Rodrigues, Durval, Jr.

2018-05-01

Realistic implementations of the Kitaev chain require, in general, the introduction of extra internal degrees of freedom. In the present work, we discuss the presence of hidden BDI symmetries for free Hamiltonians describing systems with an arbitrary number of internal degrees of freedom. We generalize results of a spinfull Kitaev chain to construct a Hamiltonian with n internal degrees of freedom and obtain the corresponding hidden chiral symmetry. As an explicit application of this generalized result, we exploit by analytical and numerical calculations the case of a spinful two-band Kitaev chain, which can host up to four Majorana bound states. We also observe the appearence of minigap states, when chiral symmetry is broken.

Dynamic modeling and optimal joint torque coordination of advanced robotic systems

NASA Astrophysics Data System (ADS)

Kang, Hee-Jun

The development is documented of an efficient dynamic modeling algorithm and the subsequent optimal joint input load coordination of advanced robotic systems for industrial application. A closed-form dynamic modeling algorithm for the general closed-chain robotic linkage systems is presented. The algorithm is based on the transfer of system dependence from a set of open chain Lagrangian coordinates to any desired system generalized coordinate set of the closed-chain. Three different techniques for evaluation of the kinematic closed chain constraints allow the representation of the dynamic modeling parameters in terms of system generalized coordinates and have no restriction with regard to kinematic redundancy. The total computational requirement of the closed-chain system model is largely dependent on the computation required for the dynamic model of an open kinematic chain. In order to improve computational efficiency, modification of an existing open-chain KIC based dynamic formulation is made by the introduction of the generalized augmented body concept. This algorithm allows a 44 pct. computational saving over the current optimized one (O(N4), 5995 when N = 6). As means of resolving redundancies in advanced robotic systems, local joint torque optimization is applied for effectively using actuator power while avoiding joint torque limits. The stability problem in local joint torque optimization schemes is eliminated by using fictitious dissipating forces which act in the necessary null space. The performance index representing the global torque norm is shown to be satisfactory. In addition, the resulting joint motion trajectory becomes conservative, after a transient stage, for repetitive cyclic end-effector trajectories. The effectiveness of the null space damping method is shown. The modular robot, which is built of well defined structural modules from a finite-size inventory and is controlled by one general computer system, is another class of evolving, highly versatile, advanced robotic systems. Therefore, finally, a module based dynamic modeling algorithm is presented for the dynamic coordination of such reconfigurable modular robotic systems. A user interactive module based manipulator analysis program (MBMAP) has been coded in C language running on 4D/70 Silicon Graphics.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Molecular dynamics simulation of the folding of single alkane chains with different lengths on single-walled carbon nanotubes and graphene.

PubMed

Liu, Yan Fang; Yang, Hua; Zhang, Hui

2018-05-31

Chain folding is an important step during polymer crystallization. In order to study the effects of the surface on chain folding, molecular dynamics simulations of the folding of different alkane chains on three kinds of single-walled carbon nanotubes (SWCNTs) and graphene were performed. The folding behaviors of the single alkane chains on these surfaces were found to be different from their folding behaviors in vacuum. The end-to-end distances of the chains were calculated to explore the chain folding. An increasing tendency to fold into two or more stems with increasing alkane chain length was observed. This result indicates that the occurrence and the stability of chain folding are related to the surface curvature, the diameter of the SWCNT, and surface texture. In addition, the angle between the direction of the alkane chain segment and the direction of the surface texture was measured on different surfaces.

Molecular, dynamic, and structural origin of inhomogeneous magnetization transfer in lipid membranes.

PubMed

Swanson, Scott D; Malyarenko, Dariya I; Fabiilli, Mario L; Welsh, Robert C; Nielsen, Jon-Fredrik; Srinivasan, Ashok

2017-03-01

To elucidate the dynamic, structural, and molecular properties that create inhomogeneous magnetization transfer (ihMT) contrast. Amphiphilic lipids, lamellar phospholipids with cholesterol, and bovine spinal cord (BSC) specimens were examined along with nonlipid systems. Magnetization transfer (MT), enhanced MT (eMT, obtained with double-sided radiofrequency saturation), ihMT (MT - eMT), and dipolar relaxation, T 1D , were measured at 2.0 and 11.7 T. The amplitude of ihMT ratio (ihMTR) is positively correlated with T 1D values. Both ihMTR and T 1D increase with increasing temperature in BSC white matter and in phospholipids and decrease with temperature in other lipids. Changes in ihMTR with temperature arise primarily from alterations in MT rather than eMT. Spectral width of MT, eMT, and ihMT increases with increasing carbon chain length. Concerted motions of phospholipids in white matter decrease proton spin diffusion leading to increased proton T 1D times and increased ihMT amplitudes, consistent with decoupling of Zeeman and dipolar spin reservoirs. Molecular specificity and dynamic sensitivity of ihMT contrast make it a suitable candidate for probing myelin membrane disorders. Magn Reson Med 77:1318-1328, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

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

DTIC Science & Technology

1978-07-01

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

DNA Molecules in Microfluidic Oscillatory Flow

PubMed Central

Chen, Y.-L.; Graham, M.D.; de Pablo, J.J.; Jo, K.; Schwartz, D.C.

2008-01-01

The conformation and dynamics of a single DNA molecule undergoing oscillatory pressure-driven flow in microfluidic channels is studied using Brownian dynamics simulations, accounting for hydrodynamic interactions between segments in the bulk and between the chain and the walls. Oscillatory flow provides a scenario under which the polymers may remain in the channel for an indefinite amount of time as they are stretched and migrate away from the channel walls. We show that by controlling the chain length, flow rate and oscillatory flow frequency, we are able to manipulate the chain extension and the chain migration from the channel walls. The chain stretch and the chain depletion layer thickness near the wall are found to increase as the Weissenberg number increases and as the oscillatory frequency decreases. PMID:19057656

Chain-reaction crash in traffic flow controlled by taillights

NASA Astrophysics Data System (ADS)

Nagatani, Takashi

2015-02-01

We study the chain-reaction crash (multiple-vehicle collision) in low-visibility condition on a road. In the traffic situation, drivers brake according to taillights of the forward vehicle. The first crash may induce more collisions. We investigate whether or not the first collision induces the chain-reaction crash, numerically and analytically. The dynamic transitions occur from no collisions through a single collision, double collisions and triple collisions, to multiple collisions with decreasing the headway. Also, we find that the dynamic transition occurs from the finite chain reaction to the infinite chain reaction when the headway is less than the critical value. We derive, analytically, the transition points and the region maps for the chain-reaction crash in traffic flow controlled by taillights.

Markovian robots: Minimal navigation strategies for active particles

NASA Astrophysics Data System (ADS)

Nava, Luis Gómez; Großmann, Robert; Peruani, Fernando

2018-04-01

We explore minimal navigation strategies for active particles in complex, dynamical, external fields, introducing a class of autonomous, self-propelled particles which we call Markovian robots (MR). These machines are equipped with a navigation control system (NCS) that triggers random changes in the direction of self-propulsion of the robots. The internal state of the NCS is described by a Boolean variable that adopts two values. The temporal dynamics of this Boolean variable is dictated by a closed Markov chain—ensuring the absence of fixed points in the dynamics—with transition rates that may depend exclusively on the instantaneous, local value of the external field. Importantly, the NCS does not store past measurements of this value in continuous, internal variables. We show that despite the strong constraints, it is possible to conceive closed Markov chain motifs that lead to nontrivial motility behaviors of the MR in one, two, and three dimensions. By analytically reducing the complexity of the NCS dynamics, we obtain an effective description of the long-time motility behavior of the MR that allows us to identify the minimum requirements in the design of NCS motifs and transition rates to perform complex navigation tasks such as adaptive gradient following, detection of minima or maxima, or selection of a desired value in a dynamical, external field. We put these ideas in practice by assembling a robot that operates by the proposed minimalistic NCS to evaluate the robustness of MR, providing a proof of concept that is possible to navigate through complex information landscapes with such a simple NCS whose internal state can be stored in one bit. These ideas may prove useful for the engineering of miniaturized robots.

Unified force-level theory of multiscale transient localization and emergent elasticity in polymer solutions and melts

NASA Astrophysics Data System (ADS)

Dell, Zachary E.; Schweizer, Kenneth S.

A unified, microscopic, theoretical understanding of polymer dynamics in concentrated liquids from segmental to macromolecular scales remains an open problem. We have formulated a statistical mechanical theory for this problem that explicitly accounts for intra- and inter-molecular forces at the Kuhn segment level. The theory is self-consistently closed at the level of a matrix of dynamical second moments of a tagged chain. Two distinct regimes of isotropic transient localization are predicted. In semidilute solutions, weak localization is predicted on a mesoscopic length scale between segment and chain scales which is a power law function of the invariant packing length. This is consistent with the breakdown of Rouse dynamics and the emergence of entanglements. The chain structural correlations in the dynamically arrested state are also computed. In dense melts, strong localization is predicted on a scale much smaller than the segment size which is weakly dependent on chain connectivity and signals the onset of glassy dynamics. Predictions of the dynamic plateau shear modulus are consistent with the known features of emergent rubbery and glassy elasticity. Generalizations to treat the effects of chemical crosslinking and physical bond formation in polymer gels are possible.

Coulomb scatter of diamagnetic dust particles in a cusp magnetic trap under microgravity conditions

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

Myasnikov, M. I., E-mail: miasnikovmi@mail.ru; D’yachkov, L. G.; Petrov, O. F.

2017-02-15

The effect of a dc electric field on strongly nonideal Coulomb systems consisting of a large number (~10{sup 4}) of charged diamagnetic dust particles in a cusp magnetic trap are carried out aboard the Russian segment of the International Space Station (ISS) within the Coulomb Crystal experiment. Graphite particles of 100–400 μm in size are used in the experiments. Coulomb scatter of a dust cluster and the formation of threadlike chains of dust particles are observed experimentally. The processes observed are simulated by the molecular dynamics (MD) method.

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

PubMed Central

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

1993-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Molecular structure of starches from maize mutants deficient in starch synthase III.

PubMed

Zhu, Fan; Bertoft, Eric; Källman, Anna; Myers, Alan M; Seetharaman, Koushik

2013-10-16

Molecular structures of starches from dull1 maize mutants deficient in starch synthase III (SSIII) with a common genetic background (W64A) were characterized and compared with the wild type. Amylose content with altered structure was higher in the nonwaxy mutants (25.4-30.2%) compared to the wild type maize (21.5%) as revealed by gel permeation chromatography. Superlong chains of the amylopectin component were found in all nonwaxy samples. Unit chain length distribution of amylopectins and their φ,β-limit dextrins (reflecting amylopectin internal structure) from dull1 mutants were also characterized by anion-exchange chromatography after debranching. Deficiency of SSIII led to an increased amount of short chains (DP ≤36 in amylopectin), whereas the content of long chains decreased from 8.4% to between 3.1 and 3.7% in both amylopectin and φ,β-limit dextrins. Moreover, both the external and internal chain lengths decreased, suggesting a difference in their cluster structures. Whereas the molar ratio of A:B-chains was similar in all samples (1.1-1.2), some ratios of chain categories were affected by the absence of SSIII, notably the ratio of "fingerprint" A-chains to "clustered" A-chains. This study highlighted the relationship between SSIII and the internal molecular structure of maize starch.

Research about vibration characteristics of timing chain system based on short-time Fourier transform

NASA Astrophysics Data System (ADS)

Xi, Jiaxin; Liu, Ning

2017-09-01

Vibration characteristic of timing chain system is very important for an engine. In this study, we used a bush roller chain drive system as an example to explain how to use mulitybody dynamic techniques and short-time Fourier transform to investigate vibration characteristics of timing chain system. Multibody dynamic simulation data as chain tension force and external excitation sources curves were provided for short-time Fourier transform study. The study results of short-time Fourier transform illustrate that there are two main vibration frequency domain of timing chain system, one is the low frequency vibration caused by crankshaft sprocket velocity and camshaft sprocket torque. Another is vibration around 1000Hz lead by hydraulic tensioner. Hence, short-time Fourier transform method is useful for basic research of vibration characteristics for timing chain system.

[Differences in dynamics of insulin and insulin-like growth I (IGF-I) receptors internalization in isolated rat hepatocytes].

PubMed

Kolychev, A P; Ternovskaya, E E; Arsenieva, A V; Shapkina, E V

2013-01-01

Insulin and IGF-I are two related peptides performing in the mammalian body functionally different roles of the metabolic and growth hormones, respectively. Internalization of the insulin-receptor complex (IRC) is the most important chain of mechanism of the action of hormone. To elucidate differences in the main stages of internalization of the two related hormones, the internalization dynamics of 125I-insulin and 125I-IGF-I was traced in isolated rat hepatocytes at 37 and 12 degrees C. There were established marked differences in the process of internalization of labeled hormones, which is stimulated by insulin and IGF-I. At 37 degrees C the insulin-stimulated internalization, unlike the process initiated by IGF-I, did not reach the maximal level for 1 h of incubation. However, essential differences in the internalization course of these two related peptide were obvious at the temperature of 12 degrees C. The internalization level of insulin receptors at 12 degrees C decreased by one third in spite of a significant increase of the insulin receptor binding on the hepatocytes plasma membrane. At 12 degrees C a slight decrease of the proportion of intracellular 125I-IGF-I correlated with a decrease in the 125I-IGF-I binding to receptors on the cell membrane. Internalization of IGF-I receptors was not affected by low temperature, as neither its level, nor the rate changed at 12 degrees C. The paradoxical decrease of the insulin-stimulated internalization at low temperature seems to represent a peculiar "inhibition mechanism" of immersion of IRC into the cell, which leads to accumulation of the complexes on the cell surface and possibly to a readjustment of the insulin biological activity. The resistance of internalization of the IGF-I receptor to cold seems to be related to the more ancient origin of this mechanism in the poikilothermal vertebrates.

Molecular dynamic heterogeneity of confined lipid films by 1H magnetization-exchange nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Buda, A.; Demco, D. E.; Jagadeesh, B.; Blümich, B.

2005-01-01

The molecular dynamic heterogeneity of monolayer to submonolayer thin lecithin films confined to submicron cylindrical pores were investigated by 1H magnetization exchange nuclear magnetic resonance. In this experiment a z-magnetization gradient was generated by a double-quantum dipolar filter. The magnetization-exchange decay and buildup curves were interpreted with the help of a theoretical model based on the approximation of a one-dimensional spin-diffusion process in a three-domain morphology. The dynamic heterogeneity of the fatty acid chains and the effects of the surface area per molecule, the diameter of the pores, and the temperature were characterized with the help of local spin-diffusion coefficients. The effect of various parameters on the molecular dynamics of the mobile region of the fatty acid chains was quantified by introducing an ad hoc Gaussian distribution function of the 1H residual dipolar couplings. For the lipid films investigated in this study, the surface induced order and the geometrical confinement affect the chain dynamics of the entire molecule. Therefore, each part of the chain independently reflects the effect of surface coverage, pore size, and temperature.

Dynamics of two disks settling in a two-dimensional narrow channel: From periodic motion to vertical chain in Oldroyd-B fluid

NASA Astrophysics Data System (ADS)

Pan, Tsorng-Whay; Glowinski, Roland

2016-11-01

In this talk we present a numerical study of the dynamics of two disks settling in a narrow vertical channel filled with an Oldroyd-B fluid. Two kinds of particle dynamics are obtained: (i) periodic interaction between two disks and (ii) the formation of the chain of two disks. For the periodic interaction of two disks, two different motions are obtained: (a) two disks stay far apart and interact is periodically, which is similar to one of the motions of two disks settling in a narrow channel filled with a Newtonian fluid discussed by Aidun & Ding and (b) two disks draft, kiss and break away periodically and the chain is not formed due to not strong enough elastic force. For the formation of two disk chain occurred at higher values of the elasticity number, it is either a tilted chain or a vertical chain. The tilted chain can be obtained for either that the elasticity number is less than the critical value for having the vertical chain or that the Mach number is greater than the critical value for a long body to fall broadside-on, which is consistent with the results for the elliptic particles settling in Oldroyd-B fluids. NSF.

Chain Dynamics in a Dilute Magnetorheological Fluid

NASA Technical Reports Server (NTRS)

Liu, Jing; Hagenbuchle, Martin

1996-01-01

The structure, formation, and dynamics of dilute, mono-dispersive ferrofluid emulsions in an external magnetic field have been investigated using dynamic light scattering techniques. In the absence of the magnetic field, the emulsion particles are randomly distributed and behave like hard spheres in Brownian motion. An applied magnetic field induces a magnetic dipole moment in each particle. Dipolar interactions between particles align them into chains where correlation functions show two decay processes. The short-time decay shows the motion of straight chains as a whole where the apparent chain length increases with the applied magnetic field and the particle volume fraction. Good scaling results are obtained showing that the apparent chain length grows with time following a power law with exponent of 0.6 and depends on the applied field, particle volume fraction, and diffusion constant of the particles. The long-time decay in the correlation function shows oscillation when the chains reach a certain length with time and stiffness with threshold field This result shows that chains not only fluctuate, but move in a periodic motion with a frequency of 364 Hz at lambda = 15. It may suggest the existence of phonons. This work is the first step in the understanding of the structure formation, especially chain coarsening mechanism, of magnetorheological (MR) fluids at higher volume fractions.

Size of the Dynamic Bead in Polymers

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

Agapov, Alexander L; Sokolov, Alexei P

2010-01-01

Presented analysis of neutron, mechanical, and MD simulation data available in the literature demonstrates that the dynamic bead size (the smallest subchain that still exhibits the Rouse-like dynamics) in most of the polymers is significantly larger than the traditionally defined Kuhn segment. Moreover, our analysis emphasizes that even the static bead size (e.g., chain statistics) disagrees with the Kuhn segment length. We demonstrate that the deficiency of the Kuhn segment definition is based on the assumption of a chain being completely extended inside a single bead. The analysis suggests that representation of a real polymer chain by the bead-and-spring modelmore » with a single parameter C cannot be correct. One needs more parameters to reflect correctly details of the chain structure in the bead-and-spring model.« less

Dynamic Self-Consistent Field Theories for Polymer Blends and Block Copolymers

NASA Astrophysics Data System (ADS)

Kawakatsu, Toshihiro

Understanding the behavior of the phase separated domain structures and rheological properties of multi-component polymeric systems require detailed information on the dynamics of domains and that of conformations of constituent polymer chains. Self-consistent field (SCF) theory is a useful tool to treat such a problem because the conformation entropy of polymer chains in inhomogeneous systems can be evaluated quantitatively using this theory. However, when we turn our attention to the dynamic properties in a non-equilibrium state, the basic assumption of the SCF theory, i.e. the assumption of equilibrium chain conformation, breaks down. In order to avoid such a difficulty, dynamic SCF theories were developed. In this chapter, we give a brief review of the recent developments of dynamic SCF theories, and discuss where the cutting-edge of this theory is.

Global dynamics in a stoichiometric food chain model with two limiting nutrients.

PubMed

Chen, Ming; Fan, Meng; Kuang, Yang

2017-07-01

Ecological stoichiometry studies the balance of energy and multiple chemical elements in ecological interactions to establish how the nutrient content affect food-web dynamics and nutrient cycling in ecosystems. In this study, we formulate a food chain with two limiting nutrients in the form of a stoichiometric population model. A comprehensive global analysis of the rich dynamics of the targeted model is explored both analytically and numerically. Chaotic dynamic is observed in this simple stoichiometric food chain model and is compared with traditional model without stoichiometry. The detailed comparison reveals that stoichiometry can reduce the parameter space for chaotic dynamics. Our findings also show that decreasing producer production efficiency may have only a small effect on the consumer growth but a more profound impact on the top predator growth. Copyright © 2017 Elsevier Inc. All rights reserved.

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

PubMed Central

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

2015-01-01

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

Influence of credit scoring on the dynamics of Markov chain

NASA Astrophysics Data System (ADS)

Galina, Timofeeva

2015-11-01

Markov processes are widely used to model the dynamics of a credit portfolio and forecast the portfolio risk and profitability. In the Markov chain model the loan portfolio is divided into several groups with different quality, which determined by presence of indebtedness and its terms. It is proposed that dynamics of portfolio shares is described by a multistage controlled system. The article outlines mathematical formalization of controls which reflect the actions of the bank's management in order to improve the loan portfolio quality. The most important control is the organization of approval procedure of loan applications. The credit scoring is studied as a control affecting to the dynamic system. Different formalizations of "good" and "bad" consumers are proposed in connection with the Markov chain model.

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.

Quantum Markov chains

NASA Astrophysics Data System (ADS)

Gudder, Stanley

2008-07-01

A new approach to quantum Markov chains is presented. We first define a transition operation matrix (TOM) as a matrix whose entries are completely positive maps whose column sums form a quantum operation. A quantum Markov chain is defined to be a pair (G,E) where G is a directed graph and E =[Eij] is a TOM whose entry Eij labels the edge from vertex j to vertex i. We think of the vertices of G as sites that a quantum system can occupy and Eij is the transition operation from site j to site i in one time step. The discrete dynamics of the system is obtained by iterating the TOM E. We next consider a special type of TOM called a transition effect matrix. In this case, there are two types of dynamics, a state dynamics and an operator dynamics. Although these two types are not identical, they are statistically equivalent. We next give examples that illustrate various properties of quantum Markov chains. We conclude by showing that our formalism generalizes the usual framework for quantum random walks.

A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins

DOE PAGES

Kim, Hanseong; Zou, Taisong; Modi, Chintan; ...

2014-12-31

In proteins, functional divergence involves mutations that modify structure and dynamics. In this paper, we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, catalytic group rearrangements, or changes in subunit assembly. Crystallographic structures were determined for several reconstructed ancestral proteins belonging to a GFP class frequently employed in superresolution microscopy. Their chain flexibility was analyzed using molecular dynamics and perturbation response scanning. The green-to-red photoconvertible phenotype appears to have arisen from a common green ancestor by migration of a knob-like anchoring region away from the active site diagonally across the βmore » barrel fold. The allosterically coupled mutational sites provide active site conformational mobility via epistasis. We propose that light-induced chromophore twisting is enhanced in a reverse-protonated subpopulation, activating internal acid-base chemistry and backbone cleavage to enlarge the chromophore. Finally, dynamics-driven hinge migration may represent a more general platform for the evolution of novel enzyme activities.« less

Dynamic light scattering and X-ray photoelectron spectroscopy characterization of PEGylated polymer nanocarriers: internal structure and surface properties.

PubMed

Celasco, Edvige; Valente, Ilaria; Marchisio, Daniele L; Barresi, Antonello A

2014-07-22

In this work, nanospheres and nanocapsules are precipitated in confined impinging jet mixers through solvent displacement and characterized. Acetone and water are used as the solvent and antisolvent, respectively, together with polymethoxypolyethylene glycol cyanoacrylate-co-hexadecylcyanoacrylate and Miglyol as the copolymer and oil, respectively. Characterization is performed with dynamic light scattering, with electrophoretic measurements, and for the first time with X-ray photoelectron spectroscopy. Results show that the presence of polyethylene glycol chains seems to be more pronounced on the surface of nanospheres than on that of nanocapsules. The thickness of the copolymer layer in nanocapsules ranges from 1 to 10 nm, depending on the value of the oil:copolymer mass ratio. Fast dilution is confirmed to have a positive effect in suppressing aggregation but can induce further copolymer precipitation.

Polymer diffusion in quenched disorder: A renormalization group approach

NASA Astrophysics Data System (ADS)

Ebert, Ute

1996-01-01

We study the diffusion of polymers through quenched short-range correlated random media by renormalization group (RG) methods, which allow us to derive universal predictions in the limit of long chains and weak disorder. We take local quenched random potentials with second moment v and the excluded-volume interaction u of the chain segments into account. We show that our model contains the relevant features of polymer diffusion in random media in the RG sense if we focus on the local entropic effects rather than on the topological constraints of a quenched random medium. The dynamic generating functional and the general structure of its perturbation expansion in u and v are derived. The distribution functions for the center-of-mass motion and the internal modes of one chain and for the correlation of the center of mass motions of two chains are calculated to one-loop order. The results allow for sufficient cross-checks to have trust in the one-loop renormalizability of the model. The general structure as well as the one-loop results of the integrated RG flow of the parameters are discussed. Universal results can be found for the effective static interaction w≔u-v≥0 and for small effective disorder couplingbar v(l) on the intermediate length scale l. As a first physical prediction from our analysis, we determine the general nonlinear scaling form of the chain diffusion constant and evaluate it explicitly as[Figure not available: see fulltext.] forbar v(l) ≪ 1.

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

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

Smith, Dayle MA; Xiong, Yijia; Straatsma, TP

2012-05-09

Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexiblemore » in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.« less

Nanostructures and dynamics of macromolecules bound to attractive filler surfaces

NASA Astrophysics Data System (ADS)

Koga, Tad; Barkley, Deborah; Jiang, Naisheng; Endoh, Maya; Masui, Tomomi; Kishimoto, Hiroyuki; Nagao, Michihiro; Satija, Sushil; Taniguchi, Takashi

We report in-situ nanostructures and dynamics of polybutadiene (PB) chains bound to carbon black (CB) fillers (the so-called ``bound polymer layer (BPL)'') in a good solvent. The BPL on the CB fillers were extracted by solvent leaching of a CB-filled PB compound and subsequently dispersed in deuterated toluene to label the BPL for small-angle neutron scattering and neutron spin echo techniques. Intriguingly, the results demonstrate that the BPL is composed of two regions regardless of molecular weights of PB: the inner unswollen region of ~ 0.5 nm thick and outer swollen region where the polymer chains display a parabolic profile with a diffuse tail. This two-layer formation on the filler surface is similar to that reported for polymer chains adsorbed on planar substrates from melts. In addition, the results show that the dynamics of the swollen bound chains can be explained by the so-called ``breathing mode'' and is generalized with the thickness of the swollen BPL. Furthermore, we will discuss how the breathing collective dynamics is affected by the presence of polymer chains in a matrix solution. We acknowledge the financial support from NSF Grant No. CMMI-1332499.

Shocks, Rarefaction Waves, and Current Fluctuations for Anharmonic Chains

DOE PAGES

Mendl, Christian B.; Spohn, Herbert

2016-10-04

The nonequilibrium dynamics of anharmonic chains is studied by imposing an initial domain-wall state, in which the two half lattices are prepared in equilibrium with distinct parameters. Here, we analyse the Riemann problem for the corresponding Euler equations and, in specific cases, compare with molecular dynamics. Additionally, the fluctuations of time-integrated currents are investigated. In analogy with the KPZ equation, their typical fluctuations should be of size t 1/3 and have a Tracy–Widom GUE distributed amplitude. The proper extension to anharmonic chains is explained and tested through molecular dynamics. Our results are calibrated against the stochastic LeRoux lattice gas.

Irreversible Markov chains in spin models: Topological excitations

NASA Astrophysics Data System (ADS)

Lei, Ze; Krauth, Werner

2018-01-01

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

Data Quality -- A Key to Successfully Implementing ECSS

DTIC Science & Technology

2009-03-01

Inventory inaccuracy and supply chain performance: A simulation study of a retail supply chain. International Journal of Production Economics , 95...Planning (ERP) System Implementations Based on Critical Success Factors (CSFs). International Journal of Production Economics , 98(2), 189- 203. Tersine

Merging constitutional and motional covalent dynamics in reversible imine formation and exchange processes.

PubMed

Kovaříček, Petr; Lehn, Jean-Marie

2012-06-06

The formation and exchange processes of imines of salicylaldehyde, pyridine-2-carboxaldehyde, and benzaldehyde have been studied, showing that the former has features of particular interest for dynamic covalent chemistry, displaying high efficiency and fast rates. The monoimines formed with aliphatic α,ω-diamines display an internal exchange process of self-transimination type, inducing a local motion of either "stepping-in-place" or "single-step" type by bond interchange, whose rate decreases rapidly with the distance of the terminal amino groups. Control of the speed of the process over a wide range may be achieved by substituents, solvent composition, and temperature. These monoimines also undergo intermolecular exchange, thus merging motional and constitutional covalent behavior within the same molecule. With polyamines, the monoimines formed execute internal motions that have been characterized by extensive one-dimensional, two-dimensional, and EXSY proton NMR studies. In particular, with linear polyamines, nondirectional displacement occurs by shifting of the aldehyde residue along the polyamine chain serving as molecular track. Imines thus behave as simple prototypes of systems displaying relative motions of molecular moieties, a subject of high current interest in the investigation of synthetic and biological molecular motors. The motional processes described are of dynamic covalent nature and take place without change in molecular constitution. They thus represent a category of dynamic covalent motions, resulting from reversible covalent bond formation and dissociation. They extend dynamic covalent chemistry into the area of molecular motions. A major further step will be to achieve control of directionality. The results reported here for imines open wide perspectives, together with other chemical groups, for the implementation of such features in multifunctional molecules toward the design of molecular devices presenting a complex combination of motional and constitutional dynamic behaviors.

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

Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph

Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less

Application of a sodium sulfur cell with dynamic sulfur electrode to a battery system

NASA Astrophysics Data System (ADS)

Tokoi, H.; Takahashi, K.; Shimoyashiki, S.

1992-01-01

The construction and performance of a sodium sulfur battery system with dynamic sulfur electrodes are described. Three cells were first connected in parallel, then two such groups were connected in series. Each cell included a liquid sodium-filled beta-double-prime-alumina tube and a system to feed liquid sulfur into the annular cathode. Low-resistance graphite felt was tightly packed around the beta-double-prime-alumina tube. Sodium pentasulfide was removed from the sulfur electrode. The battery was operated automatically and stably charged and discharged in the two-phase region. The discharged energy was 4372 Wh (capacity 1170 Ah) during a continuous operation of 19.5 h. The discharge/charge energy efficiency of the battery was 82 percent at an averaged current density of 100 mA/sq cm and operating temperature of 350 C. The deviation of the cell current in a parallel chain was less than 7 percent, and this was induced by the difference in internal resistance. In the daily charge/discharge cycle, cell capacity with the dynamic sulfur electrode was 1.5 times higher than that with the static sulfur electrode using the same active surface of beta-double-prime-alumina, because the internal resistance of the former cell was constant regardless of cell capacity. This battery system with a dynamic sulfur electrode can be applied to energy storage systems,such as large scale load leveling systems, electric vehicle batteries, and solar energy systems.

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

Liu, Siqi; Senses, Erkan; Jiao, Yang

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

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

PubMed

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

2005-08-12

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

Structure and dynamics of water inside endohedrally functionalized carbon nanotubes.

PubMed

Paul, Sanjib; Abi, T G; Taraphder, Srabani

2014-05-14

We have carried out classical molecular dynamics simulations on the formation of extended water chains inside single-walled carbon nanotubes (SWCNTs) in water in the presence of selected functional groups covalently attached to the inner wall of the tube. Analogues of polar amino acid sidechains have been chosen to carry out the endohedral functionalization of SWCNTs. Our results show a spontaneous and asymmetric filling of the nanotube with dynamical water chains in all the cases studied. The presence of Asp- and Glu-like sidechains is found to result in the formation of well-ordered water chains across the tube having the maximum number of water molecules being retained within the core with the largest residence times. The presence of methyl or methylene groups along the suspended chain is observed to disrupt the formation of water chains with higher length and/or longer residence times. The importance of hydrogen bonding in forming these water chains is assessed in terms of the relaxations of different hydrogen bond correlation functions. For a given dimension of the hydrophobic nanopore, we thus obtain a scale comparing the ability of carboxylic, alcohol, and imidazole groups in controlling the structure and dynamics of water in it. Our results also suggest that SWCNTs of varying lengths, endohedrally functionalized with Asp- and Glu-like sidechains, may be used as design templates in CNT-based water storage devices.

Conformational variety for the ansa chain of rifamycins: Comparison of observed crystal structures and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bacchi, Alessia; Pelizzi, Giancarlo

1999-07-01

The antibiotic activity (via inhibition of DNA-dependent RNA polymerase, DDRP) of rifamycins has been correlated to the conformation of the ansa chain, which can be described by means of 17 torsion angles defined along the ansa backbone. It has been shown that favourable or unfavourable conformations of the ansa chain in rifamycin crystals are generally diagnostic of activity or inactivity against isolated DDRP. The principles of structure correlation suggest that the torsional variety observed in rifamycin crystals should mimic the dynamic flexibility of the ansa chain in solution. Twenty-six crystal structures of rifamycins are grouped into two classes (active and non-active). For each class the variance of the 17 ansa backbone torsion angles is analysed. Active compounds show a well-defined common pattern, while non-active molecules are more scattered, mainly due to steric constraints forcing the molecules into unfavourable conformations. The experimental distributions of torsion angles are compared to the torsional freedom of the ansa chain simulated by molecular dynamics calculations performed at different temperatures and conditions on rifamycin S and rifamycin O, which represent a typical active and a typical sterically constrained molecule, respectively. It is shown that the torsional variety found in the crystalline state samples the dynamic behaviour of the ansa chain for active compounds. The methods of circular statistics are illustrated to describe torsion angle distributions.

Solitons riding on solitons and the quantum Newton's cradle.

PubMed

Ma, Manjun; Navarro, R; Carretero-González, R

2016-02-01

The reduced dynamics for dark and bright soliton chains in the one-dimensional nonlinear Schrödinger equation is used to study the behavior of collective compression waves corresponding to Toda lattice solitons. We coin the term hypersoliton to describe such solitary waves riding on a chain of solitons. It is observed that in the case of dark soliton chains, the formulated reduction dynamics provides an accurate an robust evolution of traveling hypersolitons. As an application to Bose-Einstein condensates trapped in a standard harmonic potential, we study the case of a finite dark soliton chain confined at the center of the trap. When the central chain is hit by a dark soliton, the energy is transferred through the chain as a hypersoliton that, in turn, ejects a dark soliton on the other end of the chain that, as it returns from its excursion up the trap, hits the central chain repeating the process. This periodic evolution is an analog of the classical Newton's cradle.

Local Dynamics of Acid- and Ion-containing Copolymer Melts

NASA Astrophysics Data System (ADS)

Winey, Karen; Middleton, Robert; Tarver, Jacob; Tyagi, Madhusudan; Soles, Christopher; Frischknecht, Amalie

Interest in acid- and ion-containing polymers arises in part from applications as single-ion conductors for selectively transporting a counter ion for battery applications. Structurally, the low dielectric constant of organic polymers and strong ionic interactions leads to ionic aggregation. Here the polymer backbone motion was investigated through quasi-elastic neutron scattering measurements (QENS) and compared with fully atomistic molecular dynamic simulations of precise poly(ethylene-acrylic acid) copolymers and their ionomers (pxAA-y%Li). The effect of carbon spacer length (x =9, 15, 21) between the acid groups and the degree of neutralization (y) with Li on PE backbone dynamics were considered. Systematic slowing in chain dynamics were observed with increasing neutralization where polymer dynamics appear constrained due to anchoring effects. Simulations provide complementary viewpoints indicating a gradient in chain dynamics as a distance away from acid groups. These results indicate that the addition of pendant acid groups inhibit typical PE backbone motion and the neutralized forms strongly suppress the fraction of mobile PE chain.

