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  • 1
    Electronic Resource
    Electronic Resource
    Response to "Comment on ‘The viscoelastic response of Brownian suspensions' " [J. Chem. Phys. 114, 3339 (2001)] (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 3341-3342 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Our original article presented computer simulation results for the viscoelastic response of a simple model colloidal suspension. We compared our results for the viscosity with a theoretical prediction of Verberg et al. [R. Verberg, I. M. de Schepper, and E. G. D. Cohen, Phys. Rev. E 55, 3143 (1997)] and found poor agreement. It is suggested in the previous comment that a comparison with a modified expression is more appropriate. In response we explain the basis of our comparison and expand on how a different interpretation could be made, leading to an expression of the form Felderhof suggests is appropriate. Nonetheless, as stated in the comment, the agreement with simulation is poor, no matter which of the two possible theoretical expressions is used. We also seek to clarify our position concerning the form of the high frequency response at low volume fraction. Our finding is that the ratio of this to the high frequency response in the zero density limit is not the radial distribution function at contact, as predicted by Verberg et al. [R. Verberg, I. M. de Schepper, M. J. Feigenbaum, and E. G. D. Cohen, J. Stat. Phys. 87, 1037 (1997)], but is a rather smaller quantity. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1338510
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  • 2
    Electronic Resource
    Electronic Resource
    Long-time tails in angular momentum correlations (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 1582-1587 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We compare computer simulation results for the angular velocity autocorrelation function (AVACF) of a colloidal particle with theoretical predictions. We consider both spherical and nonspherical particles in two and three dimensions. The theoretical prediction for the long-time decay of the AVACF in three dimensions is well known, here we also give the two-dimensional result, along with a sketch of how it was derived. For spherical particles we find excellent agreement between the simulations results and theoretical predictions in both two and three dimensions. We also find that the same expressions apply to the nonspherical particles when the particles have had time to undergo a significant angular displacement. This observation is again in agreement with theory. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469780
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  • 3
    Electronic Resource
    Electronic Resource
    The viscoelastic response of Brownian suspensions (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 8708-8720 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In a simple model for the long-time dynamical behavior of Brownian suspensions, particles diffuse independently while simultaneously undergoing direct interactions with each other. Despite its simplicity, this model forms the basis of both the Brownian dynamics computer simulation technique and apparently successful theories. Here we use the approach to study numerically the viscoelastic response of a suspension of hard spheres. At low volume fractions (10%) we find that the frequency dependence of the viscosity is in agreement with theoretical calculations based on solving the two-particle Smoluchowski equation. At a higher volume fraction (45%) we find that the model is not well described by various extensions of low density theory that have been proposed. Including hydrodynamics in a minimal way (by allowing the particles to diffuse with the short-time diffusion coefficient) and comparing with experiment, the model successfully reproduces the viscoelastic response over an intermediate range of frequencies. However, at low frequencies a significant disagreement emerges. A "slowing down" of the dynamics of the particles at longer times, more apparent in the simulations than in the experimental results, appears to be the cause of this discrepancy. Ultimately, this leads to a significant overestimate of the zero frequency (Newtonian) viscosity. The reason theories based on the approach yield such excellent agreement with experiment, we can only conclude, is because they fail to describe the model adequately. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.480211
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  • 4
    Electronic Resource
    Electronic Resource
    A stochastic technique for solving the Lorentz–Boltzmann equation for hard spheres: Application to the kinetics of gas absorption (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 5714-5722 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The Lorentz–Boltzmann equation for tagged particle motion in a hard sphere fluid may be interpreted as describing the motion of a particle propagating via a series of binary uncorrelated collisions in a structureless bath of fluid particles with a Maxwellian distribution of velocities. We describe a very general stochastic technique for solving the equation. The method can also be extended to the Enskog level, valid up to somewhat higher densities, by a simple scaling of the time. Having reproduced several known results for the Lorentz–Boltzmann equation we extend the method to a simple reaction process where there is no analytic result—the kinetics of gas absorption for a gas confined between two plates. For this process there are two simple analytic limits—the Knudsen limit (in which there are no collisions between absorbing particles) and the diffusive limit (where there are a large number of collisions between absorbing particles). We show that regardless of the Knudsen number, Kn, the Knudsen limit describes the very short time kinetics and the diffusive limit describes the long time kinetics. However, at moderate values of the Knudsen number the rate constant characterizing the long time kinetics differs from the diffusive value. This discrepancy scales away slowly (as 1/Kn) with increasing Knudsen number. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.475980
