Short-time Rheology and Diffusion in Suspensions of Yukawa-type Colloidal Particles

A comprehensive study is presented on the short-time dynamics in suspensions of charged colloidal spheres. The explored parameter space covers the major part of the fluid-state regime, with colloid concentrations extending up to the freezing transition. The particles are assumed to interact directly by a hard-core plus screened Coulomb potential, and indirectly by solvent-mediated hydrodynamic interactions (HIs). By comparison with accurate accelerated Stokesian Dynamics (ASD) simulations of the hydrodynamic function H(q), and the high-frequency viscosity, we investigate the accuracy of two fast and easy-to-implement analytical schemes. The first scheme, referred to as the pairwise additive (PA) scheme, uses exact two-body hydrodynamic mobility tensors. It is in good agreement with the ASD simulations of H(q) and the high-frequency viscosity, for smaller volume fractions up to about 10% and 20%, respectively. The second scheme is a hybrid method combining the virtues of the \delta\gamma-scheme by Beenakker and Mazur with those of the PA scheme. It leads to predictions in good agreement with the simulation data, for all considered concentrations, combining thus precision with computational efficiency. The hybrid method is used to test the accuracy of a generalized Stokes-Einstein (GSE) relation proposed by Kholodenko and Douglas, showing its severe violation in low salinity systems. For hard spheres, however, this GSE relation applies decently well

Hydrodynamic interactions in colloidal ferrofluids: A lattice Boltzmann study

We use lattice Boltzmann simulations, in conjunction with Ewald summation methods, to investigate the role of hydrodynamic interactions in colloidal suspensions of dipolar particles, such as ferrofluids. Our work addresses volume fractions $\phi$ of up to 0.20 and dimensionless dipolar interaction parameters $\lambda$ of up to 8. We compare quantitatively with Brownian dynamics simulations, in which many-body hydrodynamic interactions are absent. Monte Carlo data are also used to check the accuracy of static properties measured with the lattice Boltzmann technique. At equilibrium, hydrodynamic interactions slow down both the long-time and the short-time decays of the intermediate scattering function $S(q,t)$, for wavevectors close to the peak of the static structure factor $S(q)$, by a factor of roughly two. The long-time slowing is diminished at high interaction strengths whereas the short-time slowing (quantified via the hydrodynamic factor $H(q)$) is less affected by the dipolar interactions, despite their strong effect on the pair distribution function arising from cluster formation. Cluster formation is also studied in transient data following a quench from $\lambda = 0$; hydrodynamic interactions slow the formation rate, again by a factor of roughly two

Rab27a controls HIV-1 assembly by regulating plasma membrane levels of phosphatidylinositol 4,5-bisphosphate

During the late stages of the HIV-1 replication cycle, the viral polyprotein Pr55(Gag) is recruited to the plasma membrane (PM), where it binds phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and directs HIV-1 assembly. We show that Rab27a controls the trafficking of late endosomes carrying phosphatidylinositol 4-kinase type 2 α (PI4KIIα) toward the PM of CD4(+) T cells. Hence, Rab27a promotes high levels of PM phosphatidylinositol 4-phosphate and the localized production of PI(4,5)P2, therefore controlling Pr55(Gag) membrane association. Rab27a also controls PI(4,5)P2 levels at the virus-containing compartments of macrophages. By screening Rab27a effectors, we identified that Slp2a, Slp3, and Slac2b are required for the association of Pr55(Gag) with the PM and that Slp2a cooperates with Rab27a in the recruitment of PI4KIIα to the PM. We conclude that by directing the trafficking of PI4KIIα-positive endosomes toward the PM, Rab27a controls PI(4,5)P2 production and, consequently, HIV-1 replication.Universidad de Buenos Aires and CONICET doctoral fellowships, Agencia Nacional de Pro- moción Científica y Tecnológica (Argentina) grants: (2010-1681, 2012-00353), Creative and Novel Ideas in HIV Research Program, University of Alabama at Birmingham Center for AIDS Research funding grant P30 AI027767-24

Aspects of the dynamics of colloidal suspensions: Further results of the mode-coupling theory of structural relaxation

Results of the idealized mode-coupling theory for the structural relaxation in suspensions of hard-sphere colloidal particles are presented and discussed with regard to recent light scattering experiments. The structural relaxation becomes non-diffusive for long times, contrary to the expectation based on the de Gennes narrowing concept. A semi-quantitative connection of the wave vector dependences of the relaxation times and amplitudes of the final $\alpha$-relaxation explains the approximate scaling observed by Segr{\`e} and Pusey [Phys. Rev. Lett. {\bf 77}, 771 (1996)]. Asymptotic expansions lead to a qualitative understanding of density dependences in generalized Stokes-Einstein relations. This relation is also generalized to non-zero frequencies thereby yielding support for a reasoning by Mason and Weitz [Phys. Rev. Lett {\bf 74}, 1250 (1995)]. The dynamics transient to the structural relaxation is discussed with models incorporating short-time diffusion and hydrodynamic interactions for short times.Comment: 11 pages, 9 figures; to be published in Phys. Rev.

Chrysolina herbacea Modulates Terpenoid Biosynthesis of Mentha aquatica L.