General polytropic self-gravitating cylinder free-fall and accreting mass string with a chain of collapsed objects

NASA Astrophysics Data System (ADS)

Lou, Yu-Qing; Hu, Xu-Yao

2016-06-01

We present a theoretical model framework for general polytropic (GP) hydrodynamic cylinder under self-gravity of infinite length with axial uniformity and axisymmetry. For self-similar dynamic solutions, we derive valuable integrals, analytic asymptotic solutions, sonic critical curves, shock conditions, and global numerical solutions with or without expansion shocks. Among others, we investigate various dynamic solutions featured with central free-fall asymptotic behaviours, corresponding to a collapsed mass string with a sustained dynamic accretion from a surrounding mass reservoir. Depending on the allowed ranges of a scaling index a < -1, such cylindrical dynamic mass accretion rate could be steady, increasing with time and decreasing with time. Physically, such a collapsed mass string or filament would break up into a sequence of sub-clumps and segments as induced by gravitational Jeans instabilities. Depending on the scales involved, such sub-clumps would evolve into collapsed objects or gravitationally bound systems. In diverse astrophysical and cosmological contexts, such a scenario can be adapted on various temporal, spatial and mass scales to form a chain of collapsed clumps and/or compact objects. Examples include the formation of chains of proto-stars, brown dwarfs and gaseous planets along molecular filaments; the formation of luminous massive stars along magnetized spiral arms and circum-nuclear starburst rings in barred spiral galaxies; the formation of chains of compact stellar objects such as white dwarfs, neutron stars, and black holes along a highly condensed mass string. On cosmological scales, one can perceive the formation of chains of galaxies, chains of galaxy clusters or even chains of supermassive and hypermassive black holes in the Universe including the early Universe. All these chains referred to above include possible binaries.

Unique aspects of the structure and dynamics of elementary Iβ cellulose microfibrils revealed by computational simulations.

PubMed

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

2015-05-01

The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains. © 2015 American Society of Plant Biologists. All Rights Reserved.

Nonmuscle Myosin II Is Required for Internalization of the Epidermal Growth Factor Receptor and Modulation of Downstream Signaling*

PubMed Central

Kim, Jong Hyun; Wang, Aibing; Conti, Mary Anne; Adelstein, Robert S.

2012-01-01

Ligand-induced internalization of the epidermal growth factor receptor (EGFR) is an important process for regulating signal transduction, cellular dynamics, and cell-cell communication. Here, we demonstrate that nonmuscle myosin II (NM II) is required for the internalization of the EGFR and to trigger the EGFR-dependent activation of ERK and AKT. The EGFR was identified as a protein that interacts with NM II by co-immunoprecipitation and mass spectrometry analysis. This interaction requires both the regulatory light chain 20 (RLC20) of NM II and the kinase domain of the EGFR. Two paralogs of NM II, NM II-A, and NM II-B can act to internalize the EGFR, depending on the cell type and paralog content of the cell line. Loss (siRNA) or inhibition (25 μm blebbistatin) of NM II attenuates the internalization of the EGFR and impairs EGFR-dependent activation of ERK and AKT. Both internalization of the EGFR and downstream signaling to ERK and AKT can be partially restored in siRNA-treated cells by introduction of wild type (WT) GFP-NM II, but cannot be restored by motor mutant NM II. Taken together, these results suggest that NM II plays a role in the internalization of the EGFR and EGFR-mediated signaling pathways. PMID:22718763

A Solid-State Deuterium NMR and SFG Study of the Side Chain Dynamics of Peptides Adsorbed onto Surfaces

PubMed Central

Breen, Nicholas F.; Weidner, Tobias; Li, Kun; Castner, David G.; Drobny, Gary P.

2011-01-01

The artificial amphiphilic peptide LKα14 adopts a helical structure at interfaces, with opposite orientation of its leucine (L, hydrophobic) and lysine (K, hydrophilic) side chains. When adsorbed onto surfaces, different residue side chains necessarily have different proximities to the surface, depending on both their position in the helix and the composition of the surface itself. Deuterating the individual leucine residues (isopropyl-d7) permits the use of solid-state deuterium NMR as a site-specific probe of side chain dynamics. In conjunction with SFG as a probe of the peptide binding face, we demonstrate that the mobility of specific leucine side chains at the interface is quantifiable in terms of their surface proximity. PMID:19764755

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

Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori

Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

Chain-reaction crash on a highway in high visibility

NASA Astrophysics Data System (ADS)

Nagatani, Takashi

2016-05-01

We study the chain-reaction crash (multiple-vehicle collision) in high-visibility condition on a highway. In the traffic situation, drivers control their vehicles by both gear-changing and braking. Drivers change the gears according to the headway and brake according to taillights of the forward vehicle. We investigate whether or not the first collision induces the chain-reaction crash numerically. It is shown that dynamic transitions occur from no collisions, through a single collision, to multiple collisions with decreasing the headway. Also, we find that the dynamic transition occurs from the finite chain reaction to the infinite chain reaction when the headway is less than the critical value. We compare the multiple-vehicle collisions in high-visibility with that in low-visibility. We derive the transition points and the region maps for the chain-reaction crash in high visibility.

Selected Aspects Of The Risk In The Supply Chain In Context Of The Supplier Quality Management

NASA Astrophysics Data System (ADS)

Koblen, Ivan; Lestyánszka Škůrková, Katarína

2015-06-01

The introductory part of the paper underlines the importance of "Risk-based thinking" in the Quality Management System (QMS) and risk in the supply chain, as a principle part of the QMS. After introducing the key terms, the authors focused on the principle part of the article - explanation of the external and internal supply chain risks and the main factors concerning the supply risks, demand risks and environmental risks (as cardinal types of external supply chain risks) as well as the manufacturing and process risks, network/planning and control risks (as most important types of internal supply chain risks). The authors inform on the selected supply chain risk management tools, especially on those which are linked to the appropriate utilization of quality management tools.

Acute effects of different dynamic exercises on hamstring strain risk factors.

PubMed

Chen, Che Hsiu; Xin, Ye; Lee, Kuang Wu; Lin, Ming Ju; Lin, Jiu Jenq

2018-01-01

The purpose of the study was to examine the acute effects of different dynamic exercise interventions on hamstring muscle performance. Thirty-six young men with poor hamstring flexibility were randomly assigned to three intervention groups: jogging combined with dynamic open kinetic chain stretching (DS), jogging combined with dynamic closed kinetic chain stretching (lunge with eccentric hamstring windmills, LEC), and jogging only (CON) groups. Hamstring flexibility, muscle stiffness (area under the curve, AUC), joint position sense (JPS), maximal eccentric strength (ECC), and angle of peak torque (APT) were recorded before and immediately after the exercise interventions. The results showed that the hamstring flexibility increased in DS (p < 0.001); muscle stiffness decreased in DS and was lower than jogging (p < 0.001). Moreover, ECC increased in LEC and was higher than jogging and DS (p < 0.001). APT was different among 3 groups (p < 0.001). Decreased accuracy of JPS was found in DS and jogging (p < 0.001). In conclusion, the dynamic closed kinetic chain stretching (LEC) as compared to open kinetic chain stretching (DS) or jogging group, may be an effective technique to enhance muscle performance during the pre-competition warm-up routine.

Acute effects of different dynamic exercises on hamstring strain risk factors

PubMed Central

Xin, Ye; Lee, Kuang Wu; Lin, Ming Ju

2018-01-01

The purpose of the study was to examine the acute effects of different dynamic exercise interventions on hamstring muscle performance. Thirty-six young men with poor hamstring flexibility were randomly assigned to three intervention groups: jogging combined with dynamic open kinetic chain stretching (DS), jogging combined with dynamic closed kinetic chain stretching (lunge with eccentric hamstring windmills, LEC), and jogging only (CON) groups. Hamstring flexibility, muscle stiffness (area under the curve, AUC), joint position sense (JPS), maximal eccentric strength (ECC), and angle of peak torque (APT) were recorded before and immediately after the exercise interventions. The results showed that the hamstring flexibility increased in DS (p < 0.001); muscle stiffness decreased in DS and was lower than jogging (p < 0.001). Moreover, ECC increased in LEC and was higher than jogging and DS (p < 0.001). APT was different among 3 groups (p < 0.001). Decreased accuracy of JPS was found in DS and jogging (p < 0.001). In conclusion, the dynamic closed kinetic chain stretching (LEC) as compared to open kinetic chain stretching (DS) or jogging group, may be an effective technique to enhance muscle performance during the pre-competition warm-up routine. PMID:29390001

Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field.

PubMed

Carmelo, J M P; Sacramento, P D; Machado, J D P; Campbell, D K

2015-10-14

We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the 'pseudofermion dynamical theory' (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents ζ(τ)(k) controlling the singularities for both the longitudinal (τ = l) and transverse (τ = t) dynamical structure factors for the whole momentum range k ∈ ]0,π[, in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field

NASA Astrophysics Data System (ADS)

Carmelo, J. M. P.; Sacramento, P. D.; Machado, J. D. P.; Campbell, D. K.

2015-10-01

We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the ‘pseudofermion dynamical theory’ (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents {{\\zeta}τ}(k) controlling the singularities for both the longitudinal ≤ft(τ =l\\right) and transverse ≤ft(τ =t\\right) dynamical structure factors for the whole momentum range k\\in ]0,π[ , in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

Quality of service management framework for dynamic chaining of geographic information services

NASA Astrophysics Data System (ADS)

Onchaga, Richard

2006-06-01

Dynamic chaining of geographic information services (geo-services) is gaining popularity as a new paradigm for evolving flexible geo-information systems and for providing on-demand access to geo-information. In dynamic chaining, disparate geo-services are discovered and composed at run time to yield more elaborate functionality and create value-added geo-information. Common approaches to service chaining discover and compose disparate geo-services based on the functional capability of individual geo-services. The primary concern of common approaches is thus the emergent behavior of the resulting composite geo-service. However, as geo-services become mundane and take on a greater and more strategic role in mission critical processes, deliverable quality of service (QoS) becomes an important concern. QoS concerns operational characteristics of a service that determine its utility in an application context. To address pertinent QoS requirements, a new approach to service chaining becomes necessary. In this paper we propose a QoS-aware chaining approach in which geo-services are discovered, composed and executed considering both functional and QoS requirements. We prescribe a QoS management framework that defines fundamental principles, concepts and mechanisms which can be applied to evolve an effective distributed computing platform for QoS-aware chaining of geo-services - the so-called geo-service infrastructure. The paper also defines an extensible QoS model for services delivered by dynamic compositions of geo-services. The process of orthophoto generation is used to demonstrate the applicability of the prescribed framework to service-oriented geographic information processing.

Green certification, e-commerce, and low-carbon economy for international tourist hotels.

PubMed

Chen, Long-Fei

2018-05-22

Increasing population and over-consumption are placing unprecedented demands on agriculture and natural resources. The Earth is suffering from global warning and environmental destruction while our agricultural systems are concurrently degrading land, water, biodiversity, and climate on a global scale. For a sustainable future, green certification, e-commerce, and environment education can boost low-carbon economy with decreasing carbon emissions, but very few researches address them for the hotel industry. This research studies the performance impact of e-commerce, international hotel chain, local hotel chain, and green certification for carbon emission reductions of international tourist hotels of Taiwan. It reveals that, after a sufficiently long time, there is an improvement in the environmental and economic performance of the green-certified hotel group. In addition, it reveals that, as recommended by the operation policy, the international hotel chain group together with e-commerce has better performance than local hotel chain. It is also discussed how to sustain the continuing improvement in low-carbon performance of the hotel industry.

Strategy to Enhance International Supply Chain Security

DTIC Science & Technology

2007-07-01

as part of the effort to secure air passenger travel . The security assessment crew traveling by air, land or sea cannot be considered only a travel ...threats through its traveler screening and worker credentialing programs. The strategy to secure the supply chain reflects the larger security strategy of...living or traveling abroad. • Assisting U.S. businesses in the international marketplace. • Coordinating and providing support for international

Transition records of stationary Markov chains.

PubMed

Naudts, Jan; Van der Straeten, Erik

2006-10-01

In any Markov chain with finite state space the distribution of transition records always belongs to the exponential family. This observation is used to prove a fluctuation theorem, and to show that the dynamical entropy of a stationary Markov chain is linear in the number of steps. Three applications are discussed. A known result about entropy production is reproduced. A thermodynamic relation is derived for equilibrium systems with Metropolis dynamics. Finally, a link is made with recent results concerning a one-dimensional polymer model.

Determining rotational dynamics of the guanidino group of arginine side chains in proteins by carbon-detected NMR† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7cc04821a

PubMed Central

Gerecht, Karola; Figueiredo, Angelo Miguel

2017-01-01

Arginine residues are imperative for many active sites and protein-interaction interfaces. A new NMR-based method is presented to determine the rotational dynamics around the Nε–Cζ bond of arginine side chains. An application to a 19 kDa protein shows that the strengths of interactions involving arginine side chains can be characterised. PMID:28840203

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

PubMed

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

2018-01-01

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

Network evolution model for supply chain with manufactures as the core

PubMed Central

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

2018-01-01

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

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

PubMed

Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-03-10

Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

78 FR 50394 - Advisory Committee on Supply Chain Competitiveness: Notice of Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-19

... DEPARTMENT OF COMMERCE International Trade Administration Advisory Committee on Supply Chain... discussion for a public meeting of the Advisory Committee on Supply Chain Competitiveness (Committee). DATES... growth competitiveness, foster national economic competitiveness, and improve U.S. supply chain...

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.

Ligand Binding Properties of the Lentil Lipid Transfer Protein: Molecular Insight into the Possible Mechanism of Lipid Uptake.

PubMed

Shenkarev, Zakhar O; Melnikova, Daria N; Finkina, Ekaterina I; Sukhanov, Stanislav V; Boldyrev, Ivan A; Gizatullina, Albina K; Mineev, Konstantin S; Arseniev, Alexander S; Ovchinnikova, Tatiana V

2017-03-28

The lentil lipid transfer protein, designated as Lc-LTP2, was isolated from Lens culinaris seeds. The protein belongs to the LTP1 subfamily and consists of 93 amino acid residues. Its spatial structure includes four α-helices (H1-H4) and a long C-terminal tail. Here, we report the ligand binding properties of Lc-LTP2. The fluorescent 2-p-toluidinonaphthalene-6-sulfonate binding assay revealed that the affinity of Lc-LTP2 for saturated and unsaturated fatty acids was enhanced with a decrease in acyl-chain length. Measurements of boundary potential in planar lipid bilayers and calcein dye leakage in vesicular systems revealed preferential interaction of Lc-LTP2 with the negatively charged membranes. Lc-LTP2 more efficiently transferred anionic dimyristoylphosphatidylglycerol (DMPG) than zwitterionic dimyristoylphosphatidylcholine. Nuclear magnetic resonance experiments confirmed the higher affinity of Lc-LTP2 for anionic lipids and those with smaller volumes of hydrophobic chains. The acyl chains of the bound lysopalmitoylphosphatidylglycerol (LPPG), DMPG, or dihexanoylphosphatidylcholine molecules occupied the internal hydrophobic cavity, while their headgroups protruded into the aqueous environment between helices H1 and H3. The spatial structure and backbone dynamics of the Lc-LTP2-LPPG complex were determined. The internal cavity was expanded from ∼600 to ∼1000 Å 3 upon the ligand binding. Another entrance into the internal cavity, restricted by the H2-H3 interhelical loop and C-terminal tail, appeared to be responsible for the attachment of Lc-LTP2 to the membrane or micelle surface and probably played an important role in the lipid uptake determining the ligand specificity. Our results confirmed the previous assumption regarding the membrane-mediated antimicrobial action of Lc-LTP2 and afforded molecular insight into its biological role in the plant.

Microscopic insights into the NMR relaxation based protein conformational entropy meter

PubMed Central

Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua

2013-01-01

Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven pro! teins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy. PMID:24007504

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

NASA Astrophysics Data System (ADS)

Matsypura, Dmytro

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

Design of multi-phase dynamic chemical networks

NASA Astrophysics Data System (ADS)

Chen, Chenrui; Tan, Junjun; Hsieh, Ming-Chien; Pan, Ting; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.

2017-08-01

Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.

Finding the Missing Physics: Simulating Polydisperse Polymer Melts

NASA Astrophysics Data System (ADS)

Rorrer, Nichoals; Dorgan, John

2014-03-01

A Monte Carlo algorithm has been developed to model polydisperse polymer melts. For the first time, this enables the specification of a predetermined molecular weight distribution for lattice based simulations. It is demonstrated how to map an arbitrary probability distributions onto a discrete number of chains residing on an fcc lattice. The resulting algorithm is able to simulate a wide variety of behaviors for polydisperse systems including confinement effects, shear flow, and parabolic flow. The dynamic version of the algorithm accurately captures Rouse dynamics for short polymer chains, and reptation-like dynamics for longer chain lengths.1 When polydispersity is introduced, smaller Rouse times and broadened the transition between different scaling regimes are observed. Rouse times also decrease under confinement for both polydisperse and monodisperse systems and chain length dependent migration effects are observed. The steady-state version of the algorithm enables the simulation of flow and when polydisperse systems are subject to parabolic (Poiseulle) flow, a migration phenomenon based on chain length is again present. These and other phenomena highlight the importance of including polydispersity in obtaining physically realistic simulations of polymeric melts. 1. Dorgan, J.R.; Rorrer, N.A.; Maupin, C.M., Macromolecules 2012, 45(21), 8833-8840. Work funded by the Fluid Dynamics program of the National Science Foundation under grant CBET-1067707.

77 FR 58811 - Advisory Committee on Supply Chain Competitiveness Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-24

... DEPARTMENT OF COMMERCE International Trade Administration Advisory Committee on Supply Chain... open meeting. SUMMARY: This notice announces a public meeting of the Advisory Committee on Supply Chain..., Washington, DC 20230. Public comments may be mailed to Advisory Committee on Supply Chain Competitiveness...

Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution.

PubMed

Eibinger, Manuel; Zahel, Thomas; Ganner, Thomas; Plank, Harald; Nidetzky, Bernd

2016-01-01

Enzymatic hydrolysis of cellulose involves the spatiotemporally correlated action of distinct polysaccharide chain cleaving activities confined to the surface of an insoluble substrate. Because cellulases differ in preference for attacking crystalline compared to amorphous cellulose, the spatial distribution of structural order across the cellulose surface imposes additional constraints on the dynamic interplay between the enzymes. Reconstruction of total system behavior from single-molecule activity parameters is a longstanding key goal in the field. We have developed a stochastic, cellular automata-based modeling approach to describe degradation of cellulosic material by a cellulase system at single-molecule resolution. Substrate morphology was modeled to represent the amorphous and crystalline phases as well as the different spatial orientations of the polysaccharide chains. The enzyme system model consisted of an internally chain-cleaving endoglucanase (EG) as well as two processively acting, reducing and non-reducing chain end-cleaving cellobiohydrolases (CBHs). Substrate preference (amorphous: EG, CBH II; crystalline: CBH I) and characteristic frequencies for chain cleavage, processive movement, and dissociation were assigned from biochemical data. Once adsorbed, enzymes were allowed to reach surface-exposed substrate sites through "random-walk" lateral diffusion or processive motion. Simulations revealed that slow dissociation of processive enzymes at obstacles obstructing further movement resulted in local jamming of the cellulases, with consequent delay in the degradation of the surface area affected. Exploiting validation against evidence from atomic force microscopy imaging as a unique opportunity opened up by the modeling approach, we show that spatiotemporal characteristics of cellulose surface degradation by the system of synergizing cellulases were reproduced quantitatively at the nanometer resolution of the experimental data. This in turn gave useful prediction of the soluble sugar release rate. Salient dynamic features of cellulose surface degradation by different cellulases acting in synergy were reproduced in simulations in good agreement with evidence from high-resolution visualization experiments. Due to the single-molecule resolution of the modeling approach, the utility of the presented model lies not only in predicting system behavior but also in elucidating inherently complex (e.g., stochastic) phenomena involved in enzymatic cellulose degradation. Thus, it creates synergy with experiment to advance the mechanistic understanding for improved application.

Markov model of the loan portfolio dynamics considering influence of management and external economic factors

NASA Astrophysics Data System (ADS)

Bozhalkina, Yana; Timofeeva, Galina

2016-12-01

Mathematical model of loan portfolio in the form of a controlled Markov chain with discrete time is considered. It is assumed that coefficients of migration matrix depend on corrective actions and external factors. Corrective actions include process of receiving applications, interaction with existing solvent and insolvent clients. External factors are macroeconomic indicators, such as inflation and unemployment rates, exchange rates, consumer price indices, etc. Changes in corrective actions adjust the intensity of transitions in the migration matrix. The mathematical model for forecasting the credit portfolio structure taking into account a cumulative impact of internal and external changes is obtained.

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Butler, Jason E.; Shaqfeh, Eric S. G.

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions.

PubMed

Butler, Jason E; Shaqfeh, Eric S G

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions. (c) 2005 American Institute of Physics.

Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels

PubMed Central

Armstrong, Craig T.; Mason, Philip E.; Anderson, J. L. Ross; Dempsey, Christopher E.

2016-01-01

Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD. PMID:26899474

Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels

NASA Astrophysics Data System (ADS)

Armstrong, Craig T.; Mason, Philip E.; Anderson, J. L. Ross; Dempsey, Christopher E.

2016-02-01

Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD.

Topological dynamics of optical singularities in speckle-fields induced by photorefractive scattering in a LiNbO{sub 3} : Fe crystal

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

Vasil'ev, Vasilii I; Soskin, M S

2013-02-28

A natural singular dynamics of elliptically polarised speckle-fields induced by the 'optical damage' effect in a photorefractive crystal of lithium niobate by a passing beam of a helium - neon laser is studied by the developed methods of singular optics. For the polarisation singularities (C points), a new class of chain reactions, namely, singular chain reactions are discovered and studied. It is shown that they obey the topological charge and sum Poincare index conservation laws. In addition, they exist for all the time of crystal irradiation. They consist of a series of interlocking chains, where singularity pairs arising in amore » chain annihilate with singularities from neighbouring independently created chains. Less often singular 'loop' reactions are observed where arising pairs of singularities annihilate after reversible transformations in within the boundaries of a single speckle. The type of a singular reaction is determined by a topology and dynamics of the speckles, in which the reactions are developing. (laser optics 2012)« less

INTERNAL AMPLIFICATION CONTROL FOR USE IN QUANTITATIVE POLYMERASE CHAIN REACTION FECAL INDICATOR BACTERIA ASSAYS

EPA Science Inventory

Quantitative polymerase chain reaction (QPCR) can be used as a rapid method for detecting fecal indicator bacteria. Because false negative results can be caused by PCR inhibitors that co-extract with the DNA samples, an internal amplification control (IAC) should be run with eac...

78 FR 11155 - Advisory Committee on Supply Chain Competitiveness: Notice of Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-15

... DEPARTMENT OF COMMERCE International Trade Administration Advisory Committee on Supply Chain... discussion for a public meeting of the Advisory Committee on Supply Chain Competitiveness (Committee). DATES... national economic competitiveness, and improve U.S. supply chain competitiveness in the domestic and global...

76 FR 68159 - Establishment of the Advisory Committee on Supply Chain Competitiveness and Solicitation of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-03

... on Supply Chain Competitiveness and Solicitation of Nominations for Membership AGENCY: International Trade Administration, DOC. ACTION: Notice of establishment of the Advisory Committee on Supply Chain... the establishment of the Advisory Committee on Supply Chain Competitiveness (the Committee) by the...

Branching, Chain Scission, and Solution Stability of Worm-Like Micelles

NASA Astrophysics Data System (ADS)

Beaucage, Greg; Vogtt, Karsten; Jiang, Hanqui

As salt is added to a simple micelle solution such as SDS or SLES, the zero shear rate specific viscosity rises rapidly followed by a maximum and decay. The rapid rise in viscosity is associated with formation of elliptical and extended chain worm-like micelles, WLMs. Entanglement of these long chain micelles leads to the viscoelastic behavior we associate with shampoo and body wash. The plateau and drop in viscosity at high salt concentrations is caused by a special type of topological branching where the branch points have no energy penalty to motion along the chain according to Cates theory. These have some similarity to catenane crosslinks. Predictive dynamic theories for WLMs rely on structural details; the diameter, persistence length, contour length, branch length, segment length between branch points, and mesh size. Further, since the contour length and other large scale features are in kinetic equilibrium, with frequent chain breakage and formation, the thermodynamics of these long chain structures are of interest both in terms of chain scission as well as in terms of the stability of the colloidal solution as a whole. Recent structural studies of WLMs using static neutron scattering based on new scattering models will be presented demonstrating that these input parameters for dynamic models of complex topological systems are quantitatively and directly available. In this context it is important to consider a comparison between dynamic features, for instance entanglement, and their static analogs, chain overlap.

Complexity of the international agro-food trade network and its impact on food safety.

PubMed

Ercsey-Ravasz, Mária; Toroczkai, Zoltán; Lakner, Zoltán; Baranyi, József

2012-01-01

With the world's population now in excess of 7 billion, it is vital to ensure the chemical and microbiological safety of our food, while maintaining the sustainability of its production, distribution and trade. Using UN databases, here we show that the international agro-food trade network (IFTN), with nodes and edges representing countries and import-export fluxes, respectively, has evolved into a highly heterogeneous, complex supply-chain network. Seven countries form the core of the IFTN, with high values of betweenness centrality and each trading with over 77% of all the countries in the world. Graph theoretical analysis and a dynamic food flux model show that the IFTN provides a vehicle suitable for the fast distribution of potential contaminants but unsuitable for tracing their origin. In particular, we show that high values of node betweenness and vulnerability correlate well with recorded large food poisoning outbreaks.

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.

Molecular Dynamics Simulations of Poly(ethylene oxide) Grafted onto Silica Immersed in Melt of Homopolymers.

PubMed

Benková, Zuzana; Cordeiro, M Natália D S

2015-09-22

Tuning of surface properties plays an important role in applications ranging from material engineering to biomedicine/chemistry. The interactions of chains grafted to a solid support and exposed to a matrix of chemically identical chains represent an intriguing issue. In this work, the behavior of poly(ethylene oxide) (PEO) chains grafted irreversibly onto an amorphous silica and immersed in the matrix of free PEO chains of different polymerization degree is studied using molecular dynamics simulations. The density distributions of grafted and free PEO chains, the height of the grafted layer, overlap parameters, and orientation order parameters depend not only on the grafting density but also on the length of free chains which confirm the entropic nature of the interactions between the grafted and free chains. In order to achieve a complete expulsion of the free chains from the grafted layer, a grafting density as high as 3.5 nm(-2) is necessary. Free PEO chains of 9 monomers leave the grafted layer at lower grafting densities than the longer PEO chains of 18 monomers in contrast with the theoretical predictions. The height of the grafted layer evolves with the grafting density in the presence of free chains in qualitative agreement with the theoretical phase diagram.

Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity.

PubMed

Huculeci, Radu; Cilia, Elisa; Lyczek, Agatha; Buts, Lieven; Houben, Klaartje; Seeliger, Markus A; van Nuland, Nico; Lenaerts, Tom

2016-11-01

Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role in the activation process. Here, we show through experimental methyl dynamic results and predicted changes in side-chain conformational couplings that the SH2 structure of Fyn contains a dynamic network capable of propagating binding information. We reveal that binding the phosphorylated tail of Fyn perturbs a residue cluster near the linker connecting the SH2 and SH3 domains of Fyn, which is known to be relevant in the regulation of the activity of Fyn. Biochemical perturbation experiments validate that those residues are essential for inhibition of Fyn, leading to a gain of function upon mutation. These findings reveal how side-chain dynamics may facilitate the allosteric regulation of the different members of the Src kinase family. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents.

PubMed

Hezaveh, Samira; Samanta, Susruta; Milano, Giuseppe; Roccatano, Danilo

2012-03-28

In this paper, the conformation and dynamics properties of polyethylene oxide (PEO) and polypropylene oxide (PPO) polymer chains at 298 K have been studied in the melt and at infinite dilution condition in water, methanol, chloroform, carbon tetrachloride, and n-heptane using molecular dynamics simulations. The calculated density of PEO melt with chain lengths of n = 2, 3, 4, 5 and, for PPO, n = 7 are in good agreement with the available experimental data. The conformational properties of PEO and PPO show an increasing gauche preference for the O-C-C-O dihedral in the following order water>methanol>chloroform>carbon tetrachloride = n-heptane. On the contrary, the preference for trans conformation has a maximum in carbon tetrachloride and n-heptane followed in the order by chloroform, methanol, and water. The PEO conformational preferences are in qualitative agreement with results of NMR studies. PEO chains formed different types of hydrogen bonds with polar solvent molecules. In particular, the occurrence of bifurcated hydrogen bonding in chloroform was also observed. Radii of gyration of PEO chains of length larger than n = 9 monomers showed a good agreement with light scattering data in water and in methanol. For the shorter chains the observed deviations are probably due to the enhanced hydrophobic effects caused by the terminal methyl groups. For PEO the fitting of end-to-end distance distributions with the semi-flexible chain model at 298 K provided persistence lengths of 0.375 and 0.387 nm in water and methanol, respectively. Finally, the radius of gyration of Pluronic P85 turned out to be 2.25 ± 0.4 nm at 293 K in water in agreement with experimental data.

Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents

NASA Astrophysics Data System (ADS)

Hezaveh, Samira; Samanta, Susruta; Milano, Giuseppe; Roccatano, Danilo

2012-03-01

In this paper, the conformation and dynamics properties of polyethylene oxide (PEO) and polypropylene oxide (PPO) polymer chains at 298 K have been studied in the melt and at infinite dilution condition in water, methanol, chloroform, carbon tetrachloride, and n-heptane using molecular dynamics simulations. The calculated density of PEO melt with chain lengths of n = 2, 3, 4, 5 and, for PPO, n = 7 are in good agreement with the available experimental data. The conformational properties of PEO and PPO show an increasing gauche preference for the O-C-C-O dihedral in the following order water>methanol>chloroform>carbon tetrachloride = n-heptane. On the contrary, the preference for trans conformation has a maximum in carbon tetrachloride and n-heptane followed in the order by chloroform, methanol, and water. The PEO conformational preferences are in qualitative agreement with results of NMR studies. PEO chains formed different types of hydrogen bonds with polar solvent molecules. In particular, the occurrence of bifurcated hydrogen bonding in chloroform was also observed. Radii of gyration of PEO chains of length larger than n = 9 monomers showed a good agreement with light scattering data in water and in methanol. For the shorter chains the observed deviations are probably due to the enhanced hydrophobic effects caused by the terminal methyl groups. For PEO the fitting of end-to-end distance distributions with the semi-flexible chain model at 298 K provided persistence lengths of 0.375 and 0.387 nm in water and methanol, respectively. Finally, the radius of gyration of Pluronic P85 turned out to be 2.25 ± 0.4 nm at 293 K in water in agreement with experimental data.

77 FR 7133 - Advisory Committee on Supply Chain Competitiveness Solicitation of Nominations for Membership

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-10

... DEPARTMENT OF COMMERCE International Trade Administration Advisory Committee on Supply Chain... Organizations or Entities, Including Ports, To Apply for Membership on the Advisory Committee on Supply Chain... organizations or entities, including ports, to serve as members of the Advisory Committee on Supply Chain...

Energy exchange dynamics of the discrete nonlinear Schrödinger equation lattice and intrinsic formation of strongly localized states

NASA Astrophysics Data System (ADS)

Hennig, D.

1997-09-01

We study the dynamics of excitation energy transfer along a lattice chain modeled by the discrete nonlinear Schrödinger (DNLS) equation. We prove that a segment carrying resonant motion can be decoupled from the remainder of the chain supporting quasiperiodic dynamics. The resonant segment from the extended chain is taken to be a four-site element, viz., a tetramer. First, we focus interest on the energy exchange dynamics along the tetramer viewed as two weakly coupled DNLS dimers. Hamiltonian methods are used to investigate the phase-space dynamics. We pay special attention to the role of the diffusion of the action variables inside resonance layers for the energy migration. When distributing the energy initially equally between the two dimers one observes a directed irreversible flow of energy from one dimer into the other assisted by action diffusion. Eventually on one dimer a stable self-trapped excitation of large amplitude forms at a single site while the other dimer exhibits equal energy partition over its two sites. Finally, we study the formation of localized structure on an extended DNLS lattice chain. In particular we explore the stability of the so-called even-parity and odd-parity localized modes, respectively, and explain their different stability properties by means of phase-space dynamics. The global instability of the even-parity mode is shown. For the excited even-parity mode a symmetry-breaking perturbation of the pattern leads to an intrinsic collapse of the even-parity mode to the odd-parity one. The latter remains stable with respect to symmetry-breaking perturbations. In this way we demonstrate that the favored stable localized states for the DNLS lattice chain correspond to one-site localized excitations.

Structure and dynamics of ionic micelles: MD simulation and neutron scattering study.

PubMed

Aoun, B; Sharma, V K; Pellegrini, E; Mitra, S; Johnson, M; Mukhopadhyay, R

2015-04-16

Fully atomistic molecular dynamics (MD) simulations have been carried out on sodium dodecyl sulfate (SDS), an anionic micelle, and three cationic (CnTAB; n = 12, 14, 16) micelles, investigating the effects of size, the form of the headgroup, and chain length. They have been used to analyze neutron scattering data. MD simulations confirm the dynamical model of global motion of the whole micelle, segmental motion (headgroup and alkyl chain), and fast torsional motion associated with the surfactants that is used to analyze the experimental data. It is found that the solvent surrounding the headgroups results in their significant mobility, which exceeds that of the tails on the nanosecond time scale. The middle of the chain is found to be least mobile, consolidating the micellar configuration. This dynamical feature is similar for all the ionic micelles investigated and therefore independent of headgroup form and charge and chain length. Diffusion constants for global and segmental motion of the different micelles are consistent with experimentally obtained values as well as known structural features. This work provides a more realistic model of micelle dynamics and offers new insight into the strongly fluctuating surface of micelles which is important in understanding micelle dispersion and related functionality, like drug delivery.

Phase diagram and quench dynamics of the cluster-XY spin chain

NASA Astrophysics Data System (ADS)

Montes, Sebastián; Hamma, Alioscia

2012-08-01

We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

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.

Phase diagram and quench dynamics of the cluster-XY spin chain.

PubMed

Montes, Sebastián; Hamma, Alioscia

2012-08-01

We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

Chain registry and load-dependent conformational dynamics of collagen.

