1,074 research outputs found
Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. II. Charge separation processes
A new approach to carry out molecular dynamics simulations of chemical reactions in solution using combined density functional theory/molecular mechanics potentials is presented. We focus our attention on the analysis of reactive trajectories, dynamic solvent effects and transmission coefficient rather than on the evaluation of free energy which is another important topic that will be examined elsewhere. In a previous paper we have described the generalities of this hybrid molecular dynamics method and it has been employed to investigate low energy barrier proton transfer process in water. The study of processes with activation energies larger than a few kT requires the use of specific techniques adapted to ârare eventsâ simulations. We describe here a method that consists in the simulation of short trajectories starting from an equilibrated transition state in solution, the structure of which has been approximately established. This calculation is particularly efficient when carried out with parallel computers since the study of a reactive process is decomposed in a set of short time trajectories that are completely independent. The procedure is close to that used by other authors in the context of classical molecular dynamics but present the advantage of describing the chemical system with rigorous quantum mechanical calculations. It is illustrated through the study of the first reaction step in electrophilic bromination of ethylene in water. This elementary process is representative of many charge separation reactions for which static and dynamic solvent effects play a fundamental [email protected]
Forced Stratified Turbulence: Successive Transitions with Reynolds Number
Numerical simulations are made for forced turbulence at a sequence of
increasing values of Reynolds number, R, keeping fixed a strongly stable,
volume-mean density stratification. At smaller values of R, the turbulent
velocity is mainly horizontal, and the momentum balance is approximately
cyclostrophic and hydrostatic. This is a regime dominated by so-called pancake
vortices, with only a weak excitation of internal gravity waves and large
values of the local Richardson number, Ri, everywhere. At higher values of R
there are successive transitions to (a) overturning motions with local
reversals in the density stratification and small or negative values of Ri; (b)
growth of a horizontally uniform vertical shear flow component; and (c) growth
of a large-scale vertical flow component. Throughout these transitions, pancake
vortices continue to dominate the large-scale part of the turbulence, and the
gravity wave component remains weak except at small scales.Comment: 8 pages, 5 figures (submitted to Phys. Rev. E
Alternative splicing modifies the effect of mutations in COL11A1 and results in recessive type 2 Stickler syndrome with profound hearing loss.
BACKGROUND: Stickler syndromes types 1, 2 and 3 are usually dominant disorders caused by mutations in the genes COL2A1, COL11A1 and COL11A2 that encode the fibrillar collagens types II and XI present in cartilage and vitreous. Rare recessive forms of Stickler syndrome exist that are due to mutations in genes encoding type IX collagen (COL9A1 type 4 Stickler syndrome and COL9A2 type 5 Stickler syndrome). Recently, recessive mutations in the COL11A1 gene have been demonstrated to result in fibrochondrogenesis, a much more severe skeletal dysplasia, which is often lethal. Here we demonstrate that some mutations in COL11A1 are recessive, modified by alternative splicing and result in type 2 Stickler syndrome rather than fibrochondrogenesis. METHODS: Patients referred to the national Stickler syndrome diagnostic service for England, UK were assessed clinically and subsequently sequenced for mutations in COL11A1. Additional in silico and functional studies to assess the effect of sequence variants on pre-mRNA processing and collagen structure were performed. RESULTS: In three different families, heterozygous COL11A1 biallelic null, null/missense or silent/missense mutations, were found. They resulted in a recessive form of type 2 Stickler syndrome characterised by particularly profound hearing loss and are clinically distinct from the recessive types 4 and 5 variants of Stickler syndrome. One mutant allele in each family is capable of synthesising a normal α1(XI) procollagen molecule, via variable pre-mRNA processing. CONCLUSION: This new variant has important implications for molecular diagnosis and counselling families with type 2 Stickler syndrome
Development Studies Working Paper, no. 13
In Ciskei, the development of urban housing and local authority structures has not been able to keep up with this immigration. As a result, a number of communities have sprung up in the tribal Authority areas close to this conurbation of some half a million people. These communities are neither urban nor rural, and comprise people with rural farmworker backgrounds who obtain their main source of income from employment in urban areas. In contradistinction to their true rural cousins, the breadwinners in these communities do not need to become migrants living and working far from home. Rather, they work during the week in an urban location close to home, and return on weekends to their families and children. This volume reports on one such community. The settlement of Tsweletswele is new, situated in a Tribal area, and within thirty kilometres of East London. Its residents who came from farms in the region work in East London. Their level of living is low, their access to state services minimal, and their tenure in the settlement uncertain. This report aims quite simply to establish what strategies these people choose to survive in their settlement. Subsequently, a set of recommendations are made which are aimed at improving the levels of living in the community, the delivery of essential services, and the tenure arrangements in the settlementDigitised by Rhodes University Library on behalf of the Institute of Social and Economic Research (ISER
Amelogenin Nanoparticles in Suspension: Deviations from Spherical Shape and pH-Dependent Aggregation
It is well-known that amelogenin self-assembles to form nanoparticles, usually referred to as amelogenin nanospheres, despite the fact that not much is known about their actual shape in solution. In the current paper, we combine SAXS and DLS to study the three-dimensional shape of the recombinant amelogenins rP172 and rM179. Our results show for the first time that amelogenins build oblate nanoparticles in suspension using experimental approaches that do not require the proteins to be in contact with a support material surface. The SAXS studies give evidence for the existence of isolated amelogenin nano-oblates with aspect ratios in the range of 0.45-0.5 at pH values higher than pH 7.2 and show an aggregation of these nano-oblates at lower pH values. The role of the observed oblate shape in the formation of chain-like structures at physiological conditions is discussed as a key factor in the biomineralization of dental enamel
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 of up to 0.20 and dimensionless dipolar interaction
parameters 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 , for wavevectors close to the peak of
the static structure factor , 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 ) 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 ; hydrodynamic interactions
slow the formation rate, again by a factor of roughly two
The New âHidden Abodeâ: Reflections on Value and Labour in the New Economy
In a pivotal section of Capital, volume 1, Marx (1976: 279) notes that, in order to understand the capitalist production of value, we must descend into the âhidden abode of productionâ: the site of the labour process conducted within an employment relationship. In this paper we argue that by remaining wedded to an analysis of labour that is confined to the employment relationship, Labour Process Theory (LPT) has missed a fundamental shift in the location of value production in contemporary capitalism. We examine this shift through the work of Autonomist Marxists like Hardt and Negri, Lazaratto and Arvidsson, who offer theoretical leverage to prize open a new âhidden abodeâ outside employment, for example in the âproduction of organizationâ and in consumption. Although they can open up this new âhidden abodeâ, without LPT's fine-grained analysis of control/resistance, indeterminacy and structured antagonism, these theorists risk succumbing to empirically naive claims about the ânew economyâ. Through developing an expanded conception of a ânew hidden abodeâ of production, the paper demarcates an analytical space in which both LPT and Autonomist Marxism can expand and develop their understanding of labour and value production in today's economy. </jats:p
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