Interactions between herbivorous insects and plants storing terpenoids are poorly understood. This study describes the ability of Chrysolina herbacea to use volatiles emitted by undamaged Mentha aquatica plants as attractants and the plant's response to herbivory, which involves the production of deterrent molecules. Emitted plant volatiles were analyzed by GC-MS. The insect's response to plant volatiles was tested by Y-tube olfactometer bioassays. Total RNA was extracted from control plants, mechanically damaged leaves, and leaves damaged by herbivores. The terpenoid quantitative gene expressions (qPCR) were then assayed. Upon herbivory, M. aquatica synthesizes and emits (+)-menthofuran, which acts as a deterrent to C. herbacea. Herbivory was found to up-regulate the expression of genes involved in terpenoid biosynthesis. The increased emission of (+)-menthofuran was correlated with the upregulation of (+)-menthofuran synthase

Diffusion in crowded biological environments: applications of Brownian dynamics

Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mgml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions

Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page

Utjecaj uvjeta uzgoja i dodatka soli na sastav eteričnog ulja slatkog mažurana (Origanum majorana) iz Tunisa

O. majorana shoots were investigated for their essential oil (EO) composition. Two experiments were carried out; the first on hydroponic medium in a culture chamber and the second on inert sand in a greenhouse for 20 days. Plants were cultivated for 17 days in hydroponic medium supplemented with NaCl 100 mmol L1. The results showed that the O. majorana hydroponic medium offered higher essential oil yield than that from the greenhouse. The latter increased significantly in yield (by 50 %) under saline constraint while it did not change in the culture chamber. Under greenhouse conditions and in the absence of salt treatment, the major constituents were terpinene-4-ol and trans-sabinene hydrate. However, in the culture chamber, the major volatile components were cis-sabinene hydrate and terpinene-4-ol. In the presence of NaCl, new compounds appeared, such as eicosane, spathulenol, eugenol, and phenol. In addition, in the greenhouse, with or without salt, a very important change of trans-sabinene hydrate concentration in EO occurred, whereas in the culture chamber change appeared in cis-sabinene hydrate content.U radu je opisano ispitivanje sastava eteričnog ulja izdanaka biljke O. majorana. Provedena su dva eksperimenta: prvi na hidroponom mediju u komorama za uzgoj, a drugi na inertnom pijesku u stakleniku tijekom 20 dana. Biljke su uzgajane 17 dana u hidroponom mediju u koji je dodan NaCl 100 mmol L1. Rezultati ukazuju na to da hidroponi medij O. majorana osigurava veće prinose eteričnog ulja nego staklenik. U stakleniku se prinos ulja značajno povećao dodavanjem 50 % soli dok u uzgoju u uzgojnoj komori nije bilo promjene. U uvjetima u stakleniku i u odsutnosti soli, najvažniji sastojci ulja bili su terpinen-4-ol i trans-sabinen hidrat, dok su u uvjetima uzgojne komore najvažnije hlapljive komponente bile cis-sabinen hidrat i terpinen-4-ol. U prisutnosti NaCl-a, pojavili su se novi sastojci, kao što su eikozan, spatulenol, eugenol i fenol. Dodatno je uz stakleničke uvjete, sa i bez soli, došlo do važne promjene u količini trans-sabinen hidrata u eteričnom ulju, dok se u komorama promijenio sadržaj cis-sabinen hidrata

Increased Terpenoid Accumulation in Cotton (Gossypium hirsutum) Foliage is a General Wound Response

The subepidermal pigment glands of cotton accumulate a variety of terpenoid products, including monoterpenes, sesquiterpenes, and terpenoid aldehydes that can act as feeding deterrents against a number of insect herbivore species. We compared the effect of herbivory by Spodoptera littoralis caterpillars, mechanical damage by a fabric pattern wheel, and the application of jasmonic acid on levels of the major representatives of the three structural classes of terpenoids in the leaf foliage of 4-week-old Gossypium hirsutum plants. Terpenoid levels increased successively from control to mechanical damage, herbivory, and jasmonic acid treatments, with E-β-ocimene and heliocide H1 and H4 showing the highest increases, up to 15-fold. Herbivory or mechanical damage to older leaves led to terpenoid increases in younger leaves. Leaf-by-leaf analysis of terpenes and gland density revealed that higher levels of terpenoids were achieved by two mechanisms: (1) increased filling of existing glands with terpenoids and (2) the production of additional glands, which were found to be dependent on damage intensity. As the relative response of individual terpenoids did not differ substantially among herbivore, mechanical damage, and jasmonic acid treatments, the induction of terpenoids in cotton foliage appears to represent a non-specific wound response mediated by jasmonic acid

Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package

<p>Abstract</p> <p>Background</p> <p>Brownian Dynamics (BD) is a coarse-grained implicit-solvent simulation method that is routinely used to investigate binary protein association dynamics, but due to its efficiency in handling large simulation volumes and particle numbers it is well suited to also describe many-protein scenarios as they often occur in biological cells.</p> <p>Results</p> <p>Here we introduce our "brownmove" simulation package which was designed to handle many-particle problems with varying particle numbers and allows for a very flexible definition of rigid and flexible protein and polymer models. Both a Brownian and a Langevin dynamics (LD) propagation scheme can be used and hydrodynamic interactions are treated efficiently with our recently introduced TEA-HI ansatz [Geyer, Winter, JCP 130 (2009) 114905]. With simulations of constrained polymers and flexible models of spherical proteins we demonstrate that it is crucial to include hydrodynamics when multi-bead models are used in BD or LD simulations. Only then both the translational and the rotational diffusion coefficients and the timescales of the internal dynamics can be reproduced correctly. In the third example project we show how constant density boundary conditions [Geyer et al, JCP 120 (2004) 4573] can be used to set up a non-equilibrium simulation of diffusional transport across an array of fixed obstacles. Finally, we demonstrate how the agglomeration dynamics of multiple particles with attractive patches can be analysed conveniently with the help of a dynamic interaction network.</p> <p>Conclusions</p> <p>Combining BD and LD propagation, fast hydrodynamics, a flexible protein model, and interfaces for "open" simulation settings, our freely available "brownmove" simulation package constitutes a new platform for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes.</p