PubMed

Teng, Xiaojing; Hwang, Wonmuk

2014-08-11

Degradation of fibrillar collagen is critical for tissue maintenance. Yet, understanding collagen catabolism has been challenging partly due to a lack of atomistic picture for its load-dependent conformational dynamics, as both mechanical load and local unfolding of collagen affect its cleavage by matrix metalloproteinase (MMP). We use molecular dynamics simulation to find the most cleavage-prone arrangement of α chains in a collagen triple helix and find amino acids that modulate stability of the MMP cleavage domain depending on the chain registry within the molecule. The native-like state is mechanically inhomogeneous, where the cleavage site interfaces a stiff region and a locally unfolded and flexible region along the molecule. In contrast, a triple helix made of the stable glycine-proline-hydroxyproline motif is uniformly flexible and is dynamically stabilized by short-lived, low-occupancy hydrogen bonds. These results provide an atomistic basis for the mechanics, conformation, and stability of collagen that affect catabolism.

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions.

PubMed

Li, Hui; Li, Wei; Li, Shuhua; Ma, Jing

2008-06-12

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.

Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor

NASA Astrophysics Data System (ADS)

Brooks, Bernard; Karplus, Martin

1983-11-01

A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibitor in the full conformational space of the molecule (1,740 degrees of freedom); that is, all bond lengths and angles, as well as dihedral angles, are included for the 580-atom system consisting of all heavy atoms and polar hydrogens. The heavy-atom frequency spectrum shows a dense distribution between 3 and 1,800 cm-1, with 350 modes below 216 cm-1. Most of the low-frequency modes, of which many have significant anharmonic character, are found to be delocalized over the protein. The root-mean-square amplitudes of the atomic fluctuations are calculated at 300 K from the normal modes and compared with those obtained from a solution molecular dynamics simulation based on the same potential function; very good agreement is obtained for the variation in the main-chain fluctuations as a function of residue number, though larger differences occur for the side chains. The fluctuations are generally, though not always, dominated by frequencies below 30 cm-1, in accord with the results of the dynamics simulation. The vibrational contributions to the thermodynamic properties of the protein are calculated as a function of temperature; the effects of perturbations on the spectrum, suggested for ligand or substrate binding, are examined. The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.

Brownian dynamics simulation of a polymer chain in a solid-state nanopore attached to a molecular stop

NASA Astrophysics Data System (ADS)

Wells, Craig; Hulings, Zachery; Melnikov, Dmitriy; Gracheva, Maria

We study a nanopore inside a silicon dioxide membrane submerged in a KCl solution with a negatively charged polymer chain of varying lengths whose movement is described using Brownian dynamics. The polymer is attached to a molecule with a radius larger than that of the nanopore's which acts as a molecular stop, allowing the chain to thread the nanopore but preventing it from translocating. We found that the polymer chain's variation of movement along the nanopore decreased when increasing applied biases and chain lengths for portions of the chain closest to the molecular stop. The chain displacement within the pore is also compared to a freely translocating polymer where preliminary results show the free polymer having a greater variation in the radial direction. Overall, our preliminary results indicate that the radial direction of the polymer chain is dominated by the confinement in the narrow nanopore with restrictions imposed by the molecular stop and bias playing a lesser role. Understanding the interaction behavior of the polymer chain-stop molecule may lead to methods that decrease movement variation, facilitating an improvement on characterizing and identification of molecules. NSF DMR and CBET Grant No. 1352218.

How tension propagates for a driven semi-flexible chain while translocating through a nano-pore

NASA Astrophysics Data System (ADS)

Adhikari, Ramesh; Bhattacharya, Aniket

2013-03-01

Driven translocation of a stiff chain through a nano-pore is studied using Langevin dynamics in two dimension (2D). We observe that for a given chain length N the mean first passage time (MFPT) < τ > increases for a stiffer chain and the translocation exponent α (< τ > ~Nα) satisfies the inequality 2 ν < α < 1 + ν , where ν is the equilibrium Flory exponent for a given chain stiffness. We calculate the residence time of the individual monomers and observe that the peak position of the residence time W (m) as a function of the monomer index m shifts at a lower m-value with increasing chain stiffness κb. Finally, we provide qualitative physical explanation for dependence of various quantities on chain stiffness κb by using ideas from Sakaue's tension propagation(TP) theory [Phys. Rev. E 76, 021803 (2007)] and its recent implementation into a Brownian dynamics tension propagation (BDTP) scheme for a finite chain by Ikonen et al. [J. Chem. Phys. 137, 085101 (2012); Phys. Rev. E 85, 051803 (2012)]for a semi-flexible chain. Partially supported by UCF Office of Research and Commercialization & College of Science SEED grant.

Handling target obscuration through Markov chain observations

NASA Astrophysics Data System (ADS)

Kouritzin, Michael A.; Wu, Biao

2008-04-01

Target Obscuration, including foliage or building obscuration of ground targets and landscape or horizon obscuration of airborne targets, plagues many real world filtering problems. In particular, ground moving target identification Doppler radar, mounted on a surveillance aircraft or unattended airborne vehicle, is used to detect motion consistent with targets of interest. However, these targets try to obscure themselves (at least partially) by, for example, traveling along the edge of a forest or around buildings. This has the effect of creating random blockages in the Doppler radar image that move dynamically and somewhat randomly through this image. Herein, we address tracking problems with target obscuration by building memory into the observations, eschewing the usual corrupted, distorted partial measurement assumptions of filtering in favor of dynamic Markov chain assumptions. In particular, we assume the observations are a Markov chain whose transition probabilities depend upon the signal. The state of the observation Markov chain attempts to depict the current obscuration and the Markov chain dynamics are used to handle the evolution of the partially obscured radar image. Modifications of the classical filtering equations that allow observation memory (in the form of a Markov chain) are given. We use particle filters to estimate the position of the moving targets. Moreover, positive proof-of-concept simulations are included.

Benchmarking Operations to Promote Learning: An Internal Supply Chain Perspective

ERIC Educational Resources Information Center

Benton, Helen; Binder, Mario; Egel-Hess, Wolfgang

2007-01-01

Despite the widespread discussion of organisational learning, there is little scholarly contribution on promoting learning through the practical application of management tools. This is especially true in a complex internal supply chain context of an organisation. This paper seeks to address this gap by exploring and analysing the capability of…

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.

Economic Development Policymaking Down the Global Commodity Chain: Attracting an Auto Industry to Silao, Mexico

ERIC Educational Resources Information Center

Rothstein, Jeffrey S.

2005-01-01

This article applies the global commodity chain approach to analyze the way policymakers encouraged an automotive commodity chain to touch down in Silao, Mexico. The article explains that the changing dynamics of the global auto industry have transformed it into an "assembler-driven" commodity chain. It notes how policymakers in the…

Dynamical heterogeneities of rotational motion in room temperature ionic liquids evidenced by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Usui, Kota; Hunger, Johannes; Bonn, Mischa; Sulpizi, Marialore

2018-05-01

Room temperature ionic liquids (RTILs) have been shown to exhibit spatial heterogeneity or structural heterogeneity in the sense that they form hydrophobic and ionic domains. Yet studies of the relationship between this structural heterogeneity and the ˜picosecond motion of the molecular constituents remain limited. In order to obtain insight into the time scales relevant to this structural heterogeneity, we perform molecular dynamics simulations of a series of RTILs. To investigate the relationship between the structures, i.e., the presence of hydrophobic and ionic domains, and the dynamics, we gradually increase the size of the hydrophobic part of the cation from ethylammonium nitrate (EAN), via propylammonium nitrate (PAN), to butylammonium nitrate (BAN). The two ends of the organic cation, namely, the charged Nhead-H group and the hydrophobic Ctail-H group, exhibit rotational dynamics on different time scales, evidencing dynamical heterogeneity. The dynamics of the Nhead-H group is slower because of the strong coulombic interaction with the nitrate counter-ionic anions, while the dynamics of the Ctail-H group is faster because of the weaker van der Waals interaction with the surrounding atoms. In particular, the rotation of the Nhead-H group slows down with increasing cationic chain length, while the rotation of the Ctail-H group shows little dependence on the cationic chain length, manifesting that the dynamical heterogeneity is enhanced with a longer cationic chain. The slowdown of the Nhead-H group with increasing cationic chain length is associated with a lower number of nitrate anions near the Nhead-H group, which presumably results in the increase of the energy barrier for the rotation. The sensitivity of the Nhead-H rotation to the number of surrounding nitrate anions, in conjunction with the varying number of nitrate anions, gives rise to a broad distribution of Nhead-H reorientation times. Our results suggest that the asymmetry of the cations and the larger excluded volume for longer cationic chain are important for both the structural heterogeneity and the dynamical heterogeneities. The observed dynamical heterogeneities may affect the rates of chemical reactions depending on where the reactants are solvated in ionic liquids and provide an additional guideline for the design of RTILs as solvents.

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.

Molecular dynamics simulations of polyethers and a quaternary ammonium ionic liquid as CO2 absorbers

NASA Astrophysics Data System (ADS)

Cardoso, Piercarlo Fortunato; Fernandez, Juan S. L. C.; Lepre, Luiz Fernando; Ando, Rômulo Augusto; Costa Gomes, Margarida F.; Siqueira, Leonardo J. A.

2018-04-01

The properties of mixtures of butyltrimethylammonium bis(trifluoromethylsulfonyl)imide, [N4111][NTf2], with poly(ethyleneglycol) dimethyl ether, PEO, were described as a function of PEO chain size by molecular dynamics simulations. Both PEO chain size and mixture composition revealed to play a significant role in determining the structure and the dynamics of the fluids. The remarkably higher viscosity observed for mixtures composed by 0.25 mole fraction of PEO was attributed to the increase in the gauche population of OCCO dihedral of the polyether of longer chains. The negative solvation enthalpy (ΔsolH < 0) and entropy (ΔsolS < 0) revealed a favorable CO2 absorption by the neat and mixture systems. The CO2 absorption was higher in neat PEO, particularly considering longer chains. The gas solubility in the mixtures presented intermediate values in comparison to the neat PEO and neat ionic liquid. The CO2 solutions had their structures discussed in the light of the calculated radial and spatial distribution functions.

Molecular dynamics simulations of polyethers and a quaternary ammonium ionic liquid as CO2 absorbers.

PubMed

Cardoso, Piercarlo Fortunato; Fernandez, Juan S L C; Lepre, Luiz Fernando; Ando, Rômulo Augusto; Costa Gomes, Margarida F; Siqueira, Leonardo J A

2018-04-07

The properties of mixtures of butyltrimethylammonium bis(trifluoromethylsulfonyl)imide, [N 4111 ][NTf 2 ], with poly(ethyleneglycol) dimethyl ether, PEO, were described as a function of PEO chain size by molecular dynamics simulations. Both PEO chain size and mixture composition revealed to play a significant role in determining the structure and the dynamics of the fluids. The remarkably higher viscosity observed for mixtures composed by 0.25 mole fraction of PEO was attributed to the increase in the gauche population of OCCO dihedral of the polyether of longer chains. The negative solvation enthalpy (Δ sol H < 0) and entropy (Δ sol S < 0) revealed a favorable CO 2 absorption by the neat and mixture systems. The CO 2 absorption was higher in neat PEO, particularly considering longer chains. The gas solubility in the mixtures presented intermediate values in comparison to the neat PEO and neat ionic liquid. The CO 2 solutions had their structures discussed in the light of the calculated radial and spatial distribution functions.

Decision support for green supply chain operations by integrating dynamic simulation and LCA indicators: diaper case study.

PubMed

Adhitya, Arief; Halim, Iskandar; Srinivasan, Rajagopalan

2011-12-01

As the issue of environmental sustainability is becoming an important business factor, companies are now looking for decision support tools to assess the fuller picture of the environmental impacts associated with their manufacturing operations and supply chain (SC) activities. Lifecycle assessment (LCA) is widely used to measure the environmental consequences assignable to a product. However, it is usually limited to a high-level snapshot of the environmental implications over the product value chain without consideration of the dynamics arising from the multitiered structure and the interactions along the SC. This paper proposes a framework for green supply chain management by integrating a SC dynamic simulation and LCA indicators to evaluate both the economic and environmental impacts of various SC decisions such as inventories, distribution network configuration, and ordering policy. The advantages of this framework are demonstrated through an industrially motivated case study involving diaper production. Three distinct scenarios are evaluated to highlight how the proposed approach enables integrated decision support for green SC design and operation.

Configurations and Dynamics of Semi-Flexible Polymers in Good and Poor Solvents

NASA Astrophysics Data System (ADS)

Larson, Ronald

We develop coarse-graining procedures for determining the conformational and dynamic behavior of semi-flexible chains with and without flow using Brownian dynamics (BD) simulations that are insensitive to the degree of coarse-graining. In the absence of flow, in a poor solvent, we find three main collapsed states: torus, bundle, and globule over a range of dimensionless ratios of the three energy parameters, namely solvent-polymer surface energy, energy of polymer folds, and polymer bending energy or persistence length. A theoretical phase diagram, confirmed by BD simulations, captures the general phase behavior of a single long chain (>10 Kuhn lengths) at moderately high (order unity) dimensionless temperature, which is the ratio of thermal energy to the attractive interaction between neighboring monomers. We also find converged results for polymer conformations in shear or extensional flow in solvents of various qualities and determine scaling laws for chain dimensions for low, moderate, and high Weissenberg numbers Wi. We also derive scaling laws to describe chains dimensions and tumbling rates in these regimes.

Surface water retardation around single-chain polymeric nanoparticles: critical for catalytic function?

PubMed

Stals, Patrick J M; Cheng, Chi-Yuan; van Beek, Lotte; Wauters, Annelies C; Palmans, Anja R A; Han, Songi; Meijer, E W

2016-03-01

A library of water-soluble dynamic single-chain polymeric nanoparticles (SCPN) was prepared using a controlled radical polymerisation technique followed by the introduction of functional groups, including probes at targeted positions. The combined tools of electron paramagnetic resonance (EPR) and Overhauser dynamic nuclear polarization (ODNP) reveal that these SCPNs have structural and surface hydration properties resembling that of enzymes.

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

NASA Astrophysics Data System (ADS)

Rozairo, Damith; Croll, Andrew

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

Dynamics and order-disorder transitions in bidisperse diblock copolymer blends

NASA Astrophysics Data System (ADS)

Wang, Yueqiang; Li, Xuan; Tang, Ping; Yang, Yuliang

2011-03-01

We employ the dynamic extension of self-consistent field theory (DSCFT) to study dynamics and order-disorder transitions (ODT) in AB diblock copolymer binary mixtures of two different monodisperse chain lengths by imitating the dynamic storage modulus G‧ corresponding to any given morphology in the oscillatory shear measurements. The different polydispersity index (PDI) is introduced by binary blending AB diblock copolymers with variations in chain lengths and chain number fractions. The simulation results show that the increase of polydispersity in the minority or symmetric block introduces a decrease in the segregation strength at the ODT, ( χN) ODT, whereas the increase of polydispersity in the majority block results in a decrease, then increase and final decrease again in ( χN) ODT. To the best of our knowledge, our DSCFT simulations, for the first time, predict an increase in ( χN) ODT with the PDI in the majority block, which produces the experimental results. The simulations by previous SCFT, which generally speaking, is capable of describing equilibrium morphologies, however, contradict the experimental data. The polydispersity acquired by properly tuning the chain lengths and number fractions of binary diblock copolymer blends should be a convenient and efficient way to control the microphase separation strength at the ODT.

Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of 13C NMR Relaxation Times and Their Distributions.

PubMed

Chen, Pan; Terenzi, Camilla; Furó, István; Berglund, Lars A; Wohlert, Jakob

2018-05-15

Macromolecular dynamics in biological systems, which play a crucial role for biomolecular function and activity at ambient temperature, depend strongly on moisture content. Yet, a generally accepted quantitative model of hydration-dependent phenomena based on local relaxation and diffusive dynamics of both polymer and its adsorbed water is still missing. In this work, atomistic-scale spatial distributions of motional modes are calculated using molecular dynamics simulations of hydrated xyloglucan (XG). These are shown to reproduce experimental hydration-dependent 13 C NMR longitudinal relaxation times ( T 1 ) at room temperature, and relevant features of their broad distributions, which are indicative of locally heterogeneous polymer reorientational dynamics. At low hydration, the self-diffusion behavior of water shows that water molecules are confined to particular locations in the randomly aggregated XG network while the average polymer segmental mobility remains low. Upon increasing water content, the hydration network becomes mobile and fully accessible for individual water molecules, and the motion of hydrated XG segments becomes faster. Yet, the polymer network retains a heterogeneous gel-like structure even at the highest level of hydration. We show that the observed distribution of relaxations times arises from the spatial heterogeneity of chain mobility that in turn is a result of heterogeneous distribution of water-chain and chain-chain interactions. Our findings contribute to the picture of hydration-dependent dynamics in other macromolecules such as proteins, DNA, and synthetic polymers, and hold important implications for the mechanical properties of polysaccharide matrixes in plants and plant-based materials.

Modeling the dynamics of backyard chicken flows in traditional trade networks in Thailand: implications for surveillance and control of avian influenza.

PubMed

Wiratsudakul, Anuwat; Paul, Mathilde Cécile; Bicout, Dominique Joseph; Tiensin, Thanawat; Triampo, Wannapong; Chalvet-Monfray, Karine

2014-06-01

In Southeast Asia, traditional poultry marketing chains have been threatened by epidemics caused by the highly pathogenic avian influenza H5N1 (HPAI H5N1) virus. In Thailand, the trade of live backyard chickens is based on the activities of traders buying chickens from villages and supplying urban markets with chicken meat. This study aims to quantify the flows of chickens traded during a 1-year period in a province of Thailand. A compartmental stochastic dynamic model was constructed to illustrate trade flows of live chickens from villages to slaughterhouses. Live poultry movements present important temporal variations with increased activities during the 15 days preceding the Chinese New Year and, to a lesser extent, other festivals (Qingming Festival, Thai New Year, Hungry Ghost Festival, and International New Year). The average distance of poultry movements ranges from 4 to 25 km, defining a spatial scale for the risk of avian influenza that spread through traditional poultry marketing chains. Some characteristics of traditional poultry networks in Thailand, such as overlapping chicken supply zones, may facilitate disease diffusion over longer distances through combined expansion and relocation processes. This information may be of use in tailoring avian influenza and other emerging infectious poultry disease surveillance and control programs provided that the cost-effectiveness of such scenarios is also evaluated in further studies.

Exact wave packet dynamics of singlet fission in unsubstituted and substituted polyene chains within long-range interacting models

NASA Astrophysics Data System (ADS)

Prodhan, Suryoday; Ramasesha, S.

2017-08-01

Singlet fission (SF) is a potential pathway for significant enhancement of efficiency in organic solar cells (OSC). In this paper, we study singlet fission in a pair of polyene molecules in two different stacking arrangements employing exact many-body wave packet dynamics. In the noninteracting model, the SF yield is absent. The individual molecules are treated within Hubbard and Pariser-Parr-Pople (PPP) models and the interaction between them involves transfer terms, intersite electron repulsions, and site-charge-bond-charge repulsion terms. Initial wave packet is constructed from excited singlet state of one molecule and ground state of the other. Time development of this wave packet under the influence of intermolecular interactions is followed within the Schrödinger picture by an efficient predictor-corrector scheme. In unsubstituted Hubbard and PPP chains, 2 1A excited singlet state leads to significant SF yield while the 1 1B state gives negligible fission yield. On substitution by donor-acceptor groups of moderate strength, the lowest excited state will have sufficient 2 1A character and hence results in significant SF yield. Because of rapid internal conversion, the nature of the lowest excited singlet will determine the SF contribution to OSC efficiency. Furthermore, we find the fission yield depends considerably on the stacking arrangement of the polyene molecules.

Rate-Dependent Behavior of the Amorphous Phase of Spider Dragline Silk

PubMed Central

Patil, Sandeep P.; Markert, Bernd; Gräter, Frauke

2014-01-01

The time-dependent stress-strain behavior of spider dragline silk was already observed decades ago, and has been attributed to the disordered sequences in silk proteins, which compose the soft amorphous matrix. However, the actual molecular origin and magnitude of internal friction within the amorphous matrix has remained inaccessible, because experimentally decomposing the mechanical response of the amorphous matrix from the embedded crystalline units is challenging. Here, we used atomistic molecular dynamics simulations to obtain friction forces for the relative sliding of peptide chains of Araneus diadematus spider silk within bundles of these chains as a representative unit of the amorphous matrix in silk fibers. We computed the friction coefficient and coefficient of viscosity of the amorphous phase to be in the order of 10−6 Ns/m and 104 Ns/m2, respectively, by extrapolating our simulation data to the viscous limit. Finally, we used a finite element method for the amorphous phase, solely based on parameters derived from molecular dynamics simulations including the newly determined coefficient of viscosity. With this model the time scales of stress relaxation, creep, and hysteresis were assessed, and found to be in line with the macroscopic time-dependent response of silk fibers. Our results suggest the amorphous phase to be the primary source of viscosity in silk and open up the avenue for finite element method studies of silk fiber mechanics including viscous effects. PMID:24896131

Hidden regularity and universal classification of fast side chain motions in proteins

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

Rajeshwar, Rajitha; Smith, Jeremy C.; Krishnam, Marimuthu

Proteins display characteristic dynamical signatures that appear to be universal across all proteins regardless of topology and size. Here, we systematically characterize the universal features of fast side chain motions in proteins by examining the conformational energy surfaces of individual residues obtained using enhanced sampling molecular dynamics simulation (618 free energy surfaces obtained from 0.94 s MD simulation). The side chain conformational free energy surfaces obtained using the adaptive biasing force (ABF) method for a set of eight proteins with different molecular weights and secondary structures are used to determine the methyl axial NMR order parameters (O axis 2), populationsmore » of side chain rotamer states (ρ), conformational entropies (S conf), probability fluxes, and activation energies for side chain inter-rotameric transitions. The free energy barriers separating side chain rotamer states range from 0.3 to 12 kcal/mol in all proteins and follow a trimodal distribution with an intense peak at ~5 kcal/mol and two shoulders at ~3 and ~7.5 kcal/mol, indicating that some barriers are more favored than others by proteins to maintain a balance between their conformational stability and flexibility. The origin and the influences of the trimodal barrier distribution on the distribution of O axis 2 and the side chain conformational entropy are discussed. A hierarchical grading of rotamer states based on the conformational free energy barriers, entropy, and probability flux reveals three distinct classes of side chains in proteins. A unique nonlinear correlation is established between O axis 2 and the side chain rotamer populations (ρ). In conclusion, the apparent universality in O axis 2 versus correlation, trimodal barrier distribution, and distinct characteristics of three classes of side chains observed among all proteins indicates a hidden regularity (or commonality) in the dynamical heterogeneity of fast side chain motions in proteins.« less

Hemoglobin Dynamics in Red Blood Cells: Correlation to Body Temperature

PubMed Central

Stadler, A. M.; Digel, I.; Artmann, G. M.; Embs, J. P.; Zaccai, G.; Büldt, G.

2008-01-01

A transition in hemoglobin behavior at close to body temperature has been discovered recently by micropipette aspiration experiments on single red blood cells (RBCs) and circular dichroism spectroscopy on hemoglobin solutions. The transition temperature was directly correlated to the body temperatures of a variety of species. In an exploration of the molecular basis for the transition, we present neutron scattering measurements of the temperature dependence of hemoglobin dynamics in whole human RBCs in vivo. The data reveal a change in the geometry of internal protein motions at 36.9°C, at human body temperature. Above that temperature, amino acid side-chain motions occupy larger volumes than expected from normal temperature dependence, indicating partial unfolding of the protein. Global protein diffusion in RBCs was also measured and the findings compared favorably with theoretical predictions for short-time self-diffusion of noncharged hard-sphere colloids. The results demonstrated that changes in molecular dynamics in the picosecond time range and angstrom length scale might well be connected to a macroscopic effect on whole RBCs that occurs at body temperature. PMID:18708462

Slowing down of ring polymer diffusion caused by inter-ring threading.

PubMed

Lee, Eunsang; Kim, Soree; Jung, YounJoon

2015-06-01

Diffusion of long ring polymers in a melt is much slower than the reorganization of their internal structures. While direct evidence for entanglements has not been observed in the long ring polymers unlike linear polymer melts, threading between the rings is suspected to be the main reason for slowing down of ring polymer diffusion. It is, however, difficult to define the threading configuration between two rings because the rings have no chain end. In this work, evidence for threading dynamics of ring polymers is presented by using molecular dynamics simulation and applying a novel analysis method. The simulation results are analyzed in terms of the statistics of persistence and exchange times that have proved useful in studying heterogeneous dynamics of glassy systems. It is found that the threading time of ring polymer melts increases more rapidly with the degree of polymerization than that of linear polymer melts. This indicates that threaded ring polymers cannot diffuse until an unthreading event occurs, which results in the slowing down of ring polymer diffusion. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hemoglobin dynamics in red blood cells: correlation to body temperature.

PubMed

Stadler, A M; Digel, I; Artmann, G M; Embs, J P; Zaccai, G; Büldt, G

2008-12-01

A transition in hemoglobin behavior at close to body temperature has been discovered recently by micropipette aspiration experiments on single red blood cells (RBCs) and circular dichroism spectroscopy on hemoglobin solutions. The transition temperature was directly correlated to the body temperatures of a variety of species. In an exploration of the molecular basis for the transition, we present neutron scattering measurements of the temperature dependence of hemoglobin dynamics in whole human RBCs in vivo. The data reveal a change in the geometry of internal protein motions at 36.9 degrees C, at human body temperature. Above that temperature, amino acid side-chain motions occupy larger volumes than expected from normal temperature dependence, indicating partial unfolding of the protein. Global protein diffusion in RBCs was also measured and the findings compared favorably with theoretical predictions for short-time self-diffusion of noncharged hard-sphere colloids. The results demonstrated that changes in molecular dynamics in the picosecond time range and angstrom length scale might well be connected to a macroscopic effect on whole RBCs that occurs at body temperature.

Numerical study of two disks settling in an Oldroyd-B fluid: From periodic interaction to chaining

NASA Astrophysics Data System (ADS)

Pan, Tsorng-Whay; Glowinski, Roland

2017-12-01

In this article, we present a numerical study of the dynamics of two disks sedimenting in a narrow vertical channel filled with an Oldroyd-B fluid. Two kinds of particle dynamics are observed: (i) a periodic interaction between the two disks, and (ii) the formation of a two-disk chain. For the periodic interaction of the two disks, two different motions are observed: (a) the two disks stay far apart and interact periodically, and (b) the two disks interact closely and then far apart in a periodic way, like the drafting, kissing, and tumbling of two disks sedimenting in a Newtonian fluid, due to a weak elastic force. Concerning the formation of a two-disk chain occurring at higher values of the elasticity number, either a tilted chain or a vertical chain is observed. Our simulations show that, as expected, the values of the elasticity and Mach numbers are the determining factors concerning the particle chain formation and its orientation.

Spheres settling in an Oldroyd-B fluid

NASA Astrophysics Data System (ADS)

Pan, Tsorng-Whay; Glowinski, Roland

2017-11-01

In this talk we present a numerical study of the dynamics of balls settling in a vertical channel with a square cross-section filled with an Oldroyd-B fluid. For the case of two balls, two typical kinds of particle dynamics are obtained: (i) periodic interaction between two balls and (ii) the formation of a vertical chain of two balls. For the periodic interaction of two balls occurred at lower values of the elasticity number, two balls draft, kiss and break away periodically and the chain is not formed due to not strong enough elastic force. For slightly higher values of the elasticity number, two balls draft, kiss and break away a couple times first and then form a chain. Such chain finally becomes a vertical one after the oscillation damps out. For higher values of the elasticity number, two balls draft, kiss and form a vertical chain right away. The formation of three ball chain can be obtained at higher values of the elasticity number. This work was supported by NSF (Grant DMS-1418308).

Numerical study of two disks settling in an Oldroyd-B fluid: From periodic interaction to chaining.

PubMed

Pan, Tsorng-Whay; Glowinski, Roland

2017-12-01

In this article, we present a numerical study of the dynamics of two disks sedimenting in a narrow vertical channel filled with an Oldroyd-B fluid. Two kinds of particle dynamics are observed: (i) a periodic interaction between the two disks, and (ii) the formation of a two-disk chain. For the periodic interaction of the two disks, two different motions are observed: (a) the two disks stay far apart and interact periodically, and (b) the two disks interact closely and then far apart in a periodic way, like the drafting, kissing, and tumbling of two disks sedimenting in a Newtonian fluid, due to a weak elastic force. Concerning the formation of a two-disk chain occurring at higher values of the elasticity number, either a tilted chain or a vertical chain is observed. Our simulations show that, as expected, the values of the elasticity and Mach numbers are the determining factors concerning the particle chain formation and its orientation.

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

NASA Astrophysics Data System (ADS)

Woelki, Stefan; Kohler, Hans-Helmut

2003-09-01

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

Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore

NASA Astrophysics Data System (ADS)

Wells, Craig C.; Melnikov, Dmitriy V.; Gracheva, Maria E.

2017-08-01

We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore.

PubMed

Wells, Craig C; Melnikov, Dmitriy V; Gracheva, Maria E

2017-08-07

We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

A Langevin dynamics simulation study of the tribology of polymer loop brushes.

PubMed

Yin, Fang; Bedrov, Dmitry; Smith, Grant D; Kilbey, S Michael

2007-08-28

The tribology of surfaces modified with doubly bound polymer chains (loops) has been investigated in good solvent conditions using Langevin dynamics simulations. The density profiles, brush interpenetration, chain inclination, normal forces, and shear forces for two flat substrates modified by doubly bound bead-necklace polymers and equivalent singly bound polymers (twice as many polymer chains of 12 the molecular weight of the loop chains) were determined and compared as a function of surface separation, grafting density, and shear velocity. The doubly bound polymer layers showed less interpenetration with decreasing separation than the equivalent singly bound layers. Surprisingly, this difference in interpenetration between doubly bound polymer and singly bound polymer did not result in decreased friction at high shear velocity possibly due to the decreased ability of the doubly bound chains to deform in response to the applied shear. However, at lower shear velocity, where deformation of the chains in the flow direction is less pronounced and the difference in interpenetration is greater between the doubly bound and singly bound chains, some reduction in friction was observed.

Implementation of system dynamic simulation method to optimize profit in supply chain network of vegetable product

NASA Astrophysics Data System (ADS)

Tama, I. P.; Akbar, Z.; Eunike, A.

2018-04-01

Vegetables are categorized as a perishable product, which is a product with short lifespan thus requires proper handling and planning to reduce losses caused by the short lifespan. In order to reduce the losses, coordination among the players in the supply chain is required. On the other hand, the decision in the supply chain of vegetables and other farming products in the traditional market of developing country is independent among the players. This research is conducted by using System Dynamic Simulation method to develop model and scenario by coordinating the supply quantity amongst players in the supply chain. The scenarios are developed based on newsboy inventory model. This study aims to compare scenarios combining tiers involved in coordination program. The result shows that coordination in supply chain increases total supply chain profit, although there will always be players who experienced decrements in profit. The scenario of coordination among the farmer, the distributor, and the wholesaler resulted in the highest increase in total supply chain profit compared to other coordination scenarios, with an increased value of 10.49%.

Effect of PEO molecular weight on the miscibility and dynamics in epoxy/PEO blends.

PubMed

Lu, Shoudong; Zhang, Rongchun; Wang, Xiaoliang; Sun, Pingchuan; Lv, Weifeng; Liu, Qingjie; Jia, Ninghong

2015-11-01

In this work, the effect of poly(ethylene oxide) (PEO) molecular weight in blends of epoxy (ER) and PEO on the miscibility, inter-chain weak interactions and local dynamics were systematically investigated by multi-frequency temperature modulation DSC and solid-state NMR techniques. We found that the molecular weight (M(w)) of PEO was a crucial factor in controlling the miscibility, chain dynamics and hydrogen bonding interactions between PEO and ER. A critical PEO molecular weight (M(crit)) around 4.5k was found. PEO was well miscible with ER when the molecular weight was below M(crit), where the chain motion of PEO was restricted due to strong inter-chain hydrogen bonding interactions. However, for the blends with high molecular weight PEO (M(w) > M(crit)), the miscibility between PEO and ER was poor, and most of PEO chains were considerably mobile. Finally, polarization inversion spin exchange at magic angle (PISEMA) solid-state NMR experiment further revealed the different mobility of the PEO in ER/PEO blends with different molecular weight of PEO at molecular level. Based on the DSC and NMR results, a tentative model was proposed to illustrate the miscibility in ER/PEO blends.

Dealing with large-scale supply lines when introducing new regimens.

PubMed

Malati, Christine; Rosenfeld, Joshua; Mowafy, Sherif; Rittmiller, Trevor; Kuritsky, Joel; Crowley, John

2017-07-01

As programs plan the introduction of a new antiretroviral as part of a regimen for HIV treatment, supply chain considerations need to be taken into account. The key to success is balancing the introduction of a new regimen with the phasing out of an old regimen in a manner that does not result in either a shortage or an excess supply of either product while ensuring that patients continue receiving their medications. This necessitates that country programs, donors, and procurement entities possess an appreciation of the global antiretroviral market and understand the dynamics that the manufacturing of new antiretrovirals will have on the transition. Supply, demand, and financial considerations affect the capacity of the supply chain to facilitate a successful antiretroviral transition. Although this commentary draws on United States Agency for International Development experiences under the President's Emergency Plan for AIDS Relief from earlier antiretroviral treatment shifts, the approaches are applicable to other institutions and to future transitions. Three approaches were employed: ensuring the engagement of all key stakeholders in transition planning and execution, including clinicians, advocacy groups, supply chain professionals, ministry, and donors; conducting and updating regularly the national quantification and supply plans for all regimens; and introducing antiretroviral products into programs from regional warehouses based on firm orders. Extensive planning and accounting for supply chain factors is essential to ensuring a smooth transition to a new regimen and to enable the global antiretroviral market to respond adequately.

Environmental Management Competitive Pressure Effect on SME Environmental Innovation Activities: A Green Supply Chain Perspective

NASA Astrophysics Data System (ADS)

Rashid, A. A.; Sidek, A. A.; Suffian, S. A.; Daud, M. R. C.

2018-01-01

The idea of assimilating green supply chain is to integrate and establish environmental management into the supply chain practices. The study aims to explore how environmental management competitive pressure influences a SME company in Malaysia to incorporate green supply chain integration, which is an efficient platform to develop environmental innovation. This study further advances green supply chain management research in Malaysia by using the method of quantitative analysis to analyze the model developed which data will be collected based on a sample of SMEs in Malaysia in manufacturing sector. The model developed in this study illustrates how environmental management competitive pressure from main competitors affects three fundamental dimensions of green supply chain integration. The research findings suggest that environmental management competitive pressure is a vital driving force for a SME company to incorporate internal and external collaboration in developing green product innovation. From the analysis conducted, the study strongly demonstrated that the best way for a company to counteract competitor’s environmental management success is to first implement strong internal green product development process then move to incorporate external environmental management innovation between their suppliers and customers. The findings also show that internal integration of green product innovation fully mediates the relationship of environmental management competitive pressure and the external integration of green product innovation.