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  • 5
    Electronic Resource
    Electronic Resource
    Response to "Comment on ‘Long-time tails in angular momentum correlations' '' [J. Chem. Phys. 104, 7363 (1996)] (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 7364-7365 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.471403
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  • 6
    Electronic Resource
    Electronic Resource
    Magnetochemistry of the tetrahaloferrate (III) ions: Crystal structure and magnetic ordering in [(4-chloropyridinium)FeCl4]2⋅4-chloropyridinium chloride and related salts (abstract) (1990)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 67 (1990), S. 5862-5862 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The yellow compound of stoichiometry (4-chloropyridinium)3Fe2Cl9 belongs to the space group P21/n with four formula units in the unit cell. Structural analysis shows that the iron is present as the FeX4− ion. Magnetic measurements on single crystals show that the material orders as a canted antiferromagnet at 2.725 K. Replacement of the 4-chloro cation by the 4-bromo analog yields an isomorphous material and shifts the transition temperature to 2.34 K. The phase diagrams of both salts have also been determined. For [(4-chloropyridinium)FeCl4]2⋅4-chloropyridinium chloride, the bicritical point is at 2.40 K and 7 kOe, and HSF(0)=5.5 kOe. With Hc(0)=56 kOe, α=HA/HE=1.9×10−2. In the case of [(4-bromopyridinium)FeCl4]2⋅4-bromopyridinium chloride, HSF(0)=3 kOe, Hc(0)=42 kOe, α=1.0×10−2, and the bicritical point is at 2.24 K and 4.2 kOe. Crystallographic investigations at 25 K are reported on the isomorphous (4-chloropyridinium)3Fe2Br9 and on (4-bromopyridinium)3Fe2Cl1.3Br7.7. Magnetic measurements on single crystals show that (4-bromopyridinium)3Fe2Cl1.3Br7.7 orders as a canted antiferromagnet at 5.67 K, while (4-chloropyridinium)3Fe2Br9 orders similarly at 7.96 K. These compounds behave approximately as S=5/2, three-dimensional Heisenberg antiferromagnets.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.345993
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  • 7
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    Characterization of the Cadherin-Catenin Complex of the Sea Anemone Nematostella vectensis and Implications for the Evolution of Metazoan Cell-Cell Adhesion (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-19
    Description: The cadherin–catenin complex (CCC) mediates cell–cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-binding properties of the CCC are conserved in a nonbilaterian animal, the sea anemone Nematostella vectensis . We demonstrated that N. vectensis has a complete repertoire of cadherin–catenin proteins, including two classical cadherins, one α-catenin, and one β-catenin. Using size-exclusion chromatography and multi-angle light scattering, we showed that α-catenin and β-catenin formed a heterodimer that bound N. vectensis Cadherin-1 and -2. Nematostella vectensis α-catenin bound F-actin with equivalent affinity as either a monomer or an α/β-catenin heterodimer, and its affinity for F-actin was, in part, regulated by a novel insert between the N- and C-terminal domains. Nematostella vectensis α-catenin inhibited Arp2/3 complex-mediated nucleation of actin filaments, a regulatory property previously thought to be unique to mammalian αE-catenin. Thus, despite significant differences in sequence, the key interactions of the CCC are conserved between bilaterians and cnidarians, indicating that the core function of the CCC as a link between cell adhesions and the actin cytoskeleton is ancestral in the eumetazoans.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    NF-{kappa}B directly mediates epigenetic deregulation of common microRNAs in Epstein-Barr virus-mediated transformation of B-cells and in lymphomas (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-27
    Description: MicroRNAs (miRNAs) have negative effects on gene expression and are major players in cell function in normal and pathological conditions. Epstein-Barr virus (EBV) infection of resting B lymphocytes results in their growth transformation and associates with different B cell lymphomas. EBV-mediated B cell transformation involves large changes in gene expression, including cellular miRNAs. We performed miRNA expression analysis in growth transformation of EBV-infected B cells. We observed predominant downregulation of miRNAs and upregulation of a few miRNAs. We observed similar profiles of miRNA expression in B cells stimulated with CD40L/IL-4, and those infected with EBNA-2- and LMP-1-deficient EBV particles, suggesting the implication of the NF-kB pathway, common to all four situations. In fact, the NF-kB subunit p65 associates with the transcription start site (TSS) of both upregulated and downregulated miRNAs following EBV infection This occurs together with changes at histone H3K27me3 and histone H3K4me3. Inhibition of the NF-kB pathway impairs changes in miRNA expression, NF-kB binding and changes at the above histone modifications near the TSS of these miRNA genes. Changes in expression of these miRNAs also occurred in diffuse large B cell lymphomas (DLBCL), which are strongly NF-kB dependent. Our results highlight the relevance of the NF-kB pathway in epigenetically mediated miRNA control in B cell transformation and DLBCL.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-20
    Description: The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements and 100% of the nonkeratin feather gene set were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near insulin-like growth factor binding protein (IGFBP) 2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Oxyrrhis marina growth, sex and reproduction (2010)
    Oxford University Press
    Details
    Publication Date: 2010-08-26
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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