Exploring the folding pattern of a polymer chain in a single crystal by combining single-molecule force spectroscopy and steered molecular dynamics simulations.

PubMed

Song, Yu; Feng, Wei; Liu, Kai; Yang, Peng; Zhang, Wenke; Zhang, Xi

2013-03-26

Understanding the folding pattern of a single polymer chain within its single crystal will shed light on the mechanism of crystallization. Here, we use the combined techniques of atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations to study the folding pattern of a polyethylene oxide (PEO) chain in its single crystal. Our results show that the folding pattern of a PEO chain in the crystal formed in dilute solution follows the adjacent re-entry folding model. While in the crystal obtained from the melt, the nonadjacent folding with large and irregular loops contributes to big force fluctuations in the force-extension curves. The method established here can offer a novel strategy to directly unravel the chain-folding pattern of polymer single crystals at single-molecule level.

Locations of Racism in Education: A Speech Act Analysis of a Policy Chain

ERIC Educational Resources Information Center

Arneback, Emma; Quennerstedt, Ann

2016-01-01

This article explores how racism is located in an educational policy chain and identifies how its interpretation changes throughout the chain. A basic assumption is that the policy formation process can be seen as a chain in which international, national and local policies are "links"--separate entities yet joined. With Sweden as the…

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.

Anomalous dynamical phase in quantum spin chains with long-range interactions

NASA Astrophysics Data System (ADS)

Homrighausen, Ingo; Abeling, Nils O.; Zauner-Stauber, Valentin; Halimeh, Jad C.

2017-09-01

The existence or absence of nonanalytic cusps in the Loschmidt-echo return rate is traditionally employed to distinguish between a regular dynamical phase (regular cusps) and a trivial phase (no cusps) in quantum spin chains after a global quench. However, numerical evidence in a recent study (J. C. Halimeh and V. Zauner-Stauber, arXiv:1610.02019) suggests that instead of the trivial phase, a distinct anomalous dynamical phase characterized by a novel type of nonanalytic cusps occurs in the one-dimensional transverse-field Ising model when interactions are sufficiently long range. Using an analytic semiclassical approach and exact diagonalization, we show that this anomalous phase also arises in the fully connected case of infinite-range interactions, and we discuss its defining signature. Our results show that the transition from the regular to the anomalous dynamical phase coincides with Z2-symmetry breaking in the infinite-time limit, thereby showing a connection between two different concepts of dynamical criticality. Our work further expands the dynamical phase diagram of long-range interacting quantum spin chains, and can be tested experimentally in ion-trap setups and ultracold atoms in optical cavities, where interactions are inherently long range.

Dynamics of metastable breathers in nonlinear chains in acoustic vacuum

NASA Astrophysics Data System (ADS)

Sen, Surajit; Mohan, T. R. Krishna

2009-03-01

The study of the dynamics of one-dimensional chains with both harmonic and nonlinear interactions, as in the Fermi-Pasta-Ulam and related problems, has played a central role in efforts to identify the broad consequences of nonlinearity in these systems. Nevertheless, little is known about the dynamical behavior of purely nonlinear chains where there is a complete absence of the harmonic term, and hence sound propagation is not admissible, i.e., under conditions of “acoustic vacuum.” Here we study the dynamics of highly localized excitations, or breathers, which are known to be initiated by the quasistatic stretching of the bonds between adjacent particles. We show via detailed particle-dynamics-based studies that many low-energy pulses also form in the vicinity of the perturbation, and the breathers that form are “fragile” in the sense that they can be easily delocalized by scattering events in the system. We show that the localized excitations eventually disperse, allowing the system to attain an equilibrium-like state that is realizable in acoustic vacuum. We conclude with a discussion of how the dynamics is affected by the presence of acoustic oscillations.

Dynamical behavior of a single polymer chain under nanometric confinement

NASA Astrophysics Data System (ADS)

Lagrené, K.; Zanotti, J.-M.; Daoud, M.; Farago, B.; Judeinstein, P.

2010-10-01

We address the dynamical behavior of a single polymer chain under nanometric confinement. We consider a polymer melt made of a mixture of hydrogenated and deuterated high molecular mass Poly(Ethylene Oxide) (PEO). The confining material is a membrane of Anodic Aluminum Oxide (AAO), a macroscopically highly ordered confining system made of parallel cylindrical channels. We use Neutron Spin-Echo (NSE) under the Zero Average Contrast (ZAC) condition to, all at once, i) match the intense porous AAO detrimental elastic SANS (Small Angle Neutron Scattering) contribution to the total intermediate scattering function I(Q,t) and ii) measure the Q dependence of the dynamical modes of a single chain under confinement. The polymer dynamics is probed on an extremely broad spacial ([2.2 10-2 Å-1, 0.2 Å-1]) and temporal ([0.1 ns, 600 ns]) ranges. We do not detect any influence of confinement on the polymer dynamics. This result is discussed in the framework of the debate on the existence of a "corset effect" recently suggested by NMR relaxometry data.

Dynamics of Surface Reorganization of Poly(methyl methacrylate) in Contact with Water

NASA Astrophysics Data System (ADS)

Horinouchi, Ayanobu; Atarashi, Hironori; Fujii, Yoshihisa; Tanaka, Keiji

2013-03-01

New tools for tailor-made diagnostics, such as DNA arrays and tips for micro-total-analysis systems, are generally made from polymers. In these applications, the polymer surface is in contact with a water phase. However, despite the importance of detailed knowledge of the fundamental interactions of polymer interfaces with liquids, such studies are very limited. As an initial benchmark for designing and constructing specialized biomedical surfaces containing polymer, aggregation states and dynamics of chains at the water interface should be systematically examined. We here apply time-resolved contact angle measurement to study the dynamics of the surface reorganization of poly(methyl methacrylate) (PMMA) in contact with water. By doing the measurements at various temperatures, it is possible to discuss the surface dynamics of PMMA based on the apparent activation energy. Also, sum-frequency generation spectroscopy revealed that the surface reorganization involves the conformational changes in the main chain part as well as the side chains. Hence, the dynamics observed here may reflect the segmental motion at the outermost region of the PMMA film, in which water plays as a plasticizer.

Performance of Kobryn-Gusarov-Kovalenko closure from a thermodynamic viewpoint for one-component Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Miyata, Tatsuhiko; Tange, Kentaro

2018-05-01

The performance of Kobryn-Gusarov-Kovalenko (KGK) closure was examined in terms of the thermodynamics for one-component Lennard-Jones fluids. The result was compared to molecular dynamics simulation as well as to hypernetted chain, Kovalenko-Hirata (KH), Percus-Yevick and Verlet-modified closures. As the density increases, the error of KGK closure shows a turnover, regarding the excess internal energy, pressure and isothermal compressibility. On the other hand, it was numerically confirmed that the energy and the virial equations are consistent under both KH and KGK closures. The accuracies of density-derivative and temperature-derivative of the radial distribution function are also discussed.

Adsorption of poly(ethylene succinate) chain onto graphene nanosheets: A molecular simulation.

PubMed

Kelich, Payam; Asadinezhad, Ahmad

2016-09-01

Understanding the interaction between single polymer chain and graphene nanosheets at local and global length scales is essential for it underlies the mesoscopic properties of polymer nanocomposites. A computational attempt was then performed using atomistic molecular dynamics simulation to gain physical insights into behavior of a model aliphatic polyester, poly(ethylene succinate), single chain near graphene nanosheets, where the effects of the polymer chain length, graphene functionalization, and temperature on conformational properties of the polymer were studied comparatively. Graphene functionalization was carried out through extending the parameters set of an all-atom force field. The results showed a significant conformational transition of the polymer chain from three-dimensional statistical coil, in initial state, to two-dimensional fold, in final state, during adsorption on graphene. The conformational order, overall shape, end-to-end separation statistics, and mobility of the polymer chain were found to be influenced by the graphene functionalization, temperature, and polymer chain length. Furthermore, the polymer chain dynamics mode during adsorption on graphene was observed to transit from normal diffusive to slow subdiffusive mode. The findings from this computational study could shed light on the physics of the early stages of aliphatic polyester chain organization induced by graphene. Copyright © 2016 Elsevier Inc. All rights reserved.

Chaotic dynamics of Heisenberg ferromagnetic spin chain with bilinear and biquadratic interactions

NASA Astrophysics Data System (ADS)

Blessy, B. S. Gnana; Latha, M. M.

2017-10-01

We investigate the chaotic dynamics of one dimensional Heisenberg ferromagnetic spin chain by constructing the Hamiltonian equations of motion. We present the trajectory and phase plots of the system with bilinear and also biquadratic interactions. The stability of the system is analysed in both cases by constructing the Jacobian matrix and by measuring the Lyapunov exponents. The results are illustrated graphically.

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.

Pulse propagation in granular chains

NASA Astrophysics Data System (ADS)

Rosas, Alexandre; Lindenberg, Katja

2018-03-01

In this comprehensive review we present, discuss, and compare a number of theoretical approaches to the propagation of impulses in granular chains found in the literature, emphasizing the strengths and weaknesses of each. Experimental and numerical results are compared, and common features of the dynamics of pulse propagation for distinct chain setups are highlighted.

NMR studies of structure, hydrogen exchange, and main-chain dynamics in a disrupted-core mutant of thioredoxin.

PubMed Central

De Lorimier, R.; Hellinga, H. W.; Spicer, L. D.

1996-01-01

Core-packing mutants of proteins often approach molten globule states, and hence may have attributes of folding intermediates. We have studied a core-packing mutant of thioredoxin, L78K, in which a leucine residue is substituted by lysine, using 15N heteronuclear two- and three-dimensional NMR. Chemical shift differences between the mutant and wild-type main-chain resonances reveal that structural changes caused by the mutation are localized within 12 A of the altered side chain. The majority of resonances are unchanged, as are many 1H-1H NOEs indicative of the main-chain fold, suggesting that the structure of L78K is largely similar to wild type. Hydrogen exchange studies reveal that residues comprising the central beta-sheet of both mutant and wild-type proteins constitute a local unfolding unit, but with the unfolding/folding equilibrium approximately 12 times larger in L78K. The dynamics of main-chain NH bonds in L78K were studied by 15N spin relaxation and compared with a previous study of wild type. Order parameters for angular motion of NH bonds in the mutant are on average lower than in wild type, suggesting greater spatial freedom on a rapid time scale, but may also be related to different rotational correlation times in the two proteins. There is also evidence of greater conformational exchange in the mutant. Differences between mutant and wild type in hydrogen exchange and main-chain dynamics are not confined to the vicinity of the mutation. We infer that mispacking of the protein core in one location affects local dynamics and stability throughout. PMID:8976564

Main-chain metallopolymers at the static-dynamic boundary based on nickelocene

NASA Astrophysics Data System (ADS)

Musgrave, Rebecca A.; Russell, Andrew D.; Hayward, Dominic W.; Whittell, George R.; Lawrence, Paul G.; Gates, Paul J.; Green, Jennifer C.; Manners, Ian

2017-08-01

Interactions between metal ions and ligands in metal-containing polymers involve two bonding extremes: persistent covalent bonding, in which the polymers are essentially static in nature, or labile coordination bonding, which leads to dynamic supramolecular materials. Main-chain polymetallocenes based on ferrocene and cobaltocene fall into the former category because of the presence of strong metal-cyclopentadienyl bonds. Herein, we describe a main-chain polynickelocene—formed by ring-opening polymerization of a moderately strained [3]nickelocenophane monomer—that can be switched between static and dynamic states because of the relatively weak nickel-cyclopentadienyl ligand interactions. This is illustrated by the observation that, at a low concentration or at an elevated temperature in a coordinating or polar solvent, depolymerization of the polynickelocene occurs. A study of this dynamic polymer-monomer equilibrium by 1H NMR spectroscopy allowed the determination of the associated thermodynamic parameters. Microrheology data, however, indicated that under similar conditions the polynickelocene is considered to be static on the shorter rheological timescale.

Rotational dynamics of coumarin-153 and 4-aminophthalimide in 1-ethyl-3-methylimidazolium alkylsulfate ionic liquids: effect of alkyl chain length on the rotational dynamics.

PubMed

Das, Sudhir Kumar; Sarkar, Moloy

2012-01-12

Rotational dynamics of two neutral organic solutes, coumarin-153 (C-153) and 4-aminophthalimide (AP), with only the latter having hydrogen-bond-donating ability, has been investigated in a series of 1-ethyl-3-methylimidazolium alkyl sulfate ionic liquids as a function of temperature. The ionic liquids differ only in the length of the linear alkyl side chain (alkyl = ethyl, butyl, hexyl, and octyl) on the anionic moiety. The present study has been undertaken to examine the role of alkyl side chains on the rotational dynamics of the two solutes in these ionic liquids. Analysis of the results using Stokes-Einstein-Debye hydrodynamic theory indicates that the rotational dynamics of C-153 lies between the stick and slip boundary condition in the ethyl analogue and finally reaches subslip condition as in case of the octyl substituent. The observed rotational behavior of C-153 has been explained on the basis of an increase in the size of the solvent, which offers lower friction for solute rotation. On the other hand, AP shows superstick behavior in the ethyl system and exceeds the stick limit in the octyl derivative. Superstick behavior of AP has been attributed to the specific hydrogen-bonding interaction between AP and the sulfate moiety. Proton NMR investigation confirms the hydrogen-bonding interaction between the N-H hydrogen of AP and the ionic liquid. The decrease in rotational coupling constant values for AP with increasing length of alkyl side chains has been attributed to the decrease in the solute-solvent-specific interaction with an increase in the alkyl side chain length on the sulfate moiety.

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

NASA Astrophysics Data System (ADS)

Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

2017-10-01

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.

75 FR 22412 - Food and Drug Administration/Xavier University Global Outsourcing Conference

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-28

... relationships and supply chain control, as well as expectations from global regulators. Pharmaceutical companies...; Quality Agreement Development throughout the product and process lifecycle; Supply Chain Transparency and Pedigree; How to Audit the Supply Chain; Rx-360 and International Pharmaceutical Excipients Council...

Molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2017-02-20

Quinoa starch has very small granules with unique properties. However, the molecular structure of quinoa starch remains largely unknown. In this study, composition and amylopectin molecular structure of 9 quinoa starch samples were characterised by chromatographic techniques. In particular, the amylopectin internal molecular structure, represented by φ, β-limit dextrins (LDs), was explored. Great variations in the composition and molecular structures were recorded among samples. Compared with other amylopectins, quinoa amylopectin showed a high ratio of short chain to long chains (mean:14.6) and a high percentage of fingerprint A-chains (A fp ) (mean:10.4%). The average chain length, external chain length, and internal chain length of quinoa amylopectin were 16.6, 10.6, and 5.00 glucosyl residues, respectively. Pearson correlation and principal component analysis revealed some inherent correlations among structural parameters and a similarity of different samples. Overall, quinoa amylopectins are structurally similar to that from starches with A-type polymorph such as oat and amaranth starches. Copyright © 2016 Elsevier Ltd. All rights reserved.

Anomalous critical slowdown at a first order phase transition in single polymer chains.

PubMed

Zhang, Shuangshuang; Qi, Shuanhu; Klushin, Leonid I; Skvortsov, Alexander M; Yan, Dadong; Schmid, Friederike

2017-08-14

Using Brownian dynamics, we study the dynamical behavior of a polymer grafted onto an adhesive surface close to the mechanically induced adsorption-stretching transition. Even though the transition is first order (in the infinite chain length limit, the stretching degree of the chain jumps discontinuously), the characteristic relaxation time is found to grow according to a power law as the transition point is approached. We present a dynamic effective interface model which reproduces these observations and provides an excellent quantitative description of the simulation data. The generic nature of the theoretical model suggests that the unconventional mixing of features that are characteristic for first-order transitions (a jump in an order parameter) and features that are characteristic of critical points (an anomalous slowdown) may be a common phenomenon in force-driven phase transitions of macromolecules.

Bose-Fermi mapping and a multibranch spin-chain model for strongly interacting quantum gases in one dimension: Dynamics and collective excitations

NASA Astrophysics Data System (ADS)

Yang, Li; Pu, Han

2016-09-01

We show that the wave function in one spatial sector x1

Overshoot in biological systems modelled by Markov chains: a non-equilibrium dynamic phenomenon.

PubMed

Jia, Chen; Qian, Minping; Jiang, Daquan

2014-08-01

A number of biological systems can be modelled by Markov chains. Recently, there has been an increasing concern about when biological systems modelled by Markov chains will perform a dynamic phenomenon called overshoot. In this study, the authors found that the steady-state behaviour of the system will have a great effect on the occurrence of overshoot. They showed that overshoot in general cannot occur in systems that will finally approach an equilibrium steady state. They further classified overshoot into two types, named as simple overshoot and oscillating overshoot. They showed that except for extreme cases, oscillating overshoot will occur if the system is far from equilibrium. All these results clearly show that overshoot is a non-equilibrium dynamic phenomenon with energy consumption. In addition, the main result in this study is validated with real experimental data.

Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains

NASA Astrophysics Data System (ADS)

Zhang, Shuangshuang; Qi, Shuanhu; Klushin, Leonid I.; Skvortsov, Alexander M.; Yan, Dadong; Schmid, Friederike

2018-01-01

We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an attraction parameter ɛ and the other is the loop-stretch transition in a chain with one end attached to a repulsive substrate, driven by an external end-force F applied to the free end. Specifically, we compare the behavior of the respective order parameters of the transitions, i.e., the mean number of surface contacts in the case of the adsorption transition and the mean position of the chain end in the case of the loop-stretch transition. Close to the transition points, both the static behavior and the dynamic behavior of chains with different length N are very well described by a scaling ansatz with the scaling parameters (ɛ - ɛ*)Nϕ (adsorption transition) and (F - F*)Nν (loop-stretch transition), respectively, where ϕ is the crossover exponent of the adsorption transition and ν is the Flory exponent. We show that both the loop-stretch and the loop adsorption transitions provide an exceptional opportunity to construct explicit analytical expressions for the crossover functions which perfectly describe all simulation results on static properties in the finite-size scaling regime. Explicit crossover functions are based on the ansatz for the analytical form of the order parameter distributions at the respective transition points. In contrast to the close similarity in equilibrium static behavior, the dynamic relaxation at the two transitions shows qualitative differences, especially in the strongly ordered regimes. This is attributed to the fact that the surface contact dynamics in a strongly adsorbed chain is governed by local processes, whereas the end height relaxation of a strongly stretched chain involves the full spectrum of Rouse modes.

Internal friction and mode relaxation in a simple chain model.

PubMed

Fugmann, S; Sokolov, I M

2009-12-21

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

Paige Jadun | NREL

Science.gov Websites

dynamics. She has performed research in sustainable mobility, network optimization, supply chain analysis Experience Supply Chain Design Consultant, LLamasoft, Ann Arbor, MI Featured Publications Laura J

Mass dependence of the activation enthalpy and entropy of unentangled linear alkane chains

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

Jeong, Cheol; Douglas, Jack F.

2015-10-14

The mass scaling of the self-diffusion coefficient D of polymers in the liquid state, D ∼ M{sup β}, is one of the most basic characteristics of these complex fluids. Although traditional theories such as the Rouse and reptation models of unentangled and entangled polymer melts, respectively, predict that β is constant, this exponent for alkanes has been estimated experimentally to vary from −1.8 to −2.7 upon cooling. Significantly, β changes with temperature T under conditions where the chains are not entangled and at temperatures far above the glass transition temperature T{sub g} where dynamic heterogeneity does not complicate the descriptionmore » of the liquid dynamics. Based on atomistic molecular dynamics simulations on unentangled linear alkanes in the melt, we find that the variation of β with T can be directly attributed to the dependence of the enthalpy ΔH{sub a} and entropy ΔS{sub a} of activation on the number of alkane backbone carbon atoms, n. In addition, we find a sharp change in the melt dynamics near a “critical” chain length, n ≈ 17. A close examination of this phenomenon indicates that a “buckling transition” from rod-like to coiled chain configurations occurs at this characteristic chain length and distinct entropy-enthalpy compensation relations, ΔS{sub a} ∝ ΔH{sub a}, hold on either side of this polymer conformational transition. We conclude that the activation free energy parameters exert a significant influence on the dynamics of polymer melts that is not anticipated by either the Rouse and reptation models. In addition to changes of ΔH{sub a} and ΔS{sub a} with M, we expect changes in these free energy parameters to be crucial for understanding the dynamics of polymer blends, nanocomposites, and confined polymers because of changes of the fluid free energy by interfacial interactions and geometrical confinement.« less

Who Is the Dynamic Duo? How Infants Learn about the Identity of Objects in a Causal Chain

ERIC Educational Resources Information Center

Rakison, David H.; Smith, Gabriel Tobin; Ali, Areej

2016-01-01

Four experiments investigated infants' and adults' knowledge of the identity of objects in a causal sequence of events. In Experiments 1 and 2, 18- and 22-month-olds in the visual habituation procedure were shown a 3-step causal chain event in which the relation between an object's part (dynamic or static) and its causal role was either consistent…

Spin dynamics of random Ising chain in coexisting transverse and longitudinal magnetic fields

NASA Astrophysics Data System (ADS)

Liu, Zhong-Qiang; Jiang, Su-Rong; Kong, Xiang-Mu; Xu, Yu-Liang

2017-05-01

The dynamics of the random Ising spin chain in coexisting transverse and longitudinal magnetic fields is studied by the recursion method. Both the spin autocorrelation function and its spectral density are investigated by numerical calculations. It is found that system's dynamical behaviors depend on the deviation σJ of the random exchange coupling between nearest-neighbor spins and the ratio rlt of the longitudinal and the transverse fields: (i) For rlt = 0, the system undergoes two crossovers from N independent spins precessing about the transverse magnetic field to a collective-mode behavior, and then to a central-peak behavior as σJ increases. (ii) For rlt ≠ 0, the system may exhibit a coexistence behavior of a collective-mode one and a central-peak one. When σJ is small (or large enough), system undergoes a crossover from a coexistence behavior (or a disordered behavior) to a central-peak behavior as rlt increases. (iii) Increasing σJ depresses effects of both the transverse and the longitudinal magnetic fields. (iv) Quantum random Ising chain in coexisting magnetic fields may exhibit under-damping and critical-damping characteristics simultaneously. These results indicate that changing the external magnetic fields may control and manipulate the dynamics of the random Ising chain.

Dynamics in Polymer Nanocomposites

NASA Astrophysics Data System (ADS)

Clarke, Nigel

2015-03-01

Since nanoparticles are increasingly being added to polymers to impart mechanical and functional properties, we are exploring how nanoparticles impact polymer dynamics with a focus on the diffusion coefficients. In high molecular weight polymer melts, chain diffusion is well described by the reptation model. Motion proceeds as a snake-like diffusion of the chain as a whole, along the contour of a tube that mimics the role of physical entanglements, or topological constraints, with other chains. In polymer nanocomposites there are additional constraints due to the dispersed nanoparticles in the polymer matrix. Chain motion can be altered by nanoparticle size, shape , aspect ratio, surface area, loading and the nature of the interactions between the nanoparticles and the polymer matrix. We have observed a minimum in the diffusion coefficient as a function of nanoparticle concentration when the nanoparticles are rod-like and a collapse of the diffusion coefficient onto a master curve when the nanoparticles are spherical. We are simulating the dynamics using molecular and dissipative particle simulations in order to provide physical insight into the local structure and dynamics, and have also carried out highly coarse grained Monte Carlo simulations of entangled polymers to explore how reptation is affected by the presence of larger scale obstacles. We acknowledge support from the NSF/EPSRC Materials World Network Program.

Free energy landscapes of short peptide chains using adaptively biased molecular dynamics

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2009-03-01

We present the results of a computational study of the free energy landscapes of short polypeptide chains, as a function of several reaction coordinates meant to distinguish between several known types of helices. The free energy landscapes were calculated using the recently developed adaptively biased molecular dynamics method followed up with equilibrium ``umbrella correction'' runs. Specific polypeptides investigated include small chains of pure and mixed alanine, glutamate, leucine, lysine and methionine (all amino acids with strong helix-forming propensities), as well as glycine, proline(having a low helix forming propensities), tyrosine, serine and arginine. Our results are consistent with the existing experimental and other theoretical evidence.

Research on Duplication Dynamics and Evolutionary Stable of Reverse Supply Chain

NASA Astrophysics Data System (ADS)

Huizhong, Dong; Hongli, Song

An evolutionary game model of Reverse Supply Chain(RSC) is established based on duplication dynamics function and evolutionary stable strategy. Using the model framework, this paper provides insights into a deeper understanding on how each supplier make strategic decision independently in reverse supply chain to determine their performance. The main conclusion is as follow: Under the market mechanism, not unless the extra income derived from the implementation of RSC exceeds zero point would the suppliers implement RSC strategy. When those suppliers are passive to RSC, the effective solution is that the government takes macro-control measures, for example, to force those suppliers implement RSC through punishment mechanism.

Efficient dynamic modeling of manipulators containing closed kinematic loops

NASA Astrophysics Data System (ADS)

Ferretti, Gianni; Rocco, Paolo

An approach to efficiently solve the forward dynamics problem for manipulators containing closed chains is proposed. The two main distinctive features of this approach are: the dynamics of the equivalent open loop tree structures (any closed loop can be in general modeled by imposing some additional kinematic constraints to a suitable tree structure) is computed through an efficient Newton Euler formulation; the constraint equations relative to the most commonly adopted closed chains in industrial manipulators are explicitly solved, thus, overcoming the redundancy of Lagrange's multipliers method while avoiding the inefficiency due to a numerical solution of the implicit constraint equations. The constraint equations considered for an explicit solution are those imposed by articulated gear mechanisms and planar closed chains (pantograph type structures). Articulated gear mechanisms are actually used in all industrial robots to transmit motion from actuators to links, while planar closed chains are usefully employed to increase the stiffness of the manipulators and their load capacity, as well to reduce the kinematic coupling of joint axes. The accuracy and the efficiency of the proposed approach are shown through a simulation test.

Ultrafast exciton migration in an HJ-aggregate: Potential surfaces and quantum dynamics

NASA Astrophysics Data System (ADS)

Binder, Robert; Polkehn, Matthias; Ma, Tianji; Burghardt, Irene

2017-01-01

Quantum dynamical and electronic structure calculations are combined to investigate the mechanism of exciton migration in an oligothiophene HJ aggregate, i.e., a combination of oligomer chains (J-type aggregates) and stacked aggregates of such chains (H-type aggregates). To this end, a Frenkel exciton model is parametrized by a recently introduced procedure [Binder et al., J. Chem. Phys. 141, 014101 (2014)] which uses oligomer excited-state calculations to perform an exact, point-wise mapping of coupled potential energy surfaces to an effective Frenkel model. Based upon this parametrization, the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method is employed to investigate ultrafast dynamics of exciton transfer in a small, asymmetric HJ aggregate model composed of 30 sites and 30 active modes. For a partially delocalized initial condition, it is shown that a torsional defect confines the trapped initial exciton, and planarization induces an ultrafast resonant transition between an HJ-aggregated segment and a covalently bound "dangling chain" end. This model is a minimal realization of experimentally investigated mixed systems exhibiting ultrafast exciton transfer between aggregated, highly planarized chains and neighboring disordered segments.

Molecular dynamics studies on the interaction and encapsulation processes of the nucleotide and peptide chains inside of a carbon nanotube matrix with inclusion of gold nanoparticles

NASA Astrophysics Data System (ADS)

Kholmurodov, Kholmirzo; Dushanov, Eric; Khusenov, Mirzoaziz; Rahmonov, Khaiyom; Zelenyak, Tatyana; Doroshkevich, Alexander; Majumder, Subrata

2017-05-01

Studying of molecular systems as single nucleotides, nucleotide and peptide chains, RNA and DNA interacting with metallic nanoparticles within a carbon nanotube matrix represents a great interest in modern research. In this respect it is worth mentioning the development of the electronics diagnostic apparatus, the biochemical and biotechnological application tools (nanorobotic design, facilities of drug delivery in a living cell), so on. In the present work using molecular dynamics (MD) simulation method the interaction process of small nucleotide chains (NCs) and elongated peptide chains with different sets of metallic nanoparticles (NPs) on a matrix from carbon nanotube (CNT) were simulated to study their mechanisms of encapsulation and folding processes. We have performed a series of the MD calculations with different NC,peptides-NP-CNT models that were aimed on the investigation of the peculiarities of NC,peptide-NP interactions, the formation of bonds and structures in the system, as well as the dynamical behavior in an environment confined by the CNT matrix.

Note: A simple picture of subdiffusive polymer motion from stochastic simulations

NASA Astrophysics Data System (ADS)

Gniewek, Pawel; Kolinski, Andrzej

2011-02-01

Entangled polymer solutions and melts exhibit unusual frictional properties. In the entanglement limit self-diffusion coefficient of long flexible polymers decays with the second power of chain length and viscosity increases with 3-3.5 power of chain length.1 It is very difficult to provide detailed molecular-level explanation of the entanglement effect.2 Perhaps, the problem of many entangled polymer chains is the most complex multibody issue of classical physics. There are different approaches to polymer melt dynamics. Some of these recognize hydrodynamic interactions as a dominant term, while topological constraints for polymer chains are assumed as a secondary factor. Other theories consider the topological constraints as the most important factors controlling polymer dynamics. Herman and co-workers describe polymer dynamics in melts, as a lateral sliding of a chain along other chains until complete mutual disentanglement. Despite the success in explaining the power-laws for viscosity, the model has some limitations. First of all, memory effects are ignored, that is, polymer segments are treated independently. Also, each entanglement/obstacle is treated as a separate entity, which is certainly a simplification of the memory effect problem. In addition to that, correlated motions of segments are addressed within the framework of renormalized Rouse-chain theory,7 without calling any topological entanglements in advance. This approach leads to the generalized Langevin equation characterized by distinct memory kernels describing local and nonlocal segment correlations or to the Smoluchowski equation in which the segments' mobility is treated as a stochastic variable.11 Both models describe the polymer segments motion at a microscopic level. An interesting alternative is to solve the integrodifferential equation for the chain relaxation with a sophisticated kernel function.12 The design of the kernel function is based on a mesoscopic description of the polymer melt. These theories explain some experimental data, although the description of the crossover between the Rouse and non-Rouse behavior is not satisfactory. Obviously, within the scope of a short note we cannot review all theoretical concepts of the polymer melt dynamics. Here we focus just on the interpretation of the observed single segment autocorrelation function.

Block and Gradient Copoly(2-oxazoline) Micelles: Strikingly Different on the Inside.

PubMed

Filippov, Sergey K; Verbraeken, Bart; Konarev, Petr V; Svergun, Dmitri I; Angelov, Borislav; Vishnevetskaya, Natalya S; Papadakis, Christine M; Rogers, Sarah; Radulescu, Aurel; Courtin, Tim; Martins, José C; Starovoytova, Larisa; Hruby, Martin; Stepanek, Petr; Kravchenko, Vitaly S; Potemkin, Igor I; Hoogenboom, Richard

2017-08-17

Herein, we provide a direct proof for differences in the micellar structure of amphiphilic diblock and gradient copolymers, thereby unambiguously demonstrating the influence of monomer distribution along the polymer chains on the micellization behavior. The internal structure of amphiphilic block and gradient co poly(2-oxazolines) based on the hydrophilic poly(2-methyl-2-oxazoline) (PMeOx) and the hydrophobic poly(2-phenyl-2-oxazoline) (PPhOx) was studied in water and water-ethanol mixtures by small-angle X-ray scattering (SAXS), small-angle neutron scattering (SANS), static and dynamic light scattering (SLS/DLS), and 1 H NMR spectroscopy. Contrast matching SANS experiments revealed that block copolymers form micelles with a uniform density profile of the core. In contrast to popular assumption, the outer part of the core of the gradient copolymer micelles has a distinctly higher density than the middle of the core. We attribute the latter finding to back-folding of chains resulting from hydrophilic-hydrophobic interactions, leading to a new type of micelles that we refer to as micelles with a "bitterball-core" structure.

On the mesoscopic origins of high viscosities in some polyelectrolyte-surfactant mixtures

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

Hoffmann, Ingo, E-mail: ingo.hoffmann@tu-berlin.de; Institut Max von Laue-Paul Langevin; Farago, Bela

Oppositely charged polyelectrolyte (PE) surfactant mixtures allow the control of rheological parameters of a solution even at fairly low concentrations. For example, addition of 0.3 wt. % of anionic surfactant to a 1 wt. % solution of the polycation JR 400 increases the viscosity by 4 orders of magnitude. Recently, we could show that this increase is related to the formation of mixed, rod-like PE/surfactant aggregates which interconnect several polyelectrolyte chains [Hoffmann et al., Europhys. Lett. 104, 28001 (2013)]. In this paper, we refine our structural model of the aggregates to obtain a more consistent picture of their internal structure for differentmore » anionic surfactants. Combining small angle neutron scattering (SANS) and neutron spin-echo (NSE) allows us to determine the size of the aggregates. By comparing different contrasts, the internal structure of the aggregates can be elucidated and it is seen that the PE in the aggregates retains a relatively high freedom of movement. We proceeded to investigate the influence of the surfactant concentration and the surfactant type on structure and dynamics of the mixed aggregates. It is seen that the structural parameters of the aggregates depend very little on the surfactant concentration and headgroup. However, it is crucial to incorporate a sufficient amount of PE in the aggregates to increase the viscosity of the aggregates. By comparing viscous samples at 1 wt. % PE concentration with samples at a PE concentration of 0.3 wt. %, where no significant increase in viscosity is observed, we find that similar aggregates are formed already at this lower PE concentrations. However, the amount of PE incorporated in them is insufficient to interconnect several PE chains and therefore, they do not increase viscosity. So, our detailed investigation combining contrast variation SANS and NSE does not only allow to explain the viscosity behavior but also to deduced detailed information regarding the structures and the dynamics especially of the polyelectrolyte within the complexes.« less

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.

Exploring the Dynamics of Globalization: Supply Chain Vulnerability to Natural Disasters

ERIC Educational Resources Information Center

Kalafsky, Ronald V.; Conner, Neil

2015-01-01

Global supply chains play an increasingly important role in the economy and should therefore be addressed within geography coursework, especially given concerns that geographers have not fully explored various angles of globalization. This article explores the use of an online case study on supply chains and their vulnerability to natural…

Micro-Hall magnetometry on a Co-organic chain compound

NASA Astrophysics Data System (ADS)

Rolland, L.; Simonet, V.; Wernsdorfer, W.; Bogani, L.; Sessoli, R.

2004-05-01

The static and dynamical properties of Co-organic chains, with strong magnetic anisotropy, are studied by micro-Hall magnetometry. The low-temperature hysteresis cycles are discussed with respect to the helical structure of the chains. Thermally activated relaxation of the magnetization is observed, compatible with the Glauber model for a 1D Ising system.

Geometric modelling of the contact point between the bushing and sprocket in chain drives

NASA Astrophysics Data System (ADS)

Saulescu, R.; Velicu, R.; Lates, M.

2017-02-01

An important problem of the bush chains dynamics is represented by the calculus of the normal and transversal forces on all the contacts; these forces are producing vibrations in the chain and due to this, the chain is affected by the wear. One aspect of that dynamics is referring directly on the sprockets geometry and on the bushing and sprocket contact. The paper presents a calculus method for the contact angle between the bushing and the sprocket; this angle is a variable one depending on the bushing’s number being in contact (i) and on the specific elongation of the chain (x) due to the functioning of it. Based on the presented calculus model, a comparative analysis is proposed for these factors by using sprockets with different teeth numbers and different specific elongations of the chain. The results of the numerical simulations allow the dissemination of recommendations regarding the contact angle’s evolution, from the beginning to the end of the contact and regarding the influence of the chain’s specific elongations on the out of use of it.

Peptide adsorption on the hydrophobic surface: A free energy perspective

NASA Astrophysics Data System (ADS)

Sheng, Yuebiao; Wang, Wei; Chen, P.

2011-05-01

Protein adsorption is a very attractive topic which relates to many novel applications in biomaterials, biotechnology and nanotechnology. Ionic complementary peptides are a group of novel nano-biomaterials with many biomedical applications. In this work, molecular dynamics simulations of the ionic-complementary peptide EAK16-II on a hydrophobic graphite surface were performed under neutral, acidic and basic solution conditions. Adsorption free energy contour maps were obtained by analyzing the dynamical trajectories. Hydrophobic interactions were found to govern the adsorption of the first peptide molecule, and both hydrophobic and electrostatic interactions contributed to the adsorption of the second peptide molecule. Especially under acidic and basic solution conditions, interplay existed among chain-chain hydrophobic, chain-surface hydrophobic and chain-chain electrostatic interactions during the adsorption of the second peptide molecule. Non-charged residues were found to lie on the graphite surface, while charged residue side-chains oriented towards the solution after the peptide deposited on the surface. These results provide a basis for understanding peptide adsorption on the hydrophobic surface under different solution conditions, which is useful for novel applications such as bioactive implant devices and drug delivery material design.

Polymer chain dynamics under nanoscopic confinements.

PubMed

Kimmich, Rainer; Fatkullin, Nail; Mattea, Carlos; Fischer, Elmar

2005-02-01

It is shown that the confinement of polymer melts in nanopores leads to chain dynamics dramatically different from bulk behavior. This so-called corset effect occurs both above and below the critical molecular mass and induces the dynamic features predicted for reptation. A spinodal demixing technique was employed for the preparation of linear poly(ethylene oxide) (PEO) confined to nanoscopic strands that are in turn embedded in a quasi-solid and impenetrable methacrylate matrix. Both the molecular weight of the PEO and the mean diameter of the strands were varied to a certain degree. The chain dynamics of the PEO in the molten state was examined with the aid of field-gradient NMR diffusometry (time scale, 10(-2)-10(0) s) and field-cycling NMR relaxometry (time scale, 10(-9)-10(-4) s). The dominating mechanism for translational displacements probed in the nanoscopic strands by either technique is shown to be reptation. On the time scale of spin-lattice relaxation time measurements, the frequency dependence signature of reptation (i.e., T1 approximately nu(3/4)) showed up in all samples. A "tube" diameter of only 0.6 nm was concluded to be effective on this time scale even when the strand diameter was larger than the radius of gyration of the PEO random coils. This corset effect is traced back to the lack of the local fluctuation capacity of the free volume in nanoscopic confinements. The confinement dimension is estimated at which the crossover from confined to bulk chain dynamics is expected.

Polymer translocation through a nanopore: a showcase of anomalous diffusion.

PubMed

Milchev, A; Dubbeldam, Johan L A; Rostiashvili, Vakhtang G; Vilgis, Thomas A

2009-04-01

We investigate the translocation dynamics of a polymer chain threaded through a membrane nanopore by a chemical potential gradient that acts on the chain segments inside the pore. By means of diverse methods (scaling theory, fractional calculus, and Monte Carlo and molecular dynamics simulations), we demonstrate that the relevant dynamic variable, the transported number of polymer segments, s(t), displays an anomalous diffusive behavior, both with and without an external driving force being present. We show that in the absence of drag force the time tau, needed for a macromolecule of length N to thread from the cis into the trans side of a cell membrane, scales as tauN(2/alpha) with the chain length. The anomalous dynamics of the translocation process is governed by a universal exponent alpha= 2/(2nu + 2 - gamma(1)), which contains the basic universal exponents of polymer physics, nu (the Flory exponent) and gamma(1) (the surface entropic exponent). A closed analytic expression for the probability to find s translocated segments at time t in terms of chain length N and applied drag force f is derived from the fractional Fokker-Planck equation, and shown to provide analytic results for the time variation of the statistical moments and . It turns out that the average translocation time scales as tau proportional, f(-1)N(2/alpha-1). These results are tested and found to be in perfect agreement with extensive Monte Carlo and molecular dynamics computer simulations.

Dynamical potentials for nonequilibrium quantum many-body phases

NASA Astrophysics Data System (ADS)

Roy, Sthitadhi; Lazarides, Achilleas; Heyl, Markus; Moessner, Roderich

2018-05-01

Out of equilibrium phases of matter exhibiting order in individual eigenstates, such as many-body localized spin glasses and discrete time crystals, can be characterized by inherently dynamical quantities such as spatiotemporal correlation functions. In this paper, we introduce dynamical potentials which act as generating functions for such correlations and capture eigenstate phases and order. These potentials show formal similarities to their equilibrium counterparts, namely thermodynamic potentials. We provide three representative examples: a disordered XXZ chain showing many-body localization, a disordered Ising chain exhibiting spin-glass order, and its periodically-driven cousin exhibiting time-crystalline order.

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

Mendl, Christian B.; Spohn, Herbert

The nonequilibrium dynamics of anharmonic chains is studied by imposing an initial domain-wall state, in which the two half lattices are prepared in equilibrium with distinct parameters. Here, we analyse the Riemann problem for the corresponding Euler equations and, in specific cases, compare with molecular dynamics. Additionally, the fluctuations of time-integrated currents are investigated. In analogy with the KPZ equation, their typical fluctuations should be of size t 1/3 and have a Tracy–Widom GUE distributed amplitude. The proper extension to anharmonic chains is explained and tested through molecular dynamics. Our results are calibrated against the stochastic LeRoux lattice gas.

Dynamical Binding Modes Determine Agonistic and Antagonistic Ligand Effects in the Prostate-Specific G-Protein Coupled Receptor (PSGR).

PubMed

Wolf, Steffen; Jovancevic, Nikolina; Gelis, Lian; Pietsch, Sebastian; Hatt, Hanns; Gerwert, Klaus

2017-11-22

We analysed the ligand-based activation mechanism of the prostate-specific G-protein coupled receptor (PSGR), which is an olfactory receptor that mediates cellular growth in prostate cancer cells. Furthermore, it is an olfactory receptor with a known chemically near identic antagonist/agonist pair, α- and β-ionone. Using a combined theoretical and experimental approach, we propose that this receptor is activated by a ligand-induced rearrangement of a protein-internal hydrogen bond network. Surprisingly, this rearrangement is not induced by interaction of the ligand with the network, but by dynamic van der Waals contacts of the ligand with the involved amino acid side chains, altering their conformations and intraprotein connectivity. Ligand recognition in this GPCR is therefore highly stereo selective, but seemingly lacks any ligand recognition via polar contacts. A putative olfactory receptor-based drug design scheme will have to take this unique mode of protein/ligand action into account.

Revisiting kinetic boundary conditions at the surface of fuel droplet hydrocarbons: An atomistic computational fluid dynamics simulation

PubMed Central

Nasiri, Rasoul

2016-01-01

The role of boundary conditions at the interface for both Boltzmann equation and the set of Navier-Stokes equations have been suggested to be important for studying of multiphase flows such as evaporation/condensation process which doesn’t always obey the equilibrium conditions. Here we present aspects of transition-state theory (TST) alongside with kinetic gas theory (KGT) relevant to the study of quasi-equilibrium interfacial phenomena and the equilibrium gas phase processes, respectively. A two-state mathematical model for long-chain hydrocarbons which have multi-structural specifications is introduced to clarify how kinetics and thermodynamics affect evaporation/condensation process at the surface of fuel droplet, liquid and gas phases and then show how experimental observations for a number of n-alkane may be reproduced using a hybrid framework TST and KGT with physically reasonable parameters controlling the interface, gas and liquid phases. The importance of internal activation dynamics at the surface of n-alkane droplets is established during the evaporation/condensation process. PMID:27215897

Influence of the nematic order on the rheology and conformation of stretched comb-like liquid crystalline polymers

NASA Astrophysics Data System (ADS)

Fourmaux-Demange, V.; Brûlet, A.; Boué, F.; Davidson, P.; Keller, P.; Cotton, J. P.

2000-04-01

We have studied the rheology and the conformation of stretched comb-like liquid-crystalline polymers. Both the influence of the comb-like structure and the specific effect of the nematic interaction on the dynamics are investigated. For this purpose, two isomers of a comb-like polymetacrylate polymer, of well-defined molecular weights, were synthesized: one displays a nematic phase over a wide range of temperature, the other one has only an isotropic phase. Even with high degrees of polymerization N, between 40 and 1000, the polymer chains studied were not entangled. The stress-strain curves during the stretching and relaxation processes show differences between the isotropic and nematic comb-like polymers. They suggest that, in the nematic phase, the chain dynamics is more cooperative than for a usual linear polymer. Small-angle neutron scattering has been used in order to determine the evolution of the chain conformation after stretching, as a function of the duration of relaxation t_r. The conformation can be described with two parameters only: λ_p, the global deformation of the polymer chain, and p, the number of statistical units of locally relaxed sub-chains. For the comb-like polymer, the chain deformation is pseudo-affine: λ_p is always smaller than λ (the deformation ratio of the whole sample). In the isotropic phase, λ_p has a constant value, while p increases as t_r. This latter behavior is not that expected for non-entangled chains, in which p varies as {t_r}^{1/2} (Rouse model). In the nematic phase, λ_p decreases as a stretched exponential function of t_r, while p remains constant. The dynamics of the comb-like polymers is discussed in terms of living clusters from which junctions are produced by interactions between side chains. The nematic interaction increases the lifetime of these junctions and, strikingly, the relaxation is the same at all scales of the whole polymer chain.

Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization.

PubMed

Reddy, Th Dhileep N; Mallik, Bhabani S

2017-04-19

This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site-site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of the charged entities, cations and anions, in the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic conductivities and hydrogen bonds as well as residence dynamics. The diffusion coefficients and ionic conductivity decrease with an increase in the size of the cation or anion. The effect of alkyl chain length on ionic conductivity calculated in this article is consistent with the findings of other experimental studies. Hydrogen bond lifetimes and residence times along with structure factors were also calculated, and are related to alkyl chain length.

Dynamic Game Behavior of Retailers Considering the Quality of Substitute Products Based on Delay Decision

NASA Astrophysics Data System (ADS)

Bao, Binshuo; Ma, Junhai

2017-12-01

Motivated by the Silk Road Economic Belt and the 21st-Century Maritime Silk Road project, i.e. the Belt and Road (B&R), more goods will flow around the world. With this trading platform, people can buy products at relatively cheap prices, and it is easier for people to buy various goods. The quality and quantity of products thus attract more and more attention in the supply chains. This paper discusses the quantity decision by considering the product quality in parallel supply chains where two manufacturers produce substitute products and then sell them to their downstream retailers separately. In terms of the changing quantity, as well as the different quality, this paper establishes a dynamic game model to explore the dynamic behavior when the optimal profits of two retailers have been calculated. The dynamic behaviors of the system, such as stable region, bifurcation and chaos, strange attractors and the largest Lyapunov exponents (LLE) are analyzed. The effect of the quantity adjustment parameter on the stability of the supply chain system is investigated through numerical simulations. Furthermore, a dynamic game model is established based on the quality delay decision, to investigate the influence of the quality delay parameter on the dynamic game model and the profits. Finally, the optimal decisions are obtained and analyzed.

Multi-isotope SPECT imaging of the 225Ac decay chain: feasibility studies

NASA Astrophysics Data System (ADS)

Robertson, A. K. H.; Ramogida, C. F.; Rodríguez-Rodríguez, C.; Blinder, Stephan; Kunz, Peter; Sossi, Vesna; Schaffer, Paul

2017-06-01

Effective use of the {}225Ac decay chain in targeted internal radioimmunotherapy requires the retention of both {}225Ac and progeny isotopes at the target site. Imaging-based pharmacokinetic tests of these pharmaceuticals must therefore separately yet simultaneously image multiple isotopes that may not be colocalized despite being part of the same decay chain. This work presents feasibility studies demonstrating the ability of a microSPECT/CT scanner equipped with a high energy collimator to simultaneously image two components of the {}225Ac decay chain: {}221Fr (218 keV) and {}213Bi (440 keV). Image quality phantoms were used to assess the performance of two collimators for simultaneous {}221Fr and {}213Bi imaging in terms of contrast and noise. A hotrod resolution phantom containing clusters of thin rods with diameters ranging between 0.85 and 1.70 mm was used to assess resolution. To demonstrate ability to simultaneously image dynamic {}221Fr and {}213Bi activity distributions, a phantom containing a {}213Bi generator from {}225Ac was imaged. These tests were performed with two collimators, a high-energy ultra-high resolution (HEUHR) collimator and an ultra-high sensitivity (UHS) collimator. Values consistent with activity concentrations determined independently via gamma spectroscopy were observed in high activity regions of the images. In hotrod phantom images, the HEUHR collimator resolved all rods for both {}221Fr and {}213Bi images. With the UHS collimator, no rods were resolvable in {}213Bi images and only rods  ⩾1.3 mm were resolved in {}221Fr images. After eluting the {}213Bi generator, images accurately visualized the reestablishment of transient equilibrium of the {}225Ac decay chain. The feasibility of evaluating the pharmacokinetics of the {}225Ac decay chain in vivo has been demonstrated. This presented method requires the use of a high-performance high-energy collimator.

Regime of aggregate structures and magneto-rheological characteristics of a magnetic rod-like particle suspension: Monte Carlo and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Okada, Kazuya; Satoh, Akira

2017-09-01

In the present study, we address a suspension composed ferromagnetic rod-like particles to elucidate a regime change in the aggregate structures and the magneto-rheological characteristics. Monte Carlo simulations have been employed for investigating the aggregate structures in thermodynamic equilibrium, and Brownian dynamics simulations for magneto-rheological features in a simple shear flow. The main results obtained here are summarized as follows. For the case of thermodynamic equilibrium, the rod-like particles aggregate to form thick chain-like clusters and the neighboring clusters incline in opposite directions. If the external magnetic field is increased, the thick chain-like clusters in the magnetic field direction grow thicker by adsorbing the neighboring clusters that incline in the opposite direction. Hence, a significant phase change in the particle aggregates is not induced by an increase in the magnetic field strength. For the case of a simple shear flow, even a weak shear flow induces a significant regime change from the thick chain-like clusters of thermodynamic equilibrium into wall-like aggregates composed of short raft-like clusters. A strong external magnetic field drastically changes these aggregates into wall-like aggregates composed of thick chain-like clusters rather than the short raft-like clusters. The internal structure of these aggregates is not strongly influenced by a shear flow, and the formation of the short raft-like clusters is maintained inside the aggregates. The main contribution to the net viscosity is the viscosity component due to magnetic particle-particle interaction forces in relation to the present volumetric fraction. Hence, a larger magnetic interaction strength and also a stronger external magnetic field give rise to a larger magneto-rheological effect. However, the dependence of the viscosity on these factors is governed in a complex manner by whether or not the wall-like aggregates are composed mainly of short raft-like clusters. An increase in the shear rate functions to simply decrease the effect of the magnetic particle-particle and the particle-field interactions.

Polymer dynamics: Floored by the rings

NASA Astrophysics Data System (ADS)

McLeish, Tom

2008-12-01

The tube model can explain how mutually entangled polymer chains move and interact, but it relies on the loose ends of chains to generate relaxation. Ring polymers have no ends - so how do they relax?

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.

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

PubMed

Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

2015-03-01

The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding. © 2014 Wiley Periodicals, Inc.

Live-cell and super-resolution imaging reveal that the distribution of wall-associated protein A is correlated with the cell chain integrity of Streptococcus mutans.

PubMed

Li, Y; Liu, Z; Zhang, Y; Su, Q P; Xue, B; Shao, S; Zhu, Y; Xu, X; Wei, S; Sun, Y

2015-10-01

Streptococcus mutans is a primary pathogen responsible for dental caries. It has an outstanding ability to form biofilm, which is vital for virulence. Previous studies have shown that knockout of Wall-associated protein A (WapA) affects cell chain and biofilm formation of S. mutans. As a surface protein, the distribution of WapA remains unknown, but it is important to understand the mechanism underlying the function of WapA. This study applied the fluorescence protein mCherry as a reporter gene to characterize the dynamic distribution of WapA in S. mutans via time-lapse and super-resolution fluorescence imaging. The results revealed interesting subcellular distribution patterns of WapA in single, dividing and long chains of S. mutans cells. It appears at the middle of the cell and moves to the poles as the cell grows and divides. In a cell chain, after each round of cell division, such dynamic relocation results in WapA distribution at the previous cell division sites, resulting in a pattern where WapA is located at the boundary of two adjacent cell pairs. This WapA distribution pattern corresponds to the breaking segmentation of wapA deletion cell chains. The dynamic relocation of WapA through the cell cycle increases our understanding of the mechanism of WapA in maintaining cell chain integrity and biofilm formation. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion.

PubMed

Weininger, Ulrich; Respondek, Michal; Akke, Mikael

2012-09-01

Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.

Thermodynamic description of cellulose chain collapse using coarse grain modeling

NASA Astrophysics Data System (ADS)

Das, Ritankar; Chu, Jhih-Wei

2012-11-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Local excitation-inhibition ratio for synfire chain propagation in feed-forward neuronal networks

NASA Astrophysics Data System (ADS)

Guo, Xinmeng; Yu, Haitao; Wang, Jiang; Liu, Jing; Cao, Yibin; Deng, Bin

2017-09-01

A leading hypothesis holds that spiking activity propagates along neuronal sub-populations which are connected in a feed-forward manner, and the propagation efficiency would be affected by the dynamics of sub-populations. In this paper, how the interaction between local excitation and inhibition effects on synfire chain propagation in feed-forward network (FFN) is investigated. The simulation results show that there is an appropriate excitation-inhibition (EI) ratio maximizing the performance of synfire chain propagation. The optimal EI ratio can significantly enhance the selectivity of FFN to synchronous signals, which thereby increases the stability to background noise. Moreover, the effect of network topology on synfire chain propagation is also investigated. It is found that synfire chain propagation can be maximized by an optimal interlayer linking probability. We also find that external noise is detrimental to synchrony propagation by inducing spiking jitter. The results presented in this paper may provide insights into the effects of network dynamics on neuronal computations.

Chain dynamics and nanoparticle motion in attractive polymer nanocomposites subjected to large deformations.

PubMed

Senses, Erkan; Tyagi, Madhusudan; Natarajan, Bharath; Narayanan, Suresh; Faraone, Antonio

2017-11-08

The effect of large deformation on the chain dynamics in attractive polymer nanocomposites was investigated using neutron scattering techniques. Quasi-elastic neutron backscattering measurements reveal a substantial reduction of polymer mobility in the presence of attractive, well-dispersed nanoparticles. In addition, large deformations are observed to cause a further slowing down of the Rouse rates at high particle loadings, where the interparticle spacings are slightly smaller than the chain dimensions, i.e. in the strongly confined state. No noticeable change, however, was observed for a lightly confined system. The reptation tube diameter, measured by neutron spin echo, remained unchanged after shear, suggesting that the level of chain-chain entanglements is not significantly affected. The shear-induced changes in the interparticle bridging reflect the slow nanoparticle motion measured by X-ray photon correlation spectroscopy. These results provide a first step for understanding how large shear can significantly affect the segmental motion in nanocomposites and open up new opportunities for designing mechanically responsive soft materials.

Chain dynamics and nanoparticle motion in attractive polymer nanocomposites subjected to large deformations

DOE PAGES

Senses, Erkan; Tyagi, Madhusudan; Natarajan, Bharath; ...

2017-09-28

The effect of large deformation on the chain dynamics in attractive polymer nanocomposites was investigated using neutron scattering techniques. Quasielastic neutron backscattering measurements reveal a substantial reduction of polymer mobility in the presence of attractive, well-dispersed nanoparticles. Additionally, large deformations are observed to cause a further slowing down of the Rouse rates at high particle loadings, where the interparticle spacings are slightly smaller than the chain dimensions, i.e. in the strongly confined state. No noticeable change, however, was observed for a lightly confined system. The reptation tube diameter, measured by neutron spin echo, remained unchanged after shear, suggesting that themore » level of chain-chain entanglements is not significantly affected. The shearinduced changes in the interparticle bridging reflects on the slow nanoparticle motion measured by X-ray photon correlation spectroscopy. These results provide a first step for understanding how large shear can significantly affect the segmental motion in nanocomposites and open up new opportunities for designing mechanically responsive soft materials.« less

Chain dynamics and nanoparticle motion in attractive polymer nanocomposites subjected to large deformations

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

Senses, Erkan; Tyagi, Madhusudan; Natarajan, Bharath

The effect of large deformation on the chain dynamics in attractive polymer nanocomposites was investigated using neutron scattering techniques. Quasielastic neutron backscattering measurements reveal a substantial reduction of polymer mobility in the presence of attractive, well-dispersed nanoparticles. Additionally, large deformations are observed to cause a further slowing down of the Rouse rates at high particle loadings, where the interparticle spacings are slightly smaller than the chain dimensions, i.e. in the strongly confined state. No noticeable change, however, was observed for a lightly confined system. The reptation tube diameter, measured by neutron spin echo, remained unchanged after shear, suggesting that themore » level of chain-chain entanglements is not significantly affected. The shearinduced changes in the interparticle bridging reflects on the slow nanoparticle motion measured by X-ray photon correlation spectroscopy. These results provide a first step for understanding how large shear can significantly affect the segmental motion in nanocomposites and open up new opportunities for designing mechanically responsive soft materials.« less

Nanostructures and nanosecond dynamics at the polymer/filler interface

NASA Astrophysics Data System (ADS)

Koga, Tad; Barkley, Deborah; Endoh, Maya; Masui, Tomomi; Kishimoto, Hiroyuki; Nagao, Michihiro; Taniguchi, Takashi

We report in-situ nanostructures and nanosecond dynamics of polybutadiene (PB) chains bound to carbon black (CB) fillers (the so-called ``bound polymer layer (BPL)'') in polymer solutions (from dilute to concentrated solutions). The BPL on the CB fillers were extracted by solvent leaching of a CB-filled PB compound and subsequently dispersed in deuterated toluene (a good solvent) to label the BPL for ``contrast-matching'' small-angle neutron scattering (SANS) and neutron spin echo (NSE) techniques. The SANS results demonstrate that the BPL is composed of two regions regardless of molecular weights of PB: the inner unswollen region of 0.5 nm thick and outer swollen region where the polymer chains display a parabolic profile with a diffuse tail. In addition, the NSE results show that the dynamics of the swollen bound chains in the polymer solutions can be explained by the collective dynamics, the so-called ``breathing mode''. Intriguingly, it was also indicative that the collective dynamics is independent of the polymer concentrations and is much faster than that predicted from the solution viscosity. We will discuss the mechanism at the bound polymer-free polymer interface at the nanometer scale. T.K. acknowledges the financial support from NSF Grant (CMMI-1332499).

Polymer dynamics in turbulent flow

NASA Astrophysics Data System (ADS)

Muthukumar, Murugappan

2014-03-01

Presence of dilute amounts of high-molecular weight polymers in liquids undergoing turbulent wall-bounded shear flows leads to significant drag reduction. There are two major proposed mechanisms of drag reduction in the literature. One is based on enhanced viscosity due to chain extension; the other is based on the assumption that elastic energy stored in polymer conformations is comparable to the kinetic energy in some eddies. Using the Navier-Stokes equation for the fluid and the Kirkwood-Riseman-Zimm equation for polymer chains, we have addressed the coupling between the near-wall turbulence dynamics and polymer dynamics. Our theoretical results show that the torque associated with polymer conformations contributes more significantly than the chain stretching and that the characteristic dimensions of polymer coils are much smaller than eddy sizes required for possible exchange of energy. We thus emphasize an additional mechanism to the existing two schools of thought in the search of an understanding of drag reduction.

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.

Dynamics of Polarons in Organic Conjugated Polymers with Side Radicals.

PubMed

Liu, J J; Wei, Z J; Zhang, Y L; Meng, Y; Di, B

2017-03-16

Based on the one-dimensional tight-binding Su-Schrieffer-Heeger (SSH) model, and using the molecular dynamics method, we discuss the dynamics of electron and hole polarons propagating along a polymer chain, as a function of the distance between side radicals and the magnitude of the transfer integrals between the main chain and the side radicals. We first discuss the average velocities of electron and hole polarons as a function of the distance between side radicals. It is found that the average velocities of the electron polarons remain almost unchanged, while the average velocities of hole polarons decrease significantly when the radical distance is comparable to the polaron width. Second, we have found that the average velocities of electron polarons decrease with increasing transfer integral, but the average velocities of hole polarons increase. These results may provide a theoretical basis for understanding carriers transport properties in polymers chain with side radicals.

Microscopic mechanism for the effect of adding salt on electrospinning by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Wang, Bing-Bing; Wang, Xiao-Dong; Wang, Tian-Hu

2014-09-01

Adding salts into polymer solution has been found to modulate the fiber structure and significantly improve the solution spinnability in electrospinning. However, the mechanisms have not been fully understood. This work adopted molecular dynamics method to investigate the dynamic behavior of poly(ethylene oxide) (PEO)/water droplet with or without dissolved NaCl salt under high-voltage electric field. Our simulation results agreed with the previous experimental reports well. We observed that some daughter droplets detach from the mother droplet due to the ions evaporation and hydration effect, which significantly accelerates the water evaporation and hence improves the solution spinnability. We also observed that some sodium ions are always coordinated with the ether oxygen group in the PEO chain. When these ions are accelerated by the electric field, the PEO chain segments follow the motion of the ions, inevitably stretching the chain and improving the fiber morphology.

Role of uncrosslinked chains in droplets dynamics on silicone elastomers.

PubMed

Hourlier-Fargette, Aurélie; Antkowiak, Arnaud; Chateauminois, Antoine; Neukirch, Sébastien

2017-05-21

We report an unexpected behavior in wetting dynamics on soft silicone substrates: the dynamics of aqueous droplets deposited on vertical plates of such elastomers exhibits two successive speed regimes. This macroscopic observation is found to be closely related to microscopic phenomena occurring at the scale of the polymer network: we show that uncrosslinked chains found in most widely used commercial silicone elastomers are responsible for this surprising behavior. A direct visualization of the uncrosslinked oligomers collected by water droplets is performed, evidencing that a capillarity-induced phase separation occurs: uncrosslinked oligomers are extracted from the silicone elastomer network by the water-glycerol mixture droplet. The sharp speed change is shown to coincide with an abrupt transition in surface tension of the droplets, when a critical surface concentration in uncrosslinked oligomer chains is reached. We infer that a droplet shifts to a second regime with a faster speed when it is completely covered with a homogeneous oil film.

Dynamical Negative Differential Resistance in Antiferromagnetically Coupled Few-Atom Spin Chains

NASA Astrophysics Data System (ADS)

Rolf-Pissarczyk, Steffen; Yan, Shichao; Malavolti, Luigi; Burgess, Jacob A. J.; McMurtrie, Gregory; Loth, Sebastian

2017-11-01

We present the appearance of negative differential resistance (NDR) in spin-dependent electron transport through a few-atom spin chain. A chain of three antiferromagnetically coupled Fe atoms (Fe trimer) was positioned on a Cu2 N /Cu (100 ) surface and contacted with the spin-polarized tip of a scanning tunneling microscope, thus coupling the Fe trimer to one nonmagnetic and one magnetic lead. Pronounced NDR appears at the low bias of 7 mV, where inelastic electron tunneling dynamically locks the atomic spin in a long-lived excited state. This causes a rapid increase of the magnetoresistance between the spin-polarized tip and Fe trimer and quenches elastic tunneling. By varying the coupling strength between the tip and Fe trimer, we find that in this transport regime the dynamic locking of the Fe trimer competes with magnetic exchange interaction, which statically forces the Fe trimer into its high-magnetoresistance state and removes the NDR.

Studies on the solvation dynamics of coumarin 153 in 1-ethyl-3-methylimidazolium alkylsulfate ionic liquids: dependence on alkyl chain length.

PubMed

Das, Sudhir Kumar; Sarkar, Moloy

2012-08-06

Steady-state and time-resolved fluorescence behavior of coumarin 153 (C153) is investigated in a series of 1-ethyl-3-methylimidazolium alkylsulfate ([C(2)mim][C(n)OSO(3)]) ionic liquids differing only in the length of the linear alkyl chain (n = 4, 6, and 8) in the anion. The aim of the present study is to understand the role of alkyl chain length in solute rotation and solvation dynamics of C153 in these ionic liquids. The blueshift observed in the steady-state absorption and emission maxima of C153 on going from the C(4)OSO(3) to the C(8)OSO(3) system indicates increasing nonpolar character of the microenvironment of the solute with increasing length of the alkyl side chain of the anion of the ionic liquids. The average solvation time is also found to increase on changing the substituent from butyl to octyl, and this is attributed to the increase in the bulk viscosity of the ILs. A steady blueshift of the time-zero maximum of the fluorescence spectrum with increasing alkyl chain length also indicates that the probe molecule experiences a less polar environment in the early part of the dynamics. Rotational dynamics of C153 are also analyzed by using the Stokes-Einstein-Debye (SED), Gierer-Wirtz (GW), and Dote-Kivelson-Schwartz (DKS) theories. Analyses of the results seem to suggest decoupling of the rotational motion of the probe from solvent viscosity. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chain representations of Open Quantum Systems and Lieb-Robinson like bounds for the dynamics

NASA Astrophysics Data System (ADS)

Woods, Mischa

2013-03-01

This talk is concerned with the mapping of the Hamiltonian of open quantum systems onto chain representations, which forms the basis for a rigorous theory of the interaction of a system with its environment. This mapping progresses as an interaction which gives rise to a sequence of residual spectral densities of the system. The rigorous mathematical properties of this mapping have been unknown so far. Here we develop the theory of secondary measures to derive an analytic, expression for the sequence solely in terms of the initial measure and its associated orthogonal polynomials of the first and second kind. These mappings can be thought of as taking a highly nonlocal Hamiltonian to a local Hamiltonian. In the latter, a Lieb-Robinson like bound for the dynamics of the open quantum system makes sense. We develop analytical bounds on the error to observables of the system as a function of time when the semi-infinite chain in truncated at some finite length. The fact that this is possible shows that there is a finite ``Speed of sound'' in these chain representations. This has many implications of the simulatability of open quantum systems of this type and demonstrates that a truncated chain can faithfully reproduce the dynamics at shorter times. These results make a significant and mathematically rigorous contribution to the understanding of the theory of open quantum systems; and pave the way towards the efficient simulation of these systems, which within the standard methods, is often an intractable problem. EPSRC CDT in Controlled Quantum Dynamics, EU STREP project and Alexander von Humboldt Foundation

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

NASA Astrophysics Data System (ADS)

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

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

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)].

[Status Quo, Uncertainties and Trends Analysis of Environmental Risk Assessment for PFASs].

PubMed

Hao, Xue-wen; Li, Li; Wang, Jie; Cao, Yan; Liu, Jian-guo

2015-08-01

This study systematically combed the definition and change of terms, category and application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) in international academic, focusing on the environmental risk and exposure assessment of PFASs, to comprehensively analyze the current status, uncertainties and trends of PFASs' environmental risk assessment. Overall, the risk assessment of PFASs is facing a complicated situation involving complex substance pedigrees, various types, complex derivative relations, confidential business information and risk uncertainties. Although the environmental risk of long-chain PFASs has been widely recognized, the short-chain PFASs and short-chain fluorotelomers as their alternatives still have many research gaps and uncertainties in environmental hazards, environmental fate and exposure risk. The scope of risk control of PFASs in the international community is still worth discussing. Due to trade secrets and market competition, the chemical structure and risk information of PFASs' alternatives are generally lack of openness and transparency. The environmental risk of most fluorinated and non-fluorinated alternatives is not clear. In total, the international research on PFASs risk assessment gradually transfer from long-chain perfluoroalkyl acids (PFAAs) represented by perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) to short-chain PFAAs, and then extends to other PFASs. The main problems to be solved urgently and researched continuously are: the environmental hazardous assessment indexes, such as bioaccumulation and environmental migration, optimization method, the environmental release and multimedia environmental fate of short-chain PFASs; the environmental fate of neutral PFASs and the transformation and contribution as precursors of short-chain PFASs; the risk identification and assessment of fluorinated and non-fluorinated alternatives of PFASs.

Rate-dependent behavior of the amorphous phase of spider dragline silk.

PubMed

Patil, Sandeep P; Markert, Bernd; Gräter, Frauke

2014-06-03

The time-dependent stress-strain behavior of spider dragline silk was already observed decades ago, and has been attributed to the disordered sequences in silk proteins, which compose the soft amorphous matrix. However, the actual molecular origin and magnitude of internal friction within the amorphous matrix has remained inaccessible, because experimentally decomposing the mechanical response of the amorphous matrix from the embedded crystalline units is challenging. Here, we used atomistic molecular dynamics simulations to obtain friction forces for the relative sliding of peptide chains of Araneus diadematus spider silk within bundles of these chains as a representative unit of the amorphous matrix in silk fibers. We computed the friction coefficient and coefficient of viscosity of the amorphous phase to be in the order of 10(-6) Ns/m and 10(4) Ns/m(2), respectively, by extrapolating our simulation data to the viscous limit. Finally, we used a finite element method for the amorphous phase, solely based on parameters derived from molecular dynamics simulations including the newly determined coefficient of viscosity. With this model the time scales of stress relaxation, creep, and hysteresis were assessed, and found to be in line with the macroscopic time-dependent response of silk fibers. Our results suggest the amorphous phase to be the primary source of viscosity in silk and open up the avenue for finite element method studies of silk fiber mechanics including viscous effects. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Estimating the Fully Burdened Cost of Fuel Using an Input-Output Model - A Micro-Level Analysis

DTIC Science & Technology

2011-09-01

The multilocation distribution model used by Lu and Rencheng to evaluate an international supply chain (From: Lu & Rencheng, 2007...IO model to evaluate an international supply chain specifically for a multilocation production system. Figure 2 illustrates such a system. vendor...vendor vendor Target markets Production plants Material vendor Figure 2. The multilocation distribution model used by Lu and Rencheng to

Interactions in the Metabolism of Glutamate and the Branched-Chain Amino Acids and Ketoacids in the CNS.

PubMed

Yudkoff, Marc

2017-01-01

Glutamatergic neurotransmission entails a tonic loss of glutamate from nerve endings into the synapse. Replacement of neuronal glutamate is essential in order to avoid depletion of the internal pool. In brain this occurs primarily via the glutamate-glutamine cycle, which invokes astrocytic synthesis of glutamine and hydrolysis of this amino acid via neuronal phosphate-dependent glutaminase. This cycle maintains constancy of internal pools, but it does not provide a mechanism for inevitable losses of glutamate N from brain. Import of glutamine or glutamate from blood does not occur to any appreciable extent. However, the branched-chain amino acids (BCAA) cross the blood-brain barrier swiftly. The brain possesses abundant branched-chain amino acid transaminase activity which replenishes brain glutamate and also generates branched-chain ketoacids. It seems probable that the branched-chain amino acids and ketoacids participate in a "glutamate-BCAA cycle" which involves shuttling of branched-chain amino acids and ketoacids between astrocytes and neurons. This mechanism not only supports the synthesis of glutamate, it also may constitute a mechanism by which high (and potentially toxic) concentrations of glutamate can be avoided by the re-amination of branched-chain ketoacids.

Digital Piracy: An Assessment of Consumer Piracy Risk and Optimal Supply Chain Coordination Strategies

ERIC Educational Resources Information Center

Jeong, Bong-Keun

2010-01-01

Digital piracy and the emergence of new distribution channels have changed the dynamics of supply chain coordination and created many interesting problems. There has been increased attention to understanding the phenomenon of consumer piracy behavior and its impact on supply chain profitability. The purpose of this dissertation is to better…

Understanding the effect of alkyl chains of gemini cations on the physicochemical and cellular properties of polyurethane micelles.

PubMed

Pan, Zhicheng; Fang, Danxuan; Song, Yuanqing; Song, Nijia; Ding, Mingming; Li, Jiehua; Luo, Feng; Li, Jianshu; Tan, Hong; Fu, Qiang

2018-06-06

Cationic gemini quaternary ammonium (GQA) has been used as a cell internalization promoter to improve the permeability of the cell membrane and enhance the cellular uptake. However, the effect of the alkyl chain length on the cellular properties of nanocarriers has not been elucidated yet. In this study, we developed a series of polyurethane micelles containing GQAs with various alkyl chain lengths. The alteration of the gemini alkyl chain length was found to change the distribution of GQA surfactants in the micellar structure and affect the surface charge exposure, stability, and the protein absorption properties of nanocarriers. Moreover, we also clarified the role of the alkyl chain length in tumor cell internalization and macrophage uptake of polyurethane micelles. This work provides a new understanding on the effect of the GQA alkyl chain length on the physicochemical and biological properties of nanomedicines, and offers guidance on the rational design of effective drug delivery systems where the issue of functional group exposure at the micellar surface should be considered.

Study of translational dynamics in molten polymer by variation of gradient pulse-width of PGSE.

PubMed

Stepišnik, Janez; Lahajnar, Gojmir; Zupančič, Ivan; Mohorič, Aleš

2013-11-01

Pulsed gradient spin echo is a method of measuring molecular translation. Changing Δ makes it sensitive to diffusion spectrum. Spin translation effects the buildup of phase structure during the application of gradient pulses as well. The time scale of the self-diffusion measurement shortens if this is taken into account. The method of diffusion spectrometry with variable δ is also less sensitive to artifacts caused by spin relaxation and internal gradient fields. Here the method is demonstrated in the case of diffusion spectrometry of molten polyethylene. The results confirm a model of constraint release in a system of entangled polymer chains as a sort of tube Rouse motion. Copyright © 2013 Elsevier Inc. All rights reserved.

Polymer physics experiments with single DNA molecules

NASA Astrophysics Data System (ADS)

Smith, Douglas E.

1999-11-01

Bacteriophage DNA molecules were taken as a model flexible polymer chain for the experimental study of polymer dynamics at the single molecule level. Video fluorescence microscopy was used to directly observe the conformational dynamics of fluorescently labeled molecules, optical tweezers were used to manipulate individual molecules, and micro-fabricated flow cells were used to apply controlled hydrodynamic strain to molecules. These techniques constitute a powerful new experimental approach in the study of basic polymer physics questions. I have used these techniques to study the diffusion and relaxation of isolated and entangled polymer molecules and the hydrodynamic deformation of polymers in elongational and shear flows. These studies revealed a rich, and previously unobserved, ``molecular individualism'' in the dynamical behavior of single molecules. Individual measurements on ensembles of identical molecules allowed the average conformation to be determined as well as the underlying probability distributions for molecular conformation. Scaling laws, that predict the dependence of properties on chain length and concentration, were also tested. The basic assumptions of the reptation model were directly confirmed by visualizing the dynamics of entangled chains.

Mesoscopic modeling for nucleic acid chain dynamics

PubMed Central

Sales-Pardo, M.; Guimerà, R.; Moreira, A. A.; Widom, J.; Amaral, L. A. N.

2007-01-01

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin—a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop—studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands. PMID:16089566

Surfactant mediated polyelectrolyte self-assembly

DOE PAGES

Goswami, Monojoy; Borreguero Calvo, Jose M.; Pincus, Phillip A.; ...

2015-11-25

Self-assembly and dynamics of polyelectrolyte (PE) surfactant complex (PES) is investigated using molecular dynamics simulations. The complexation is systematically studied for five different PE backbone charge densities. At a fixed surfactant concentration the PES complexation exhibits pearl-necklace to agglomerated double spherical structures with a PE chain decorating the surfactant micelles. The counterions do not condense on the complex, but are released in the medium with a random distribution. The relaxation dynamics for three different length scales, polymer chain, segmental and monomer, show distinct features of the charge and neutral species; the counterions are fastest followed by the PE chain andmore » surfactants. The surfactant heads and tails have the slowest relaxation due to their restricted movement inside the agglomerated structure. At the shortest length scale, all the charge and neutral species show similar relaxation dynamics confirming Rouse behavior at monomer length scales. Overall, the present study highlights the structure-property relationship for polymer-surfactant complexation. These results will help improve the understanding of PES complex and should aid in the design of better materials for future applications.« less

Development of an Assessment Model for Sustainable Supply Chain Management in Batik Industry

NASA Astrophysics Data System (ADS)

Mubiena, G. F.; Ma’ruf, A.

2018-03-01

This research proposes a dynamic assessment model for sustainable supply chain management in batik industry. The proposed model identifies the dynamic relationship between economic aspect, environment aspect and social aspect. The economic aspect refers to the supply chain operation reference model. The environment aspect uses carbon emissions and liquid waste as the attribute assessment, while the social aspect focus on employee’s welfare. Lean manufacturing concept was implemented as an alternative approach to sustainability. The simulation result shows that the average of sustainability score for 5 years increased from 65,3% to 70%. Future experiments will be conducted on design improvements to reach the company target on sustainability score.

Dynamics of polymers: A mean-field theory

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

Fredrickson, Glenn H.; Materials Research Laboratory, University of California, Santa Barbara, California 93106; Department of Materials, University of California, Santa Barbara, California 93106

2014-02-28

We derive a general mean-field theory of inhomogeneous polymer dynamics; a theory whose form has been speculated and widely applied, but not heretofore derived. Our approach involves a functional integral representation of a Martin-Siggia-Rose (MSR) type description of the exact many-chain dynamics. A saddle point approximation to the generating functional, involving conditions where the MSR action is stationary with respect to a collective density field ρ and a conjugate MSR response field ϕ, produces the desired dynamical mean-field theory. Besides clarifying the proper structure of mean-field theory out of equilibrium, our results have implications for numerical studies of polymer dynamicsmore » involving hybrid particle-field simulation techniques such as the single-chain in mean-field method.« less

Real-time dynamics of typical and untypical states in nonintegrable systems

NASA Astrophysics Data System (ADS)

Richter, Jonas; Jin, Fengping; De Raedt, Hans; Michielsen, Kristel; Gemmer, Jochen; Steinigeweg, Robin

2018-05-01

Understanding (i) the emergence of diffusion from truly microscopic principles continues to be a major challenge in experimental and theoretical physics. At the same time, isolated quantum many-body systems have experienced an upsurge of interest in recent years. Since in such systems the realization of a proper initial state is the only possibility to induce a nonequilibrium process, understanding (ii) the largely unexplored role of the specific realization is vitally important. Our work reports a substantial step forward and tackles the two issues (i) and (ii) in the context of typicality, entanglement as well as integrability and nonintegrability. Specifically, we consider the spin-1/2 XXZ chain, where integrability can be broken due to an additional next-nearest neighbor interaction, and study the real-time and real-space dynamics of nonequilibrium magnetization profiles for a class of pure states. Summarizing our main results, we show that signatures of diffusion for strong interactions are equally pronounced for the integrable and nonintegrable case. In both cases, we further find a clear difference between the dynamics of states with and without internal randomness. We provide an explanation of this difference by a detailed analysis of the local density of states.

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

Rai, Durgesh K.; Sharma, Veerendra K.; Anunciado, Divina

The interaction between lipid bilayers and Amyloid β peptide (Aβ) plays a critical role in proliferation of Alzheimer’s disease (AD). AD is expected to affect one in every 85 humans by 2050, and therefore, deciphering the interplay of Aβ and lipid bilayers at the molecular level is of profound importance. In this work, we applied an array of neutron scattering methods to study the structure and dynamics of Aβ(1–40) interacting 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) bilayers. In the structural investigations of lipid bilayer’s response to Aβ binding, Small Angle Neutron Scattering and Neutron Membrane Diffraction revealed that the Aβ anchors firmly to themore » highly charged DMPG bilayers in the interfacial region between water and hydrocarbon chain, and it doesn’t penetrate deeply into the bilayer. This association mode is substantiated by the dynamics studies with high resolution Quasi-Elastic Neutron Scattering experiments, showing that the addition of Aβ mainly affects the slower lateral motion of lipid molecules, especially in the fluid phase, but not the faster internal motion. The results revealed that Aβ associates with the highly charged membrane in surface with limited impact on the structure, but the altered membrane dynamics could have more influence on other membrane processes.« less

Particle size effect on strength, failure, and shock behavior in polytetrafluoroethylene-Al-W granular composite materials

NASA Astrophysics Data System (ADS)

Herbold, E. B.; Nesterenko, V. F.; Benson, D. J.; Cai, J.; Vecchio, K. S.; Jiang, F.; Addiss, J. W.; Walley, S. M.; Proud, W. G.

2008-11-01

The variation of metallic particle size and sample porosity significantly alters the dynamic mechanical properties of high density granular composite materials processed using a cold isostatically pressed mixture of polytetrafluoroethylene (PTFE), aluminum (Al), and tungsten (W) powders. Quasistatic and dynamic experiments are performed with identical constituent mass fractions with variations in the size of the W particles and pressing conditions. The relatively weak polymer matrix allows the strength and fracture modes of this material to be governed by the granular type behavior of agglomerated metal particles. A higher ultimate compressive strength was observed in relatively high porosity samples with small W particles compared to those with coarse W particles in all experiments. Mesoscale granular force chains of the metallic particles explain this unusual phenomenon as observed in hydrocode simulations of a drop-weight test. Macrocracks forming below the critical failure strain for the matrix and unusual behavior due to a competition between densification and fracture in dynamic tests of porous samples were also observed. Numerical modeling of shock loading of this granular composite material demonstrated that the internal energy, specifically thermal energy, of the soft PTFE matrix can be tailored by the W particle size distribution.

Active Site Gate Dynamics Modulate the Catalytic Activity of the Ubiquitination Enzyme E2-25K.

PubMed

Rout, Manoj K; Lee, Brian L; Lin, Aiyang; Xiao, Wei; Spyracopoulos, Leo

2018-05-03

The ubiquitin proteasome system (UPS) signals for degradation of proteins through attachment of K48-linked polyubiquitin chains, or alterations in protein-protein recognition through attachment of K63-linked chains. Target proteins are ubiquitinated in three sequential chemical steps by a three-component enzyme system. Ubiquitination, or E2 enzymes, catalyze the central step by facilitating reaction of a target protein lysine with the C-terminus of Ub that is attached to the active site cysteine of the E2 through a thioester bond. E2 reactivity is modulated by dynamics of an active site gate, whose central residue packs against the active site cysteine in a closed conformation. Interestingly, for the E2 Ubc13, which specifically catalyzes K63-linked ubiquitination, the central gate residue adopts an open conformation. We set out to determine if active site gate dynamics play a role in catalysis for E2-25K, which adopts the canonical, closed gate conformation, and which selectively synthesizes K48-linked ubiquitin chains. Gate dynamics were characterized using mutagenesis of key residues, combined with enzyme kinetics measurements, and main chain NMR relaxation. The experimental data were interpreted with all atom MD simulations. The data indicate that active site gate opening and closing rates for E2-25K are precisely balanced.

Direct Determination of Site-Specific Noncovalent Interaction Strengths of Proteins from NMR-Derived Fast Side Chain Motional Parameters.

PubMed

Rajeshwar T, Rajitha; Krishnan, Marimuthu

2017-05-25

A novel approach to accurately determine residue-specific noncovalent interaction strengths (ξ) of proteins from NMR-measured fast side chain motional parameters (O axis 2 ) is presented. By probing the environmental sensitivity of side chain conformational energy surfaces of individual residues of a diverse set of proteins, the microscopic connections between ξ, O axis 2 , conformational entropy (S conf ), conformational barriers, and rotamer stabilities established here are found to be universal among proteins. The results reveal that side chain flexibility and conformational entropy of each residue decrease with increasing ξ and that for each residue type there exists a critical range of ξ, determined primarily by the mean side chain conformational barriers, within which flexibility of any residue can be reversibly tuned from highly flexible (with O axis 2 ∼ 0) to highly restricted (with O axis 2 ∼ 1) by increasing ξ by ∼3 kcal/mol. Beyond this critical range of ξ, both side chain flexibility and conformational entropy are insensitive to ξ. The interrelationships between conformational dynamics, conformational entropy, and noncovalent interactions of protein side chains established here open up new avenues to probe perturbation-induced (for example, ligand-binding, temperature, pressure) changes in fast side chain dynamics and thermodynamics of proteins by comparing their conformational energy surfaces in the native and perturbed states.

Rapid Configurational Fluctuations in a Model of Methylcellulose

NASA Astrophysics Data System (ADS)

Li, Xiaolan; Dorfman, Kevin

Methylcellulose is a thermoresponsive polymer that undergoes a phase transition at elevated temperature, forming fibrils of a uniform diameter. However, the gelation mechanism is still unclear, in particular at higher polymer concentrations. We have investigated a coarse-grained model for methylcellulose, proposed by Larson and coworkers, that produces collapsed toroids in dilute solution with a radius close to that in experiments. Using Brownian Dynamics simulations, we demonstrate that this model's dihedral potential generates ``flipping events'', which helps the chain to avoid kinetic traps by undergoing a sudden transition between a coiled and a collapsed state. If the dihedral potential is removed, the chains cannot escape from their collapsed configuration, whereas at high dihedral potentials, the chains cannot stabilize the collapsed state. We will present quantitative results on the effect of the dihedral potential on both chain statistics and dynamic behavior, and discuss the implication of our results on the spontaneous formation of high-aspect ratio fibrils in experiments.

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

Canonical Structure and Orthogonality of Forces and Currents in Irreversible Markov Chains

NASA Astrophysics Data System (ADS)

Kaiser, Marcus; Jack, Robert L.; Zimmer, Johannes

2018-03-01

We discuss a canonical structure that provides a unifying description of dynamical large deviations for irreversible finite state Markov chains (continuous time), Onsager theory, and Macroscopic Fluctuation Theory (MFT). For Markov chains, this theory involves a non-linear relation between probability currents and their conjugate forces. Within this framework, we show how the forces can be split into two components, which are orthogonal to each other, in a generalised sense. This splitting allows a decomposition of the pathwise rate function into three terms, which have physical interpretations in terms of dissipation and convergence to equilibrium. Similar decompositions hold for rate functions at level 2 and level 2.5. These results clarify how bounds on entropy production and fluctuation theorems emerge from the underlying dynamical rules. We discuss how these results for Markov chains are related to similar structures within MFT, which describes hydrodynamic limits of such microscopic models.

Bushes of vibrational modes for Fermi-Pasta-Ulam chains

NASA Astrophysics Data System (ADS)

Chechin, G. M.; Novikova, N. V.; Abramenko, A. A.

2002-06-01

Some exact solutions and multimode invariant submanifolds were found for the Fermi-Pasta-Ulam (FPU)- β model by Poggi and Ruffo [Physica D 103 (1997) 251]. In the present paper we demonstrate how results of such a type can be obtained for an arbitraryN-particle chain with periodic boundary conditions with the aid of our group-theoretical approach [Physica D 117 (1998) 43] based on the concept of bushes of normal modes in mechanical systems with discrete symmetry. The integro-differential equation describing the FPU- α dynamics in the modal space is derived. The loss of stability of the bushes of modes for the FPU- α model, in particular, for the limiting case N→∞ for the dynamical regime with displacement pattern having period twice the lattice spacing ( π-mode) is studied. Our results for the FPU- α chain are compared with those by Poggi and Ruffo for the FPU- β chain.

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Reach and speed of judgment propagation in the laboratory.

PubMed

Moussaïd, Mehdi; Herzog, Stefan M; Kämmer, Juliane E; Hertwig, Ralph

2017-04-18

In recent years, a large body of research has demonstrated that judgments and behaviors can propagate from person to person. Phenomena as diverse as political mobilization, health practices, altruism, and emotional states exhibit similar dynamics of social contagion. The precise mechanisms of judgment propagation are not well understood, however, because it is difficult to control for confounding factors such as homophily or dynamic network structures. We introduce an experimental design that renders possible the stringent study of judgment propagation. In this design, experimental chains of individuals can revise their initial judgment in a visual perception task after observing a predecessor's judgment. The positioning of a very good performer at the top of a chain created a performance gap, which triggered waves of judgment propagation down the chain. We evaluated the dynamics of judgment propagation experimentally. Despite strong social influence within pairs of individuals, the reach of judgment propagation across a chain rarely exceeded a social distance of three to four degrees of separation. Furthermore, computer simulations showed that the speed of judgment propagation decayed exponentially with the social distance from the source. We show that information distortion and the overweighting of other people's errors are two individual-level mechanisms hindering judgment propagation at the scale of the chain. Our results contribute to the understanding of social-contagion processes, and our experimental method offers numerous new opportunities to study judgment propagation in the laboratory.

Reach and speed of judgment propagation in the laboratory

PubMed Central

Herzog, Stefan M.; Kämmer, Juliane E.; Hertwig, Ralph

2017-01-01

In recent years, a large body of research has demonstrated that judgments and behaviors can propagate from person to person. Phenomena as diverse as political mobilization, health practices, altruism, and emotional states exhibit similar dynamics of social contagion. The precise mechanisms of judgment propagation are not well understood, however, because it is difficult to control for confounding factors such as homophily or dynamic network structures. We introduce an experimental design that renders possible the stringent study of judgment propagation. In this design, experimental chains of individuals can revise their initial judgment in a visual perception task after observing a predecessor’s judgment. The positioning of a very good performer at the top of a chain created a performance gap, which triggered waves of judgment propagation down the chain. We evaluated the dynamics of judgment propagation experimentally. Despite strong social influence within pairs of individuals, the reach of judgment propagation across a chain rarely exceeded a social distance of three to four degrees of separation. Furthermore, computer simulations showed that the speed of judgment propagation decayed exponentially with the social distance from the source. We show that information distortion and the overweighting of other people’s errors are two individual-level mechanisms hindering judgment propagation at the scale of the chain. Our results contribute to the understanding of social-contagion processes, and our experimental method offers numerous new opportunities to study judgment propagation in the laboratory. PMID:28373540

Study and Simulation on Dynamics of a Risk-Averse Supply Chain Pricing Model with Dual-Channel and Incomplete Information

NASA Astrophysics Data System (ADS)

Sun, Lijian; Ma, Junhai

Under the industrial background of dual-channel, volatility in demand of consumers, we use the theory of bifurcations and numerical simulation tools to investigate the dynamic pricing game in a dual-channel supply chain with risk-averse behavior and incomplete information. Due to volatility of demand of consumers, we consider all the players in the supply chain are risk-averse. We assume there exist Bertrand game and Manufacturers’ Stackelberg in the chain which are closer to reality. The main objective of the paper is to investigate the complex influence of the decision parameters such as wholesale price adjustment speed, risk preference and service value on stability of the risk-averse supply chain and average utilities of all the players. We lay emphasis on the influence of chaos on average utilities of all the players which did not appear in previous studies. The dynamic phenomena, such as the bifurcation, chaos and sensitivity to initial values are analyzed by 2D bifurcation phase portraits, Double Largest Lyapunov exponent, basins of attraction and so on. The study shows that the manufacturers should slow down their wholesale price adjustment speed to get more utilities, if the manufacturers are willing to take on more risk, they will get more profits, but they must keep their wholesale prices in a certain range in order to maintain the market stability.

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

PubMed

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

Revealing the functionality of hypothetical protein KPN00728 from Klebsiella pneumoniae MGH78578: molecular dynamics simulation approaches

PubMed Central

2011-01-01

Background Previously, the hypothetical protein, KPN00728 from Klebsiella pneumoniae MGH78578 was the Succinate dehydrogenase (SDH) chain C subunit via structural prediction and molecular docking simulation studies. However, due to limitation in docking simulation, an in-depth understanding of how SDH interaction occurs across the transmembrane of mitochondria could not be provided. Results In this present study, molecular dynamics (MD) simulation of KPN00728 and SDH chain D in a membrane was performed in order to gain a deeper insight into its molecular role as SDH. Structural stability was successfully obtained in the calculation for area per lipid, tail order parameter, thickness of lipid and secondary structural properties. Interestingly, water molecules were found to be highly possible in mediating the interaction between Ubiquinone (UQ) and SDH chain C via interaction with Ser27 and Arg31 residues as compared with earlier docking study. Polar residues such as Asp95 and Glu101 (KPN00728), Asp15 and Glu78 (SDH chain D) might have contributed in the creation of a polar environment which is essential for electron transport chain in Krebs cycle. Conclusions As a conclusion, a part from the structural stability comparability, the dynamic of the interacting residues and hydrogen bonding analysis had further proved that the interaction of KPN00728 as SDH is preserved and well agreed with our postulation earlier. PMID:22372825

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

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.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

PubMed

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

PubMed Central

Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.

2009-01-01

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds. PMID:20160879

Conformational features of cepacian: the exopolysaccharide produced by clinical strains of Burkholderia cepacia.

PubMed

Nogueira, Carlos E Sampaio; Ruggiero, Jose R; Sist, Paola; Cescutti, Paola; Urbani, Ranieri; Rizzo, Roberto

2005-04-11

Conformational energy calculations and molecular dynamics investigations, both in water and in dimethyl sulfoxide, were carried out on the exopolysaccharide cepacian produced by the majority of the clinical strains of Burkholderia cepacia, an opportunistic pathogen causing serious lung infection in patients affected by cystic fibrosis, The investigation was aimed at defining the structural and conformational features, which might be relevant for clarification of the structure-function relationships of the polymer. The molecular dynamics calculations were carried out by Ramachandran-type energy plots of the disaccharides that constitute the polymer repeating unit. The dynamics of an oligomer composed of three repeating units were investigated in water and in Me2SO, a non-aggregating solvent. Analysis of the time persistence of hydrogen bonds showed the presence of a large number of favourable interactions in water, which were less evident in Me2SO. The calculations on the cepacian chain indicated that polymer conformational features in water were affected by the lateral chains, but were also largely dictated by the presence of solvent. Moreover, the large number of intra-chain hydrogen bonds in water disappeared in Me2SO solution, increasing the average dimension of the polymer chains.

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

A molecular model for cohesive slip at polymer melt/solid interfaces.

PubMed

Tchesnokov, M A; Molenaar, J; Slot, J J M; Stepanyan, R

2005-06-01

A molecular model is proposed which predicts wall slip by disentanglement of polymer chains adsorbed on a wall from those in the polymer bulk. The dynamics of the near-wall boundary layer is found to be governed by a nonlinear equation of motion, which accounts for such mechanisms on surface chains as convection, retraction, constraint release, and thermal fluctuations. This equation is valid over a wide range of grafting regimes, including those in which interactions between neighboring adsorbed molecules become essential. It is not closed since the dynamics of adsorbed chains is shown to be coupled to that of polymer chains in the bulk via constraint release. The constitutive equations for the layer and bulk, together with continuity of stress and velocity, are found to form a closed system of equations which governs the dynamics of the whole "bulk+boundary layer" ensemble. Its solution provides a stick-slip law in terms of the molecular parameters and extruder geometry. The model is quantitative and contains only those parameters that can be measured directly, or extracted from independent rheological measurements. The model predictions show a good agreement with available experimental data.

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 computer simulation of free-volume distributions and related structural properties in a model lipid bilayer.

PubMed Central

Xiang, T X

1993-01-01

A novel combined approach of molecular dynamics (MD) and Monte Carlo simulations is developed to calculate various free-volume distributions as a function of position in a lipid bilayer membrane at 323 K. The model bilayer consists of 2 x 100 chain molecules with each chain molecule having 15 carbon segments and one head group and subject to forces restricting bond stretching, bending, and torsional motions. At a surface density of 30 A2/chain molecule, the probability density of finding effective free volume available to spherical permeants displays a distribution with two exponential components. Both pre-exponential factors, p1 and p2, remain roughly constant in the highly ordered chain region with average values of 0.012 and 0.00039 A-3, respectively, and increase to 0.049 and 0.0067 A-3 at the mid-plane. The first characteristic cavity size V1 is only weakly dependent on position in the bilayer interior with an average value of 3.4 A3, while the second characteristic cavity size V2 varies more dramatically from a plateau value of 12.9 A3 in the highly ordered chain region to 9.0 A3 in the center of the bilayer. The mean cavity shape is described in terms of a probability distribution for the angle at which the test permeant is in contact with one of and does not overlap with anyone of the chain segments in the bilayer. The results show that (a) free volume is elongated in the highly ordered chain region with its long axis normal to the bilayer interface approaching spherical symmetry in the center of the bilayer and (b) small free volume is more elongated than large free volume. The order and conformational structures relevant to the free-volume distributions are also examined. It is found that both overall and internal motions have comparable contributions to local disorder and couple strongly with each other, and the occurrence of kink defects has higher probability than predicted from an independent-transition model. Images FIGURE 1 PMID:8241390

Modifying Effects of Plasticizer, Chain Connectivity, and Chain Adsorption on the Physical Aging and Interfacial Gradient in Dynamics in Thin Polystyrene Films

NASA Astrophysics Data System (ADS)

Thees, Michael; Roth, Connie

How the glass transition and physical aging in thin films change with confinement is nontrival, with studies in the literature showing that these effects can be modified by various factors including chain adsorption to substrate interfaces and addition of diluents. Some studies indicate that addition of plasticizer appears to eliminate confinement effects such as Tg gradients and possibly impacts chain adsorption to substrates. In contrast, how plasticizer affects physical aging in glassy polymers has been largely unexplored experimentally, despite various theoretical and simulation efforts. Previously we have shown that for neat polystyrene (PS) films, with molecular weights MW < 3000 kg/mol, physical aging rates in thin films decrease with decreasing film thickness consistent with expectations from local Tg gradients. However, we have recently found that for very high molecular weights, MW > 7000 kg/mol, the physical aging rate in thin films was more bulk like, suggesting a diminished gradient in dynamics related to chain connectivity and possibly chain adsorption to the substrate interface. Here, we explore how the addition of dioctyl phthalate (DOP) plasticizer to PS can alter the physical aging rate of thin films and possibly modify the adsorbed layer.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics

NASA Astrophysics Data System (ADS)

Mansbach, Rachael A.; Ferguson, Andrew L.

2015-03-01

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

A System-Oriented Approach for the Optimal Control of Process Chains under Stochastic Influences

NASA Astrophysics Data System (ADS)

Senn, Melanie; Schäfer, Julian; Pollak, Jürgen; Link, Norbert

2011-09-01

Process chains in manufacturing consist of multiple connected processes in terms of dynamic systems. The properties of a product passing through such a process chain are influenced by the transformation of each single process. There exist various methods for the control of individual processes, such as classical state controllers from cybernetics or function mapping approaches realized by statistical learning. These controllers ensure that a desired state is obtained at process end despite of variations in the input and disturbances. The interactions between the single processes are thereby neglected, but play an important role in the optimization of the entire process chain. We divide the overall optimization into two phases: (1) the solution of the optimization problem by Dynamic Programming to find the optimal control variable values for each process for any encountered end state of its predecessor and (2) the application of the optimal control variables at runtime for the detected initial process state. The optimization problem is solved by selecting adequate control variables for each process in the chain backwards based on predefined quality requirements for the final product. For the demonstration of the proposed concept, we have chosen a process chain from sheet metal manufacturing with simplified transformation functions.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

PubMed

Mansbach, Rachael A; Ferguson, Andrew L

2015-03-14

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

The Diffusion and Impact of Radio Frequency Identification in Supply Chains: A Multi-Method Approach

ERIC Educational Resources Information Center

Wu, Xiaoran

2012-01-01

As a promising and emerging technology for supply chain management, Radio Frequency Identification (RFID) is a new alternative to existing tracking technologies and also allows a range of internal control and supply chain coordination. RFID has generated a significant amount of interest and activities from both practitioners and researchers in…

Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

PubMed Central

Kannan, Srinivasaraghavan; Zacharias, Martin

2014-01-01

The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures. PMID:24563686

Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c.

PubMed

Clarkson, Michael W; Lee, Andrew L

2004-10-05

Long-range interactions are fundamental to protein behaviors such as cooperativity and allostery. In an attempt to understand the role protein flexibility plays in such interactions, the distribution of local fluctuations in a globular protein was monitored in response to localized, nonelectrostatic perturbations. Two valine-to-alanine mutations were introduced into the small serine protease inhibitor eglin c, and the (15)N and (2)H NMR spin relaxation properties of these variants were analyzed in terms of the Lipari-Szabo dynamics formalism and compared to those of the wild type. Significant changes in picosecond to nanosecond dynamics were observed in side chains located as much as 13 A from the point of mutation. Additionally, those residues experiencing altered dynamics appear to form contiguous surfaces within the protein. In the case of V54A, the large-to-small mutation results in a rigidification of connected residues, even though this mutation decreases the global stability. These findings suggest that dynamic perturbations arising from single mutations may propagate away from the perturbed site through networks of interacting side chains. That this is observed in eglin c, a classically nonallosteric protein, suggests that such behavior will be observed in many, if not all, globular proteins. Differences in behavior between the two mutants suggest that dynamic responses will be context-dependent.

Anisotropic magnetic interactions and spin dynamics in the spin-chain compound Cu (py) 2Br2 : An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Zeisner, J.; Brockmann, M.; Zimmermann, S.; Weiße, A.; Thede, M.; Ressouche, E.; Povarov, K. Yu.; Zheludev, A.; Klümper, A.; Büchner, B.; Kataev, V.; Göhmann, F.

2017-07-01

We compare theoretical results for electron spin resonance (ESR) properties of the Heisenberg-Ising Hamiltonian with ESR experiments on the quasi-one-dimensional magnet Cu (py) 2Br2 (CPB). Our measurements were performed over a wide frequency and temperature range giving insight into the spin dynamics, spin structure, and magnetic anisotropy of this compound. By analyzing the angular dependence of ESR parameters (resonance shift and linewidth) at room temperature, we show that the two weakly coupled inequivalent spin-chain types inside the compound are well described by Heisenberg-Ising chains with their magnetic anisotropy axes perpendicular to the chain direction and almost perpendicular to each other. We further determine the full g tensor from these data. In addition, the angular dependence of the linewidth at high temperatures gives us access to the exponent of the algebraic decay of a dynamical correlation function of the isotropic Heisenberg chain. From the temperature dependence of static susceptibilities, we extract the strength of the exchange coupling (J /kB=52.0 K ) and the anisotropy parameter (δ ≈-0.02 ) of the model Hamiltonian. An independent compatible value of δ is obtained by comparing the exact prediction for the resonance shift at low temperatures with high-frequency ESR data recorded at 4 K . The spin structure in the ordered state implied by the two (almost) perpendicular anisotropy axes is in accordance with the propagation vector determined from neutron scattering experiments. In addition to undoped samples, we study the impact of partial substitution of Br by Cl ions on spin dynamics. From the dependence of the ESR linewidth on the doping level, we infer an effective decoupling of the anisotropic component J δ from the isotropic exchange J in these systems.

Molecular dynamics simulation aiming at interfacial characteristics of polymer chains on nanotubes with different layers

NASA Astrophysics Data System (ADS)

Li, Kun; Gu, Boqin; Zhu, Wanfu

2017-03-01

A molecular dynamics (MD) simulations study is performed on multiwalled carbon nanotubes (MWNTs)/acrylonitrile-butadiene rubber (NBR) composites. The physisorption and interfacial characteristics between the various MWNTs and polymer macromolecular chains are identified. The effects of nanotube layers on the nanotubes/polymer interactions are examined. Each of the situation result and surface features is characterized by binding energy (Eb). It is shown that the binding energy (Eb) increase with the number of layers.

Protonic transport through solitons in hydrogen-bonded systems

NASA Astrophysics Data System (ADS)

Kavitha, L.; Jayanthi, S.; Muniyappan, A.; Gopi, D.

2011-09-01

We offer an alternative route for investigating soliton solutions in hydrogen-bonded (HB) chains. We invoke the modified extended tangent hyperbolic function method coupled with symbolic computation to solve the governing equation of motion for proton dynamics. We investigate the dynamics of proton transfer in HB chains through bell-shaped soliton excitations, which trigger the bio-energy transport in most biological systems. This solitonic mechanism of proton transfer could play functional roles in muscular contraction, enzymatic activity and oxidative phosphorylation.

Dynamical quadrupole structure factor of frustrated ferromagnetic chain

NASA Astrophysics Data System (ADS)

Onishi, Hiroaki

2018-05-01

We investigate the dynamical quadrupole structure factor of a spin-1/2 J1-J2 Heisenberg chain with competing ferromagnetic J1 and antiferromagnetic J2 in a magnetic field by exploiting density-matrix renormalization group techniques. In a field-induced spin nematic regime, we observe gapless excitations at q = π according to quasi-long-range antiferro-quadrupole correlations. The gapless excitation mode has a quadratic form at the saturation, while it changes into a linear dispersion as the magnetization decreases.

One-electron propagation in Fermi, Pasta, Ulam disordered chains with Gaussian acoustic pulse pumping

NASA Astrophysics Data System (ADS)

Silva, L. D. Da; Dos Santos, J. L. L.; Ranciaro Neto, A.; Sales, M. O.; de Moura, F. A. B. F.

In this work, we consider a one-electron moving on a Fermi, Pasta, Ulam disordered chain under effect of electron-phonon interaction and a Gaussian acoustic pulse pumping. We describe electronic dynamics using quantum mechanics formalism and the nonlinear atomic vibrations using standard classical physics. Solving numerical equations related to coupled quantum/classical behavior of this system, we study electronic propagation properties. Our calculations suggest that the acoustic pumping associated with the electron-lattice interaction promote a sub-diffusive electronic dynamics.

Novel spin dynamics in ferrimagnetic molecular chains from 1H NMR and μSR spin-lattice relaxation measurements

NASA Astrophysics Data System (ADS)

Micotti, E.; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L.

2004-05-01

The spin dynamics in the helical chain Co(hfac) 2NITPhOMe has been investigated by 1H NMR and μSR relaxation. In the temperature range 15

Exploring the Dynamics and Modeling National Budget as a Supply Chain System: A Proposal for Reengineering the Budgeting Process and for Developing a Management Flight Simulator

DTIC Science & Technology

2012-09-01

Elmendorf, D. W., & Gregory Mankiw , N. (1999). Government debt. Handbook of Macroeconomics , 1, 1615-1669. European Union. European financial stability...budget process, based on the supply chain demand management process principles of operations and it is introduced the idea of developing a Budget... principles of systems dynamics, a proposal for the development of a Budget Management Flight Simulator, that will operate as a learning and educational

The position 68(E11) side chain in myoglobin regulates ligand capture, bond formation with heme iron, and internal movement into the xenon cavities.

PubMed

Dantsker, David; Roche, Camille; Samuni, Uri; Blouin, George; Olson, John S; Friedman, Joel M

2005-11-18

After photodissociation, ligand rebinding to myoglobin exhibits complex kinetic patterns associated with multiple first-order geminate recombination processes occurring within the protein and a simpler bimolecular phase representing second-order ligand rebinding from the solvent. A smooth transition from cryogenic-like to solution phase properties can be obtained by using a combination of sol-gel encapsulation, addition of glycerol as a bathing medium, and temperature tuning (-15 --> 65 degrees C). This approach was applied to a series of double mutants, myoglobin CO (H64L/V68X, where X = Ala, Val, Leu, Asn, and Phe), which were designed to examine the contributions of the position 68(E11) side chain to the appearance and disappearance of internal rebinding phases in the absence of steric and polar interactions with the distal histidine. Based on the effects of viscosity, temperature, and the stereochemistry of the E11 side chain, the three major phases, B --> A, C --> A, and D --> A, can be assigned, respectively, to ligand rebinding from the following: (i) the distal heme pocket, (ii) the xenon cavities prior to large amplitude side chain conformational relaxation, and (iii) the xenon cavities after significant conformational relaxation of the position 68(E11) side chain. The relative amplitudes of the B --> A and C --> A phases depend markedly on the size and shape of the E11 side chain, which regulates sterically both ligand return to the heme iron atom and ligand migration to the xenon cavities. The internal xenon cavities provide a transient docking site that allows side chain relaxations and the entry of water into the vacated distal pocket, which in turn slows ligand recombination markedly.

Influence of solute charge and pyrrolidinium ionic liquid alkyl chain length on probe rotational reorientation dynamics.

PubMed

Guo, Jianchang; Mahurin, Shannon M; Baker, Gary A; Hillesheim, Patrick C; Dai, Sheng; Shaw, Robert W

2014-01-30

In recent years, the effect of molecular charge on the rotational dynamics of probe solutes in room-temperature ionic liquids (RTILs) has been a subject of growing interest. For the purpose of extending our understanding of charged solute behavior within RTILs, we have studied the rotational dynamics of three illustrative xanthene fluorescent probes within a series of N-alkylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([Cnmpyr][Tf2N]) RTILs with different n-alkyl chain lengths (n = 3, 4, 6, 8, or 10) using time-resolved fluorescence anisotropy decay. The rotational dynamics of the neutral probe rhodamine B (RhB) dye lies between the stick and slip boundary conditions due to the influence of specific hydrogen bonding interactions. The rotation of the negatively charged sulforhodamine 640 (SR640) is slower than that of its positively charged counterpart rhodamine 6G (R6G). An analysis based upon Stokes-Einstein-Debye hydrodynamics indicates that SR640 adheres to stick boundary conditions due to specific interactions, whereas the faster rotation of R6G is attributed to weaker electrostatic interactions. No significant dependence of the rotational dynamics on the solvent alkyl chain length was observed for any of the three dyes, suggesting that the specific interactions between dyes and RTILs are relatively independent of this solvent parameter.

Expanding AirSTAR Capability for Flight Research in an Existing Avionics Design

NASA Technical Reports Server (NTRS)

Laughter, Sean A.

2012-01-01

The NASA Airborne Subscale Transport Aircraft Research (AirSTAR) project is an Unmanned Aerial Systems (UAS) test bed for experimental flight control laws and vehicle dynamics research. During its development, the test bed has gone through a number of system permutations, each meant to add functionality to the concept of operations of the system. This enabled the build-up of not only the system itself, but also the support infrastructure and processes necessary to support flight operations. These permutations were grouped into project phases and the move from Phase-III to Phase-IV was marked by a significant increase in research capability and necessary safety systems due to the integration of an Internal Pilot into the control system chain already established for the External Pilot. The major system changes in Phase-IV operations necessitated a new safety and failsafe system to properly integrate both the Internal and External Pilots and to meet acceptable project safety margins. This work involved retrofitting an existing data system into the evolved concept of operations. Moving from the first Phase-IV aircraft to the dynamically scaled aircraft further involved restructuring the system to better guard against electromagnetic interference (EMI), and the entire avionics wiring harness was redesigned in order to facilitate better maintenance and access to onboard electronics. This retrofit and harness re-design will be explored and how it integrates with the evolved Phase-IV operations.

Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations

PubMed Central

Pastor, Nina; Amero, Carlos

2015-01-01

Proteins participate in information pathways in cells, both as links in the chain of signals, and as the ultimate effectors. Upon ligand binding, proteins undergo conformation and motion changes, which can be sensed by the following link in the chain of information. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations represent powerful tools for examining the time-dependent function of biological molecules. The recent advances in NMR and the availability of faster computers have opened the door to more detailed analyses of structure, dynamics, and interactions. Here we briefly describe the recent applications that allow NMR spectroscopy and MD simulations to offer unique insight into the basic motions that underlie information transfer within and between cells. PMID:25999971

Dynamic model of the force driving kinesin to move along microtubule-Simulation with a model system

NASA Astrophysics Data System (ADS)

Chou, Y. C.; Hsiao, Yi-Feng; To, Kiwing

2015-09-01

A dynamic model for the motility of kinesin, including stochastic-force generation and step formation is proposed. The force driving the motion of kinesin motor is generated by the impulse from the collision between the randomly moving long-chain stalk and the ratchet-shaped outer surface of microtubule. Most of the dynamical and statistical features of the motility of kinesin are reproduced in a simulation system, with (a) ratchet structures similar to the outer surface of microtubule, (b) a bead chain connected to two heads, similarly to the stalk of the real kinesin motor, and (c) the interaction between the heads of the simulated kinesin and microtubule. We also propose an experiment to discriminate between the conventional hand-over-hand model and the dynamic model.

Global value chains: Building blocks and network dynamics

NASA Astrophysics Data System (ADS)

Tsekeris, Theodore

2017-12-01

The paper employs measures and tools from complex network analysis to enhance the understanding and interpretation of structural characteristics pertaining to the Global Value Chains (GVCs) during the period 1995-2011. The analysis involves the country, sector and country-sector value chain networks to identify main drivers of structural change. The results indicate significant intertemporal changes, mirroring the increased globalization in terms of network size, strength and connectivity. They also demonstrate higher clustering and increased concentration of the most influential countries and country-sectors relative to all others in the GVC network, with the geographical dimension to prevail over the sectoral dimension in the formation of value chains. The regionalization and less hierarchical organization drive country-sector production sharing, while the sectoral value chain network has become more integrated and more competitive over time. The findings suggest that the impact of country-sector policies and/or shocks may vary with the own-group and network-wide influence of each country, take place in multiple geographical scales, as GVCs have a block structure, and involve time dynamics.

Connecting Structural and Transport Properties of Ionic Liquids with Cationic Oligoether Chains

DOE PAGES

Lall-Ramnarine, Sharon I.; Zhao, Man; Rodriguez, Chanele; ...

2017-06-01

We used X-ray diffraction and molecular dynamics simulations to probe the structures of two families of ionic liquids containing oligoether tails on the cations. Imidazolium and pyrrolidinium bis(trifluoromethylsulfonyl)amide ILs with side chains ranging from 4 to 10 atoms in length, including both linear alkyl and oligo-ethylene oxide tails, were prepared. Furthermore, their physical properties, such as viscosity, conductivity and thermal profile, were measured and compared for systematic trends. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidiniummore » ILs increases there is hardly any increase in the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. To complement the experimentally determined properties, molecular dynamics simulations were run on the two ILs with the longest ether chains. Our results point to specific aspects that could be useful for researchers designing ILs for specific applications.« less

Complex dynamics of a MC-MS pricing model for a risk-averse supply chain with after-sale investment

NASA Astrophysics Data System (ADS)

Ma, Junhai; Sun, Lijian

2015-09-01

In this paper, we investigate the pricing strategy of the manufacturers and that of a common retailer, including their after-sale investment in a risk-averse supply chain. As the demand is not always for sure, the supply chain follows Manufacturers Cooperating (MC) and Manufacturers Stackelberg (MS). The main objective of the paper is to investigate the influence of the decision parameters such as the after-sale investment, wholesale price adjustment speed and risk preference on the stability and utilities of the risk-averse supply chain. The dynamic phenomena, such as the bifurcation, chaos and sensitivity to initial values are analyzed with 2D-bifurcation diagrams, double largest Lyapunov exponent and basins of attraction. The study shows that the faster the adjustment speed is, the more profits the retailer can make, but on the other hand, it is no good to manufacturers. Risk tolerance levels (RM and RR) affect the utility of the manufacturers and that of the retailer differently. A feedback control method is used to control the chaos in the supply chain.

Amino terminal sequence of heavy and light chains from ratfish immunoglobulin.

PubMed

De Ioannes, A E; Aguila, H L

1989-01-01

The ratfish, Callorhinchus callorhinchus, a representative of the Holocephali, has a natural serum hemagglutinin (Mr 960,000), composed of heavy (Mr 71,000), light (Mr 22,500), and J (Mr 16,000) chains. To approach the mechanisms that generate diversity at this level of evolution, the amino terminal sequence of the heavy and light chains was determined by automated microsequencing. The chains are unblocked and have modest internal sequence heterogeneity. The heavy chains show sequence similarity with the terminal region of the heavy chain from the horned shark, Heterodontus francisci, and other species. In contrast to the heavy chain, the ratfish light chains display low sequence similarity with their shark kappa counterparts. However, their similarity with the variable region of the chicken lambda light chains is about 75%.

Free energy and internal energy of electron-screened plasmas in a modified hypernetted-chain approximation

NASA Astrophysics Data System (ADS)

Perrot, F.

1991-12-01

We report results of Helmholtz-free-energy and internal-energy calculations using the modified hypernetted-chain (MHNC) equation method, in the formulation of Lado, Foiles, and Ashcroft [Phys. Rev. A 28, 2374 (1983)], for a model plasma of ions linearly screened by electrons. The results are compared with HNC calculations (no Bridge term), with variational calculations using a hard-spheres reference system, and with a numerical fit of Monte Carlo simulations.

On the formation of suspended noble-metal monatomic chains

NASA Astrophysics Data System (ADS)

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

2008-09-01

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

The dynamics of food chains under climate change and nutrient enrichment.

PubMed

Binzer, Amrei; Guill, Christian; Brose, Ulrich; Rall, Björn C

2012-11-05

Warming has profound effects on biological rates such as metabolism, growth, feeding and death of organisms, eventually affecting their ability to survive. Using a nonlinear bioenergetic population-dynamic model that accounts for temperature and body-mass dependencies of biological rates, we analysed the individual and interactive effects of increasing temperature and nutrient enrichment on the dynamics of a three-species food chain. At low temperatures, warming counteracts the destabilizing effects of enrichment by both bottom-up (via the carrying capacity) and top-down (via biological rates) mechanisms. Together with increasing consumer body masses, warming increases the system tolerance to fertilization. Simultaneously, warming increases the risk of starvation for large species in low-fertility systems. This effect can be counteracted by increased fertilization. In combination, therefore, two main drivers of global change and biodiversity loss can have positive and negative effects on food chain stability. Our model incorporates the most recent empirical data and may thus be used as the basis for more complex forecasting models incorporating food-web structure.

Molecular dynamics simulations of theoretical cellulose nanotube models.

PubMed

Uto, Takuya; Kodama, Yuta; Miyata, Tatsuhiko; Yui, Toshifumi

2018-06-15

Nanotubes are remarkable nanoscale architectures for a wide range of potential applications. In the present paper, we report a molecular dynamics (MD) study of the theoretical cellulose nanotube (CelNT) models to evaluate their dynamic behavior in solution (either chloroform or benzene). Based on the one-quarter chain staggering relationship, we constructed six CelNT models by combining the two chain polarities (parallel (P) and antiparallel (AP)) and three symmetry operations (helical right (H R ), helical left (H L ), and rotation (R)) to generate a circular arrangement of molecular chains. Among the four models that retained the tubular form (P-H R , P-H L , P-R, and AP-R), the P-R and AP-R models have the lowest steric energies in benzene and chloroform, respectively. The structural features of the CelNT models were characterized in terms of the hydroxymethyl group conformation and intermolecular hydrogen bonds. Solvent structuring more clearly occurred with benzene than chloroform, suggesting that the CelNT models may disperse in benzene. Copyright © 2018 Elsevier Ltd. All rights reserved.

Investigation of the interfacial properties of polyurethane/carbon nanotube hybrid composites: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Goclon, Jakub; Panczyk, Tomasz; Winkler, Krzysztof

2018-03-01

Considering the varied applications of hybrid polymer/carbon nanotube composites and the constant progress in the synthesis methods of such materials, we report a theoretical study of interfacial layer formation between pristine single-wall carbon nanotubes (SWCNTs) and polyurethane (PU) using molecular dynamic simulations. We vary the SWCNT diameter and the number of PU chains to examine various PU-SWCNT interaction patterns. Our simulations indicate the important role of intra-chain forces in PU. No regular polymeric structures could be identified on the carbon nanotube surface during the simulations. We find that increasing the SWCNT diameter results in stronger polymer binding. However, higher surface loadings of PU lead to stronger interpenetration by the polymeric segments; this effect is more apparent for SWCNTs with small diameters. Our core finding is that the attached PU binds most strongly to the carbon nanotubes with the largest diameters. Polymer dynamics reveal the loose distribution of PU chains in these systems.

Response to ``Comment on `Unified explanation of the anomalous dynamic properties of highly asymmetric polymer blends' '' [J. Chem. Phys. 138, 197101 (2013)

NASA Astrophysics Data System (ADS)

Ngai, K. L.; Capaccioli, S.

2013-05-01

The Comment of Colmenero asserts no change in Fs(Q,t) of the poly(ethylene oxide) (PEO) chains in blends with poly(methyl methacrylate) on crossing times of about 1-2 ns in data obtained by neutron scattering experiments and simulations. The assertion is opposite to that reported in the original papers where the neutron data and simulations were published. To make this point clear, we cite the data and the very statements made in the original papers concluding that indeed in the time interval from 60 ps to 1-2 ns the dynamics of PEO chain follows approximately the Rouse model, but becomes slower and departs from the Rouse model in the dependencies on time, momentum transfer, and temperature at longer times past tc = 1-2 ns. It is noteworthy that similar crossover of chain dynamics in entangled homopolymers at the ns time scale was found by neutron scattering.

PEGylation on mixed monolayer gold nanoparticles: Effect of grafting density, chain length, and surface curvature.

PubMed

Lin, Jiaqi; Zhang, Heng; Morovati, Vahid; Dargazany, Roozbeh

2017-10-15

PEGylation on nanoparticles (NPs) is widely used to prevent aggregation and to mask NPs from the fast clearance system in the body. Understanding the molecular details of the PEG layer could facilitate rational design of PEGylated NPs that maximize their solubility and stealth ability without significantly compromising the targeting efficiency and cellular uptake. Here, we use molecular dynamics (MD) simulation to understand the structural and dynamic the PEG coating of mixed monolayer gold NPs. Specifically, we modeled gold NPs with PEG grafting densities ranging from 0-2.76chain/nm 2 , chain length with 0-10 PEG monomers, NP core diameter from 5nm to 500nm. It is found that the area accessed by individual PEG chains gradually transits from a "mushroom" to a "brush" conformation as NP surface curvature become flatter, whereas such a transition is not evident on small NPs when grafting density increases. It is shown that moderate grafting density (∼1.0chain/nm 2 ) and short chain length are sufficient enough to prevent NPs from aggregating in an aqueous medium. The effect of grafting density on solubility is also validated by dynamic light scattering measurements of PEGylated 5nm gold NPs. With respect to the shielding ability, simulations predict that increase either grafting density, chain length, or NP diameter will reduce the accessibility of the protected content to a certain size molecule. Interestingly, reducing NP surface curvature is estimated to be most effective in promoting shielding ability. For shielding against small molecules, increasing PEG grafting density is more effective than increasing chain length. A simple model that includes these three investigated parameters is developed based on the simulations to roughly estimate the shielding ability of the PEG layer with respect to molecules of different sizes. The findings can help expand our current understanding of the PEG layer and guide rational design of PEGylated gold NPs for a particular application by tuning the PEG grafting density, chain length, and particle size. Copyright © 2017 Elsevier Inc. All rights reserved.

Commitment to and preparedness for sustainable supply chain management in the oil and gas industry.

PubMed

Wan Ahmad, Wan Nurul K; Rezaei, Jafar; Tavasszy, Lóránt A; de Brito, Marisa P

2016-09-15

Our current dependency on the oil and gas (O&G) industry for economic development and social activities necessitates research into the sustainability of the industry's supply chains. At present, studies on sustainable supply chain management (SSCM) practices in the industry do not include firm-internal factors that affect the sustainability strategies employed by different functional areas of its supply chains. Our study aims to address this gap by identifying the relevant internal factors and exploring their relationship with SSCM strategies. Specifically, we discuss the commitment to and preparedness for sustainable practices of companies that operate in upstream and downstream O&G supply chain. We study the impact of these factors on their sustainability strategies of four key supply chain functions: supplier management, production management, product stewardship and logistics management. The analyses of data collected through a survey among 81 companies show that management preparedness may enhance sustainable supply chain strategies in the O&G industry more than commitment does. Among the preparedness measures, management of supply chain operational risks is found to be vital to the sustainability of all supply chain functions except for production management practices. The findings also highlight the central importance of supplier and logistics management to the achievement of sustainable O&G supply chains. Companies must also develop an organizational culture that encourages, for example, team collaboration and proactive behaviour to finding innovative sustainability solutions in order to translate commitment to sustainable practices into actions that can produce actual difference to their SSCM practices. Copyright © 2016 Elsevier Ltd. All rights reserved.

[The validation of kit of reagents for quantitative detection of DNA of human cytomegalovirus in biological material using polymerase chain reaction technique in real time operation mode].

PubMed

Sil'veĭstrova, O Iu; Domonova, É A; Shipulina, O Iu

2014-04-01

The validation of kit of reagents destined to detection and quantitative evaluation of DNA of human cytomegalovirus in biological material using polymerase chain reaction technique in real time operation mode was implemented. The comparison was made against international WHO standard--The first WHO international standard for human cytomegalovirus to implement measures the kit of reagents "AmpliSens CMV-screen/monitor-FL" and standard sample of enterprise DNA HCMV (The central research institute of epidemiology of Rospotrebnadzor) was applied. The fivefold dilution of international WHO standard and standard sample of enterprise were carried out in concentrations of DNA HCMV from 106 to 102. The arrangement of polymerase chain reaction and analysis of results were implemented using programed amplifier with system of detection of fluorescent signal in real-time mode "Rotor-Gene Q" ("Qiagen", Germany). In the total of three series of experiments, all stages of polymerase chain reaction study included, the coefficient of translation of quantitative evaluation of DNA HCMV from copy/ml to ME/ml equal to 0.6 was introduced for this kit of reagents.

Blob-Spring Model for the Dynamics of Ring Polymer in Obstacle Environment

NASA Astrophysics Data System (ADS)

Lele, Ashish K.; Iyer, Balaji V. S.; Juvekar, Vinay A.

2008-07-01

The dynamical behavior of cyclic macromolecules in a fixed obstacle (FO) environment is very different than the behavior of linear chains in the same topological environment; while the latter relax by a snake-like reptational motion from their chain ends the former can relax only by contour length fluctuations since they are endless. Duke, Obukhov and Rubinstein proposed a scaling model (the DOR model) to interpret the dynamical scaling exponents shown by Monte Carlo simulations of rings in a FO environment. We present a model (blob-spring model) to describe the dynamics of flexible and non-concatenated ring polymer in FO environment based on a theoretical formulation developed for the dynamics of an unentangled fractal polymer. We argue that the perpetual evolution of ring perimeter by the motion of contour segments results in an extra frictional load. Our model predicts self-similar dynamics with scaling exponents for the molecular weight dependence of diffusion coefficient and relaxation times that are in agreement with the scaling model proposed by Obukhov et al.

Intrachain exciton dynamics in conjugated polymer chains in solution.

PubMed

Tozer, Oliver Robert; Barford, William

2015-08-28

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

Performance measurement for supply chain management and evaluation criteria determination for reverse supply chain management

NASA Astrophysics Data System (ADS)

Kongar, N. Elif

2004-12-01

Today, since customers are able to obtain similar-quality products for similar prices, the lead time has become the only preference criterion for most of the consumers. Therefore, it is crucial that the lead time, i.e., the time spent from the raw material phase till the manufactured good reaches the customer, is minimized. This issue can be investigated under the title of Supply Chain Management (SCM). An efficiently managed supply chain can lead to reduced response time for customers. To achieve this, continuous observation of supply chain efficiency, i.e., a constant performance evaluation of the current SCM is required. Widely used conventional performance measurement methods lack the ability to evaluate a SCM since the supply chain is a dynamic system that requires a more thorough and flexible performance measurement technique. Balanced Scorecard (BS) is an efficient tool for measuring the performance of dynamic systems and has a proven capability of providing the decision makers with the appropriate feedback data. In addition to SCM, a relatively new management field, namely reverse supply chain management (RSCM), also necessitates an appropriate evaluation approach. RSCM differs from SCM in many aspects, i.e., the criteria used for evaluation, the high level of uncertainty involved etc., not allowing the usage of identical evaluation techniques used for SCM. This study proposes a generic Balanced Scorecard to measure the performance of supply chain management while defining the appropriate performance measures for SCM. A scorecard prototype, ESCAPE, is presented to demonstrate the evaluation process.

Conformation and dynamics of polymer chains on dirty surfaces: A discrete-to-continuum approach

NASA Astrophysics Data System (ADS)

Foo, Grace M.; Pandey, R. B.

1998-07-01

A discrete-to-continuum (DC) simulation approach is introduced to study the statics and dynamics of polymer chains in two dimensions with quenched barriers, a dirty surface. In our DC hybrid approach, the large-scale relaxation of polymer chains on a discrete disordered lattice is followed by off-lattice simulation using a bead-spring chain model with a finitely extensible nonlinear elastic (FENE) potential for covalent bonds and Lennard-Jones (LJ) potential for nonbonded interactions. Segregation/folding of chains, which occurs at low temperatures (T=0.2, 1.0) with LJ interaction, becomes more difficult as the concentration of barriers increases, due to a screening effect of the barriers. In contrast to the chains' contraction at high temperature (i.e., T=5) and their collapse in athermal systems, chains are elongated on increasing the barrier concentration—a barrier-induced stretching. Variations of the root-mean-square (rms) displacements of the center of mass (Rcm) of the chains and their center node (Rcn) with time (t) show power-law behaviors (Rcm˜tν1, Rcn˜tν2) with nonuniversal exponents in the range ν1≃0.40-0.05 and ν2≃0.30-0.05, respectively, depending on temperature and barrier concentration. The radius of gyration (Rg) and the average bond length () expand on increasing the barrier concentration at low temperature and contract at high temperature, which is consistent with the variation of the width of the radial distribution function.

Dynamical phases in a one-dimensional chain of heterospecies Rydberg atoms with next-nearest-neighbor interactions

NASA Astrophysics Data System (ADS)

Qian, Jing; Zhang, Lu; Zhai, Jingjing; Zhang, Weiping

2015-12-01

We theoretically investigate the dynamical phase diagram of a one-dimensional chain of laser-excited two-species Rydberg atoms. The existence of a variety of unique dynamical phases in the experimentally achievable parameter region is predicted under the mean-field approximation, and the change in those phases when the effect of the next-nearest-neighbor interaction is included is further discussed. In particular, we find that the com-petition of the strong Rydberg-Rydberg interactions and the optical excitation imbalance can lead to the presence of complex multiple chaotic phases, which are highly sensitive to the initial Rydberg-state population and the strength of the next-nearest-neighbor interactions.

Kinematics and dynamics of a six-degree-of-freedom robot manipulator with closed kinematic chain mechanism

NASA Technical Reports Server (NTRS)

Nguyen, Charles C.; Pooran, Farhad J.

1989-01-01

This paper deals with a class of robot manipulators built based on the kinematic chain mechanism (CKCM). This class of CKCM manipulators consists of a fixed and a moving platform coupled together via a number of in-parallel actuators. A closed-form solution is derived for the inverse kinematic problem of a six-degre-of-freedom CKCM manipulator designed to study robotic applications in space. Iterative Newton-Raphson method is employed to solve the forward kinematic problem. Dynamics of the above manipulator is derived using the Lagrangian approach. Computer simulation of the dynamical equations shows that the actuating forces are strongly dependent on the mass and centroid of the robot links.

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

PubMed

Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

2015-10-01

It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

PubMed Central

Dijkstra, Maurits J. J.; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

2015-01-01

It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

Complex dynamics in the Leslie-Gower type of the food chain system with multiple delays

NASA Astrophysics Data System (ADS)

Guo, Lei; Song, Zi-Gen; Xu, Jian

2014-08-01

In this paper, we present a Leslie-Gower type of food chain system composed of three species, which are resource, consumer, and predator, respectively. The digestion time delays corresponding to consumer-eat-resource and predator-eat-consumer are introduced for more realistic consideration. It is called the resource digestion delay (RDD) and consumer digestion delay (CDD) for simplicity. Analyzing the corresponding characteristic equation, the stabilities of the boundary and interior equilibrium points are studied. The food chain system exhibits the species coexistence for the small values of digestion delays. Large RDD/CDD may destabilize the species coexistence and induce the system dynamic into recurrent bloom or system collapse. Further, the present of multiple delays can control species population into the stable coexistence. To investigate the effect of time delays on the recurrent bloom of species population, the Hopf bifurcation and periodic solution are investigated in detail in terms of the central manifold reduction and normal form method. Finally, numerical simulations are performed to display some complex dynamics, which include multiple periodic solution and chaos motion for the different values of system parameters. The system dynamic behavior evolves into the chaos motion by employing the period-doubling bifurcation.

Dynamics and lithium binding energies of polyelectrolytes based on functionalized poly(para-phenylene terephthalamide).

PubMed

Grozema, F C; Best, A S; van Eijck, L; Stride, J; Kearley, G J; de Leeuw, S W; Picken, S J

2005-04-28

Polyelectrolyte materials are an interesting class of electrolytes for use in fuel cell and battery applications. Poly(para-phenylene terephthalamide) (PPTA, Kevlar) is a liquid crystalline polymer that, when sulfonated, is a polyelectrolyte that exhibits moderate ion conductivity at elevated temperatures. In this work, quasi-elastic neutron scattering (QENS) experiments were performed to gain insight into the effect of the presence of lithium counterions on the chain dynamics in the material. It was found that the addition of lithium ions decreases the dynamics of the chains. Additionally, the binding of lithium ions to the sulfonic acids groups was investigated by density functional theory (DFT) calculations. It was found that the local surroundings of the sulfonic acid group have very little effect on the lithium-ion binding energy. Binding energies for a variety of different systems were all calculated to be around 150 kcal/mol. The DFT calculations also show the existence of a structure in which a single lithium ion interacts with two sulfonic acid moieties on different chains. The formation of such "electrostatic cross-links" is believed to be the source of the increased tendency to aggregate and the reduced dynamics in the presence of lithium ions.

Dynamic SVL and body bias for low leakage power and high performance in CMOS digital circuits

NASA Astrophysics Data System (ADS)

Deshmukh, Jyoti; Khare, Kavita

2012-12-01

In this article, a new complementary metal oxide semiconductor design scheme called dynamic self-controllable voltage level (DSVL) is proposed. In the proposed scheme, leakage power is controlled by dynamically disconnecting supply to inactive blocks and adjusting body bias to further limit leakage and to maintain performance. Leakage power measurements at 1.8 V, 75°C demonstrate power reduction by 59.4% in case of 1 bit full adder and by 43.0% in case of a chain of four inverters using SVL circuit as a power switch. Furthermore, we achieve leakage power reduction by 94.7% in case of 1 bit full adder and by 91.8% in case of a chain of four inverters using dynamic body bias. The forward body bias of 0.45 V applied in active mode improves the maximum operating frequency by 16% in case of 1 bit full adder and 5.55% in case of a chain of inverters. Analysis shows that additional benefits of using the DSVL and body bias include high performance, low leakage power consumption in sleep mode, single threshold implementation and state retention even in standby mode.

Novel phase transitions in coupled dipolar chains.

NASA Astrophysics Data System (ADS)

Mellado, Paula

We study the properties of a classical magnetic system realized by two chains of U(1) rotors coupled via Coulomb interactions in the dumbbell approach. Magnets in chain I and chain II rotate in the x-z and y-z planes respectively. Ground state correlations and the system wave excitation spectrum are found using spin wave theory. The displacement ''d'' of chain II from chain I induces dynamics in the system and yields two first order magnetic phase transitions. The transitions happen at critical displacements, which notably, are independent of the magnetic charge at the tips of the magnets, suggesting a geometrical origin. This work was supported by Fondecyt under Grant No. 1160239.

77 FR 41416 - Food and Drug Administration/Xavier University Global Outsourcing Conference

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-13

... International Initiatives, FDA Inspection Trends, Supply Chain Development, Quality Agreements, Supplier... the World Establishing a Meaningful Supplier Qualification Program Supply Chain Development Finished... Agreements Business Process Management Global Standards Association Near Term Solutions The conference...

Interfacial welding of dynamic covalent network polymers

NASA Astrophysics Data System (ADS)

Yu, Kai; Shi, Qian; Li, Hao; Jabour, John; Yang, Hua; Dunn, Martin L.; Wang, Tiejun; Qi, H. Jerry

2016-09-01

Dynamic covalent network (or covalent adaptable network) polymers can rearrange their macromolecular chain network by bond exchange reactions (BERs) where an active unit replaces a unit in an existing bond to form a new bond. Such macromolecular events, when they occur in large amounts, can attribute to unusual properties that are not seen in conventional covalent network polymers, such as shape reforming and surface welding; the latter further enables the important attributes of material malleability and powder-based reprocessing. In this paper, a multiscale modeling framework is developed to study the surface welding of thermally induced dynamic covalent network polymers. At the macromolecular network level, a lattice model is developed to describe the chain density evolution across the interface and its connection to bulk stress relaxation due to BERs. The chain density evolution rule is then fed into a continuum level interfacial model that takes into account surface roughness and applied pressure to predict the effective elastic modulus and interfacial fracture energy of welded polymers. The model yields particularly accessible results where the moduli and interfacial strength of the welded samples as a function of temperature and pressure can be predicted with four parameters, three of which can be measured directly. The model identifies the dependency of surface welding efficiency on the applied thermal and mechanical fields: the pressure will affect the real contact area under the consideration of surface roughness of dynamic covalent network polymers; the chain density increment on the real contact area of interface is only dependent on the welding time and temperature. The modeling approach shows good agreement with experiments and can be extended to other types of dynamic covalent network polymers using different stimuli for BERs, such as light and moisture etc.

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

Chain Ends and the Ultimate Tensile Strength of Polyethylene Fibers

NASA Astrophysics Data System (ADS)

O'Connor, Thomas C.; Robbins, Mark O.

Determining the tensile yield mechanisms of oriented polymer fibers remains a challenging problem in polymer mechanics. By maximizing the alignment and crystallinity of polyethylene (PE) fibers, tensile strengths σ ~ 6 - 7 GPa have been achieved. While impressive, first-principal calculations predict carbon backbone bonds would allow strengths four times higher (σ ~ 20 GPa) before breaking. The reduction in strength is caused by crystal defects like chain ends, which allow fibers to yield by chain slip in addition to bond breaking. We use large scale molecular dynamics (MD) simulations to determine the tensile yield mechanism of orthorhombic PE crystals with finite chains spanning 102 -104 carbons in length. The yield stress σy saturates for long chains at ~ 6 . 3 GPa, agreeing well with experiments. Chains do not break but always yield by slip, after nucleation of 1D dislocations at chain ends. Dislocations are accurately described by a Frenkel-Kontorova model, parametrized by the mechanical properties of an ideal crystal. We compute a dislocation core size ξ = 25 . 24 Å and determine the high and low strain rate limits of σy. Our results suggest characterizing such 1D dislocations is an efficient method for predicting fiber strength. This research was performed within the Center for Materials in Extreme Dynamic Environments (CMEDE) under the Hopkins Extreme Materials Institute at Johns Hopkins University. Financial support was provided by Grant W911NF-12-2-0022.

A Bond-Fluctuation Model of Translational Dynamics of Chain-like Particles through Mucosal Scaffolds.

PubMed

Bajd, Franci; Serša, Igor

2018-06-05

Mucus scaffolds represent one of the most common barriers in targeted drug delivery and can remarkably reduce the outcome of pharmacological therapies. An efficient transport of drug particles through a mucus barrier is a precondition for an efficient drug delivery. Understanding the transport mechanism is particularly important for treatment of disorders such as cystic fibrosis. These are characterized by an onset of high-density mucus scaffolds imposing an increased steric filtering. In this study, we employed the bond-fluctuation model to analyze the effect of steric interactions on slowing the translational dynamics of compound chain-like particles traversing through scaffolds of different configurations (regular isotropic and anisotropic versus irregular random). The model, which accounts for both the geometry-imposed steric interaction as well as the intrachain steric interaction between the chain subunits, yields a transient subdiffusive motional pattern persists between the short-time and long-time Gaussian diffusion limits. The motion is analyzed in terms of a mean-squared displacement, diffusion coefficient, and radius of gyration. With higher levels of restriction or larger particles, the subdiffusive motional regime persists longer. The study also demonstrates that an important feature of the motion is also geometry-induced chain accommodation. The presented model is generic and could also be applied to studying the translational dynamics of other particles with more complex architecture such as dendrites or chain-decorated nanoparticles. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Entropic uncertainty for spin-1/2 XXX chains in the presence of inhomogeneous magnetic fields and its steering via weak measurement reversals

NASA Astrophysics Data System (ADS)

Wang, Dong; Ming, Fei; Huang, Ai-Jun; Sun, Wen-Yang; Ye, Liu

2017-09-01

The uncertainty principle configures a low bound to the measuring precision for a pair of non-commuting observables, and hence is considerably nontrivial to quantum precision measurement in the field of quantum information theory. In this letter, we consider the entropic uncertainty relation (EUR) in the context of quantum memory in a two-qubit isotropic Heisenberg spin chain. Specifically, we explore the dynamics of EUR in a practical scenario, where two associated nodes of a one-dimensional XXX-spin chain, under an inhomogeneous magnetic field, are connected to a thermal entanglement. We show that the temperature and magnetic field effect can lead to the inflation of the measuring uncertainty, stemming from the reduction of systematic quantum correlation. Notably, we reveal that, firstly, the uncertainty is not fully dependent on the observed quantum correlation of the system; secondly, the dynamical behaviors of the measuring uncertainty are relatively distinct with respect to ferromagnetism and antiferromagnetism chains. Meanwhile, we deduce that the measuring uncertainty is dramatically correlated with the mixedness of the system, implying that smaller mixedness tends to reduce the uncertainty. Furthermore, we propose an effective strategy to control the uncertainty of interest by means of quantum weak measurement reversal. Therefore, our work may shed light on the dynamics of the measuring uncertainty in the Heisenberg spin chain, and thus be important to quantum precision measurement in various solid-state systems.

Dynamics of exciton transfer in coupled polymer chains.

PubMed

Zhang, Y L; Liu, X J; Sun, Z; An, Z

2013-05-07

The dynamics of singlet and triplet exciton transfer in coupled polymer chains are investigated within the Su-Schrieffer-Heeger+Pariser-Parr-Pople model including both electron-phonon (e-p) coupling and electron-electron (e-e) interactions, using a multi-configurational time-dependent Hartree-Fock dynamic method. In order to explain the processes involved, the effects of on-site and long-range e-e interactions on the locality of the singlet and triplet excitons are first investigated on an isolated chain. It is found that the locality of the singlet exciton decreases, while the locality of the triplet exciton increases with an increase in the on-site e-e interactions. On the other hand, an increase in the long-range e-e interaction results in a more localized singlet exciton and triplet exciton. In coupled polymer chains, we then quantitatively show the yields of singlet and triplet exciton transfer products under the same interchain coupling. It is found that the yield of singlet interchain excitons is much higher than that of triplet interchain excitons, that is to say, singlet exciton transfer is significantly easier than that for triplet excitons. This results from the fact that the singlet exciton is more delocalized than the triplet exciton. In addition, hopping of electrons with opposite spins between the coupled chains can facilitate the transfer of singlet excitons. The results are of great significance for understanding the photoelectric conversion process and developing high-power organic optoelectronic applications.

Food Crises and Food Safety Incidents in European Union, United States, and Maghreb Area: Current Risk Communication Strategies and New Approaches.

PubMed

Chammem, Nadia; Issaoui, Manel; De Almeida, Ana Isabel Dâmaso; Delgado, Amélia Martins

2018-03-22

Globalization has created a dynamic market, which has dramatically intensified interchanges of goods and information as well as the flow of people among nations. This international phenomenon offers the consumer a choice between a wide variety of foods from diverse locations. However, there are challenges to improving food security and safety on a global scale; the major question is how food safety can be guaranteed while increasing the complexity of food supply chains. A food produced in a certain location usually contains ingredients, additives, and preservatives from different and distant origins. Although countries take several food control measures, their institutional and regulatory frameworks diverge widely, as do the definitions of food crisis, food incidents, and risk management approaches. The present review discusses some past food safety issues and lessons learned. Convergences and differences in the regulatory framework of food control agencies in different regions of the world are herein revealed. Emerging risks are also discussed, particularly the spread of antibiotic resistance in the food chain and the environment, as well as the rise of new antibiotic-resistant pathogenic strains with broader tolerance to environmental factors.

Model-based confirmation of alternative substrates of mitochondrial electron transport chain.

PubMed

Kleessen, Sabrina; Araújo, Wagner L; Fernie, Alisdair R; Nikoloski, Zoran

2012-03-30

Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data.

A solid-state NMR study of the dynamics and interactions of phenylalanine rings in a statherin fragment bound to hydroxyapatite crystals.

PubMed

Gibson, James M; Popham, Jennifer M; Raghunathan, Vinodhkumar; Stayton, Patrick S; Drobny, Gary P

2006-04-26

Extracellular matrix proteins regulate hard tissue growth by acting as adhesion sites for cells, by triggering cell signaling pathways, and by directly regulating the primary and/or secondary crystallization of hydroxyapatite, the mineral component of bone and teeth. Despite the key role that these proteins play in the regulation of hard tissue growth in humans, the exact mechanism used by these proteins to recognize mineral surfaces is poorly understood. Interactions between mineral surfaces and proteins very likely involve specific contacts between the lattice and the protein side chains, so elucidation of the nature of interactions between protein side chains and their corresponding inorganic mineral surfaces will provide insight into the recognition and regulation of hard tissue growth. Isotropic chemical shifts, chemical shift anisotropies (CSAs), NMR line-width information, (13)C rotating frame relaxation measurements, as well as direct detection of correlations between (13)C spins on protein side chains and (31)P spins in the crystal surface with REDOR NMR show that, in the peptide fragment derived from the N-terminal 15 amino acids of salivary statherin (i.e., SN-15), the side chain of the phenylalanine nearest the C-terminus of the peptide (F14) is dynamically constrained and oriented near the surface, whereas the side chain of the phenylalanine located nearest to the peptide's N-terminus (F7) is more mobile and is oriented away from the hydroxyapatite surface. The relative dynamics and proximities of F7 and F14 to the surface together with prior data obtained for the side chain of SN-15's unique lysine (i.e., K6) were used to construct a new picture for the structure of the surface-bound peptide and its orientation to the crystal surface.

Unique orientations and rotational dynamics of a 1-butyl-3-methyl-imidazolium hexafluorophosphate ionic liquid at the gas-liquid interface: the effects of the hydrogen bond and hydrophobic interactions.

PubMed

Yang, Deshuai; Fu, Fangjia; Li, Li; Yang, Zhen; Wan, Zheng; Luo, Yi; Hu, Na; Chen, Xiangshu; Zeng, Guixiang

2018-05-07

Here we report a series of molecular dynamics simulations for the orientations and rotational dynamics of the 1-butyl-3-methyl-imidazoliumhexafluorophosphate ([BMIM][PF 6 ]) ionic liquid (IL) at the gas-liquid interface. Compared to the bulk phase, the [BMIM] + cations at the interface prefer to orientate themselves with their imidazolium rings perpendicular to the gas-IL interface plane and their butyl chains pointing toward the vacuum phase. Such a preferential orientation can be attributed to the combined effect of the hydrophobic interactions and the optimum loss of hydrogen bonds (HBs). More interestingly, our simulation results demonstrate that the butyl chains of cations exhibit a two-stage rotational behavior at the interface, where the butyl chains are always in the vacuum phase at the first stage and the second stage corresponds to the butyl chains migrating from the vacuum phase into the liquid phase. A further detailed analysis reveals that their rotational motions at the first stage are mainly determined by the weakened HB strength at the interface while those at the second stage are dominated by their hydrophobic interactions. Such a unique rotational behavior of the butyl chains is significantly different from those of the anions and the imidazolium rings of cations at the interface due to the lack of existence of hydrophobic interaction in the cases of the latter two. In addition, a new and simple time correlation function (TCF) was constructed here for the first time to quantitatively identify the relevant hydrophobic interaction of alkyl chains. Therefore, our simulation results provide a molecular-level understanding of the effects of HB and hydrophobic interactions on the unique properties of imidazolium-based ILs at the gas-liquid interface.

Closed-kinetic chain upper-body training improves throwing performance of NCAA Division I softball players.

PubMed

Prokopy, Max P; Ingersoll, Christopher D; Nordenschild, Edwin; Katch, Frank I; Gaesser, Glenn A; Weltman, Arthur

2008-11-01

Closed-kinetic chain resistance training (CKCRT) of the lower body is superior to open-kinetic chain resistance training (OKCRT) to improve performance parameters (e.g., vertical jump), but the effects of upper-body CKCRT on throwing performance remain unknown. This study compared shoulder strength, power, and throwing velocity changes in athletes training the upper body exclusively with either CKCRT (using a system of ropes and slings) or OKCRT. Fourteen female National Collegiate Athletic Association Division I softball player volunteers were blocked and randomly placed into two groups: CKCRT and OKCRT. Blocking ensured the same number of veteran players and rookies in each training group. Training occurred three times weekly for 12 weeks during the team's supervised off-season program. Olympic, lower-body, core training, and upper-body intensity and volume in OKCRT and CKCRT were equalized between groups. Criterion variables pre- and posttraining included throwing velocity, bench press one-repetition maximum (1RM), dynamic single-leg balance, and isokinetic peak torque and power (PWR) (at 180 degrees x s(-1)) for shoulder flexion, extension, internal rotation, and external rotation (ER). The CKCRT group significantly improved throwing velocity by 2.0 mph (3.4%, p < 0.05), and the OKCRT group improved 0.3 mph (0.5%, NS). A significant interaction was observed (p < 0.05). The CKCRT group improved its 1RM bench press to the same degree (1.9 kg) as the OKCRT group (p < 0.05 within each group). The CKCRT group improved all measures of shoulder strength and power, whereas OKCRT conferred little change in shoulder torque and power scores. Although throwing is an open-chain movement, adaptations from CKCRT may confer benefits to subsequent performance. Strength coaches can incorporate upper-body CKCRT without sacrificing gains in maximal strength or performance criteria associated with an athletic open-chain movement such as throwing.

Molecular dynamics investigation of the physisorption and interfacial characteristics of NBR chains on carbon nanotubes with different characteristics

NASA Astrophysics Data System (ADS)

Li, Kun; Gu, Boqin

2017-07-01

The present study investigates the physisorption and interfacial interactions between multiwalled carbon nanotubes (MWNTs) with different characteristics, including different numbers of walls and different functional groups, and acrylonitrile-butadiene rubber (NBR) polymer chains based on molecular dynamics simulations performed using modeled MWNT/NBR compound systems. The effects of the initial orientation of NBR chains and their relative distances to nanotubes, number of nanotube layers, and the surface functional groups of nanotubes on nanotube/polymer interactions are examined. Analysis is conducted according to the final configuration obtained in conjunction with the binding energy (Eb), radius of gyration (Rg) and end-to-end distance (h). The results show that the final conformations of NBR chains adsorbed on MWNT surfaces is associated with the initial relative angle of the NBR chains and their distance from the nanotubes. For non-functionalized MWNTs, Eb is almost directly proportional to Rg under equivalent parameters. Moreover, it is observed that functional groups hinder the wrapping of NBR chains on the MWNT surfaces. This indicates that functional groups do not always benefit the macro-mechanical properties of the composites. Moreover, the type of the major interaction force has been dramatically changed into electrostatic force from vdW force because of functionalization.

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

Hybrid modeling and empirical analysis of automobile supply chain network

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Non-Destructive Evaluation of Material System Using Highly Nonlinear Acoustic Waves

NASA Astrophysics Data System (ADS)

Khatri, Devvrath

A chain of granular particles is one of the most studied examples of highly nonlinear systems deriving its response from the nonlinear Hertzian contact interaction between particles. Interest in these systems derives from their tunable dynamic response, encompassing linear, weakly nonlinear, and strongly nonlinear regimes, controlled by varying the static and dynamic load applied. In chains with a very weak (or zero) static precompression, the system supports the formation and propagation of highly nonlinear solitary waves (HNSWs). The dual-nonlinear interaction between particles (i.e., a power-law type contact potential in compression, and zero strength in tension) combined with discreteness of the system, makes the granular system highly tunable. The propagation properties of these waves, such as traveling pulse width, wave speed, number of separated pulses (single or train of pulses), etc., can be controlled by modifying one or many of the parameters, like the particle's dimension, material properties, static and dynamic force amplitude, the type and duration of the initial excitation applied to the system, and/or the periodicity of the chain. The ability to control the wave properties in such chains has been proposed for several different practical engineering applications. The dynamic properties of these granular chains have been conventionally studied using discrete particle models (DPMs) which consider the particles in the chains as point masses connected by nonlinear Hertzian springs with the neighboring particles. Although, this is a good approximation under proper circumstances, it does not capture many features of the three dimensional elastic particles such as the elastic wave propagation within the particles, the local deformation of the particles in the vicinity of the contact point, the corresponding changes in the contact area, and the collective vibrations of the particles among others. This thesis focuses on the development of a finite element model (FEM) using the commercially available software Abaqus, which takes into account many of these characteristic features. The finite element model discretizes particles by considering them as three-dimensional deformable bodies of revolution and describes the nonlinear dynamic response of one-dimensional granular chains composed of particles with various geometries and orientations. We showed that particles' geometries and orientations provide additional design parameters for controlling the dynamic response of the system, compared to chains composed of spherical particles. We also showed that the tunable and compact nature of these waves can be used to tailor the properties of HNSWs for specific application, such as information carriers for actuation and sensing of mechanical properties and boundary effects of adjoining media in Non-Destructive Evaluation (NDE) and Structural Health Monitoring (SHM). Using experiments and numerics, we characterized interface dynamics between granular media and adjoining linear elastic media, and found that the coupling produced temporary localization of the incident waves at the boundaries between the two media and their decomposition into reflected waves. We monitored the formation of reflected solitary waves propagating back from the interface and found that their properties are sensitive to the geometric and material properties of the adjoining media. The work done in this research enhances our understanding of the basic physics and tunability of nonlinear granular media, and further establishes a theoretical and numerical foundation in the applications of HNSWs as information carriers.

End-monomer Dynamics in Semiflexible Polymers

PubMed Central

Hinczewski, Michael; Schlagberger, Xaver; Rubinstein, Michael; Krichevsky, Oleg; Netz, Roland R.

2009-01-01

Spurred by an experimental controversy in the literature, we investigate the end-monomer dynamics of semiflexible polymers through Brownian hydrodynamic simulations and dynamic mean-field theory. Precise experimental observations over the last few years of end-monomer dynamics in the diffusion of double-stranded DNA have given conflicting results: one study indicated an unexpected Rouse-like scaling of the mean squared displacement (MSD) 〈r2(t)〉 ~ t1/2 at intermediate times, corresponding to fluctuations at length scales larger than the persistence length but smaller than the coil size; another study claimed the more conventional Zimm scaling 〈r2(t)〉 ~ t2/3 in the same time range. Using hydrodynamic simulations, analytical and scaling theories, we find a novel intermediate dynamical regime where the effective local exponent of the end-monomer MSD, α(t) = d log〈r2(t)〉/d log t, drops below the Zimm value of 2/3 for sufficiently long chains. The deviation from the Zimm prediction increases with chain length, though it does not reach the Rouse limit of 1/2. The qualitative features of this intermediate regime, found in simulations and in an improved mean-field theory for semiflexible polymers, in particular the variation of α(t) with chain and persistence lengths, can be reproduced through a heuristic scaling argument. Anomalously low values of the effective exponent α are explained by hydrodynamic effects related to the slow crossover from dynamics on length scales smaller than the persistence length to dynamics on larger length scales. PMID:21359118

The dynamics of commissioning across organisational and clinical boundaries.

PubMed

Baxter, Kate; Weiss, Marjorie; Le Grand, Julian

2008-01-01

The purpose of the paper is to investigate the inter- and intra-organisational relationships in the commissioning of secondary care by primary care trusts in England, using a principal-agent framework. The methodology is a qualitative study of three case studies. A total of 13 commissioning-related meetings were observed. In total, 21 managers and six consultant surgeons were interviewed. There are a number of different levels at which contractual and managerial control take place. Different strengths of control at one level can affect willingness to comply with agreements at other levels. Agreements at one level do not necessarily result in appropriate or expected action at another. The system for commissioning in the National Health Service (NHS) has changed with the introduction of payment by results and practice-based commissioning. However, the dynamics of the inter- and intra-organisational relationships studied remain. Incentives within organisations are as important as those between organisations. Within a chain of principal-agent relations, it is important that a strong link in the chain does not result in the exploitation of weaknesses in other links. If government targets and frameworks are to be met through commissioning, it may be advantageous to concentrate efforts on developing incentives that align clinician with NHS trust objectives as well as NHS trust with primary care trust (PCT) and government objectives. This paper is based on original empirical work. It uses a principal-agent framework to understand the relationships between PCTs and NHS trusts and highlights the importance of internal NHS trust governance systems in the fulfilment of commissioning agreements.

Structures and dynamics in a two-dimensional dipolar dust particle system

NASA Astrophysics Data System (ADS)

Hou, X. N.; Liu, Y. H.; Kravchenko, O. V.; Lapushkina, T. A.; Azarova, O. A.; Chen, Z. Y.; Huang, F.

2018-05-01

The effects of electric dipole moment, the number of dipolar particles, and system temperature on the structures and dynamics of a dipolar dust particle system are studied by molecular dynamics simulations. The results show that the larger electric dipole moment is favorable for the formation of a long-chain structure, the larger number of dipolar dust particles promotes the formation of the multi-chain structure, and the higher system temperature can cause higher rotation frequency. The trajectories, mean square displacement (MSD), and the corresponding spectrum functions of the MSDs are also calculated to illustrate the dynamics of the dipolar dust particle system, which is also closely related to the growth of dust particles. Some simulations are qualitatively in agreement with our experiments and can provide a guide for the study on dust growth, especially on the large-sized particles.

Dynamics in a one-dimensional ferrogel model: relaxation, pairing, shock-wave propagation.

PubMed

Goh, Segun; Menzel, Andreas M; Löwen, Hartmut

2018-05-23

Ferrogels are smart soft materials, consisting of a polymeric network and embedded magnetic particles. Novel phenomena, such as the variation of the overall mechanical properties by external magnetic fields, emerge consequently. However, the dynamic behavior of ferrogels remains largely unveiled. In this paper, we consider a one-dimensional chain consisting of magnetic dipoles and elastic springs between them as a simple model for ferrogels. The model is evaluated by corresponding simulations. To probe the dynamics theoretically, we investigate a continuum limit of the energy governing the system and the corresponding equation of motion. We provide general classification scenarios for the dynamics, elucidating the touching/detachment dynamics of the magnetic particles along the chain. In particular, it is verified in certain cases that the long-time relaxation corresponds to solutions of shock-wave propagation, while formations of particle pairs underlie the initial stage of the dynamics. We expect that these results will provide insight into the understanding of the dynamics of more realistic models with randomness in parameters and time-dependent magnetic fields.

Dielectric Properties of Poly(ethylene oxide) from Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Smith, Grant D.

1994-01-01

The order, conformations and dynamics of poly(oxyethylene) (POE) melts have been investigated through molecular dynamics simulations. The potential energy functions were determined from detailed ab initio electronic structure calculations of the conformational energies of the model molecules 1,2-dimethoxyethane (DME) and diethylether. The x-ray structure factor for POE from simulation will be compared to experiment. In terms of conformation, simulations reveal that chains are extended in the melt relative to isolated chains due to the presence of strong intermolecular O...H interactions, which occur at the expense of intramolecular O...H interactions. Conformational dynamics about the C-C bond were found to be significantly faster than in polymethylene, while conformational dynamics about the C-O bond even faster than the C-C dynamics. The faster local dynamics in POE relative to polymethylene is consistent with C-13 NMR spin-lattice relaxation experiments. Conformational transitions showed significant second-neighbor correlation, as was found for polymethylene. This correlation of transitions with C-C neighbors was found to be reduced relative to C-O neighbors. Dielectric relaxation from simulation will also be compared with experiment.

Thermalization of entanglement.

PubMed

Zhang, Liangsheng; Kim, Hyungwon; Huse, David A

2015-06-01

We explore the dynamics of the entanglement entropy near equilibrium in highly entangled pure states of two quantum-chaotic spin chains undergoing unitary time evolution. We examine the relaxation to equilibrium from initial states with either less or more entanglement entropy than the equilibrium value, as well as the dynamics of the spontaneous fluctuations of the entanglement that occur in equilibrium. For the spin chain with a time-independent Hamiltonian and thus an extensive conserved energy, we find slow relaxation of the entanglement entropy near equilibration. Such slow relaxation is absent in a Floquet spin chain with a Hamiltonian that is periodic in time and thus has no local conservation law. Therefore, we argue that slow diffusive energy transport is responsible for the slow relaxation of the entanglement entropy in the Hamiltonian system.

Effective Hamiltonian for travelling discrete breathers

NASA Astrophysics Data System (ADS)

MacKay, Robert S.; Sepulchre, Jacques-Alexandre

2002-05-01

Hamiltonian chains of oscillators in general probably do not sustain exact travelling discrete breathers. However solutions which look like moving discrete breathers for some time are not difficult to observe in numerics. In this paper we propose an abstract framework for the description of approximate travelling discrete breathers in Hamiltonian chains of oscillators. The method is based on the construction of an effective Hamiltonian enabling one to describe the dynamics of the translation degree of freedom of moving breathers. Error estimate on the approximate dynamics is also studied. The concept of the Peierls-Nabarro barrier can be made clear in this framework. We illustrate the method with two simple examples, namely the Salerno model which interpolates between the Ablowitz-Ladik lattice and the discrete nonlinear Schrödinger system, and the Fermi-Pasta-Ulam chain.

Two-dimensional heteroclinic attractor in the generalized Lotka-Volterra system

NASA Astrophysics Data System (ADS)

Afraimovich, Valentin S.; Moses, Gregory; Young, Todd

2016-05-01

We study a simple dynamical model exhibiting sequential dynamics. We show that in this model there exist sets of parameter values for which a cyclic chain of saddle equilibria, O k , k=1,\\ldots,p , have two-dimensional unstable manifolds that contain orbits connecting each O k to the next two equilibrium points O k+1 and O k+2 in the chain ({{O}p+1}={{O}1} ). We show that the union of these equilibria and their unstable manifolds form a two-dimensional surface with a boundary that is homeomorphic to a cylinder if p is even and a Möbius strip if p is odd. If, further, each equilibrium in the chain satisfies a condition called ‘dissipativity’, then this surface is asymptotically stable.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics.

PubMed

de Buyl, Pierre; Nies, Erik

2015-04-07

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics

NASA Astrophysics Data System (ADS)

de Buyl, Pierre; Nies, Erik

2015-04-01

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

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.

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor–Acceptor Polymer Single Chains

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

Lee, Franklin L.; Farimani, Amir Barati; Gu, Kevin L.

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor–acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent withmore » a globule-like conformation in a poor solvent. Altogether, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.« less

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor–Acceptor Polymer Single Chains

DOE PAGES

Lee, Franklin L.; Farimani, Amir Barati; Gu, Kevin L.; ...

2017-10-25

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor–acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent withmore » a globule-like conformation in a poor solvent. Altogether, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.« less

Thermodynamic of cellulose solvation in novel solvent mixtures

NASA Astrophysics Data System (ADS)

Das, Ritankar; Chu, Jhih-Wei

2013-04-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Thermodynamic of cellulose solvation in novel solvent mixtures

NASA Astrophysics Data System (ADS)

Das, Ritankar

2013-03-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Thermodynamics of cellulose solvation in novel solvent mixtures

NASA Astrophysics Data System (ADS)

Das, Ritankar; Chu, Jhih-Wei

2012-10-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Thermodynamic of cellulose solvation in novel solvent mixtures

NASA Astrophysics Data System (ADS)

Das, Ritankar

2012-11-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Sampling rare fluctuations of discrete-time Markov chains

NASA Astrophysics Data System (ADS)

Whitelam, Stephen

2018-03-01

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

Sampling rare fluctuations of discrete-time Markov chains.

PubMed

Whitelam, Stephen

2018-03-01

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

Nonequilibrium dynamic critical scaling of the quantum Ising chain.

PubMed

Kolodrubetz, Michael; Clark, Bryan K; Huse, David A

2012-07-06

We solve for the time-dependent finite-size scaling functions of the one-dimensional transverse-field Ising chain during a linear-in-time ramp of the field through the quantum critical point. We then simulate Mott-insulating bosons in a tilted potential, an experimentally studied system in the same equilibrium universality class, and demonstrate that universality holds for the dynamics as well. We find qualitatively athermal features of the scaling functions, such as negative spin correlations, and we show that they should be robustly observable within present cold atom experiments.

Mathematical model of the loan portfolio dynamics in the form of Markov chain considering the process of new customers attraction

NASA Astrophysics Data System (ADS)

Bozhalkina, Yana

2017-12-01

Mathematical model of the loan portfolio structure change in the form of Markov chain is explored. This model considers in one scheme both the process of customers attraction, their selection based on the credit score, and loans repayment. The model describes the structure and volume of the loan portfolio dynamics, which allows to make medium-term forecasts of profitability and risk. Within the model corrective actions of bank management in order to increase lending volumes or to reduce the risk are formalized.

An analytical approach to top predator interference on the dynamics of a food chain model

NASA Astrophysics Data System (ADS)

Senthamarai, R.; Vijayalakshmi, T.

2018-04-01

In this paper, a nonlinear mathematical model is proposed and analyzed to study of top predator interference on the dynamics of a food chain model. The mathematical model is formulated using the system of non-linear ordinary differential equations. In this model, there are three state dimensionless variables, viz, size of prey population x, size of intermediate predator y and size of top predator population z. The analytical results are compared with the numerical simulation using MATLAB software and satisfactory results are noticed.

Finite-Size Effects in Single Chain Magnets: An Experimental and Theoretical Study

NASA Astrophysics Data System (ADS)

Bogani, L.; Caneschi, A.; Fedi, M.; Gatteschi, D.; Massi, M.; Novak, M. A.; Pini, M. G.; Rettori, A.; Sessoli, R.; Vindigni, A.

2004-05-01

The problem of finite-size effects in s=1/2 Ising systems showing slow dynamics of the magnetization is investigated introducing diamagnetic impurities in a Co2+-radical chain. The static magnetic properties have been measured and analyzed considering the peculiarities induced by the ferrimagnetic character of the compound. The dynamic susceptibility shows that an Arrhenius law is observed with the same energy barrier for the pure and the doped compounds while the prefactor decreases, as theoretically predicted. Multiple spin reversal has also been investigated.

Simulation of economic agents interaction in a trade chain

NASA Astrophysics Data System (ADS)

Gimanova, I. A.; Dulesov, A. S.; Litvin, N. V.

2017-01-01

The mathematical model of economic agents interaction is offered in the work. It allowsconsidering the change of price and sales volumesin dynamics according to the process of purchase and sale in the single-product market of the trade and intermediary network. The description of data-flow processes is based on the use of the continuous dynamic market model. The application of ordinary differential equations during the simulation allows one to define areas of coefficients - characteristics of agents - and to investigate their interaction in a chain on stability.

Dynamics of polymer nanoparticles and chains.

NASA Astrophysics Data System (ADS)

Streletzky, Kiril; McKenna, John; Hillier, Gerry

2006-10-01

We present a Dynamic Light Scattering study of transport properties of the polymer chains and nanoparticles made out of the same starting solution. The spectra of both systems are highly non-exponential requiring a spectral time moment analysis. Our findings indicate the existence of several modes of relaxation in both systems. The comparison of the mean relaxation rates and diffusion coefficients of the different modes in two systems under good solvent conditions will be reported. Temperature sensitivity of the polymer nanoparticles and its possible applications in pharmaceutical, coatings, and petroleum industries will also be discussed.

Modeling competitive substitution in a polyelectrolyte complex

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

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

2015-12-28

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

Nanoscopic dynamics of phospholipid in unilamellar vesicles: Effect of gel to fluid phase transition

DOE PAGES

Sharma, V. K.; Mamontov, E.; Anunciado, D. B.; ...

2015-03-04

Dynamics of phospholipids in unilamellar vesicles (ULV) is of interest in biology, medical, and food sciences since these molecules are widely used as biocompatible agents and a mimic of cell membrane systems. We have investigated the nanoscopic dynamics of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) phospholipid in ULV as a function of temperature using elastic and quasielastic neutron scattering (QENS). The dependence of the signal on the scattering momentum transfer, which is a critical advantage of neutron scattering techniques, allows the detailed analysis of the lipid motions that cannot be carried out by other means. In agreement with a differential scanning calorimetry measurement, amore » sharp rise in the elastic scattering intensity below ca. 296 K indicates a phase transition from the high-temperature fluid phase to the low-temperature solid gel phase. The microscopic lipid dynamics exhibits qualitative differences between the solid gel phase (in a measurement at 280 K) and the fluid phase (in a measurement at a physiological temperature of 310 K). The data analysis invariably shows the presence of two distinct motions: the whole lipid molecule motion within a monolayer, or lateral diffusion, and the relatively faster internal motion of the DMPC molecule. The lateral diffusion of the whole lipid molecule is found to be Fickian in character, whereas the internal lipid motions are of localized character, consistent with the structure of the vesicles. The lateral motion slows down by an order of magnitude in the solid gel phase, whereas for the internal motion not only the time scale, but also the character of the motion changes upon the phase transition. In the solid gel phase, the lipids are more ordered and undergo uniaxial rotational motion. However, in the fluid phase, the hydrogen atoms of the lipid tails undergo confined translation diffusion rather than uniaxial rotational diffusion. The localized translational diffusion of the hydrogen atoms of the lipid tails is a manifestation of the flexibility of the chains acquired in the fluid phase. Because of this flexibility, both the local diffusivity and the confinement volume for the hydrogen atoms increase linearly from near the lipid s polar head group to the end of its hydrophobic tail. Our results present a quantitative and detailed picture of the effect of the gel-fluid phase transition on the nanoscopic lipid dynamics in ULV. Lastly, the data analysis approach developed here has a potential for probing the dynamic response of lipids to the presence of additional cell membrane components.« less

[Using Molecular Simulations to Understand Complex Nanoscale Dynamic Phenomena in Polymer Solutions

NASA Technical Reports Server (NTRS)

Smith, Grant

2004-01-01

The first half of the project concentrated on molecular simulation studies of the translocation of model molecules for single-stranded DNA through a nanosized pore. This has resulted in the publication, Translocation of a polymer chain across a nanopore: A Brownian dynamics simulation study, by Pu Tian and Grant D. Smith, JOURNAL OF CHEMICAL PHYSICS VOLUME 119, NUMBER 21 1 DECEMBER 2003, which is attached to this report. In this work we carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient) designed to mimic an electrostatic field. The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient). We focused on the latter case in our studies. Calculation of radius of gyration of the translocating chain at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tube-like pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied. Attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing field strength, and decreasing pore diameter.

Effect of vehicular size on chain-reaction crash

NASA Astrophysics Data System (ADS)

Nagatani, Takashi

2015-11-01

We present the dynamic model of the chain-reaction crash to take account of the vehicular size. Drivers brake according to taillights of the forward vehicle. We investigate the effect of the vehicular size on the chain-reaction crash (multiple-vehicle collision) in the traffic flow controlled by taillights. In the multiple-vehicle collision, the first crash induces more collisions. We investigate how the first collision induces the chain-reaction crash numerically. We derive, analytically, the transition points and the region maps for the chain-reaction crash in the traffic flow of vehicles with finite sizes. We clarify the effect of the vehicular size on the multiple-vehicle collision.

International Collaboration and Academic Exchange of the CHAIN Project in this Three Years (Period)

NASA Astrophysics Data System (ADS)

Ueno, Satoru; Shibata, Kazunari; Morita, Satoshi; Kimura, Goichi; Asai, Ayumi; Kitai, Reizaburo; Ichimoto, Kiyoshi; Nagata, Shin'ichi; Ishii, Takako; Nakatani, Yoshikazu; Masashi, Yamaguchi; et al.

2014-02-01

We will introduce contents of international collaboration and academic exchange of the CHAIN project in recent three years (ISWI period). After April of 2010, we have not obtained any enough budget for new instruments. Therefore, we have not been able to install new Flare Monitoring Telescopes (FMT) in new countries, such as Algeria. On the other hand, however, we have continued international academic exchange through scientific and educational collaboration with mainly Peru, such as data-analysis training, holding scientific workshops etc. Additionally, in this year, King Saudi University of Saudi Arabia and CRAAG of Algeria have planned to build a new FMT in their university by their own budget. Therefore, we have started some collaboration in the field of technical advices of instruments and scientific themes etc. Moreover, Pakistan Space and Upper Atmosphere Research Commission (SUPARCO) also offered us participation in the CHAIN-project. We would like to continue to consider the possibility of academic collaboration with such new positive developing nations, too.

Identification of metastable states in peptide's dynamics

NASA Astrophysics Data System (ADS)

Ruzhytska, Svitlana; Jacobi, Martin Nilsson; Jensen, Christian H.; Nerukh, Dmitry

2010-10-01

A recently developed spectral method for identifying metastable states in Markov chains is used to analyze the conformational dynamics of a four-residue peptide valine-proline-alanine-leucine. We compare our results to empirically defined conformational states and show that the found metastable states correctly reproduce the conformational dynamics of the system.

A new approach in compatibilization of the poly(lactic acid)/thermoplastic starch (PLA/TPS) blends.

PubMed

Akrami, Marzieh; Ghasemi, Ismaeil; Azizi, Hamed; Karrabi, Mohammad; Seyedabadi, Mohammad

2016-06-25

In this study, a new compatibilizer was synthesized to improve the compatibility of the poly(lactic acid)/thermoplastic starch blends. The compatibilizer was based on maleic anhydride grafted polyethylene glycol grafted starch (mPEG-g-St), and was characterized using Fourier transform infrared spectroscopy (FTIR), dynamic mechanical thermal analysis (DMTA) and back titration techniques. The results indicated successful accomplishment of the designed reactions and formation of a starch cored structure with many connections to m-PEG chains. To assess the performance of synthesized compatibilizer, several PLA/TPS blends were prepared using an internal mixer. Consequently, their morphology, dynamic-mechanical behavior, crystallization and mechanical properties were studied. The compatibilizer enhanced interfacial adhesion, possibly due to interaction between free end carboxylic acid groups of compatibilizer and active groups of TPS and PLA phases. In addition, biodegradability of the samples was evaluated by various methods consisting of weight loss, FTIR-ATR analysis and morphology. The results revealed no considerable effect of compatibilizer on biodegradability of samples. Copyright © 2016 Elsevier Ltd. All rights reserved.