Interplay between elastic fields due to gravity and a partial dislocation for a hard-sphere crystal coherently grown under gravity: driving force for defect disappearance

We previously observed that an intrinsic staking fault shrunk through a glide of a Shockley partial dislocation terminating its lower end in a hard-sphere crystal under gravity coherently grown in by Monte Carlo simulations [Mori et al., Molec. Phys. 105, 1377 (2007)]; it was an answer to a one-decade long standing question why the stacking disorder in colloidal crystals reduced under gravity [Zhu et al., Nature 387, 883 (1997)]. Here, we present an elastic energy calculation; in addition to the self-energy of the partial dislocation [Mori et al., Prog. Theor. Phys. Suppl. 178, 33 (2009)] we calculate the cross-coupling term between elastic field due to gravity and that due to a Shockley partial dislocation. The cross term is a increasing function of the linear dimension R over which the elastic field expands, showing that a driving force arises for the partial dislocation moving toward the upper boundary of a grain.Comment: 8pages, 4figures, to be published in Molecular Physic

How simple can a model of an empty viral capsid be? Charge distributions in viral capsids

We investigate and quantify salient features of the charge distributions on viral capsids. Our analysis combines the experimentally determined capsid geometry with simple models for ionization of amino acids, thus yielding the detailed description of spatial distribution for positive and negative charge across the capsid wall. The obtained data is processed in order to extract the mean radii of distributions, surface charge densities and dipole moment densities. The results are evaluated and examined in light of previously proposed models of capsid charge distributions, which are shown to have to some extent limited value when applied to real viruses.Comment: 10 pages, 10 figures; accepted for publication in Journal of Biological Physic

Direct entropy determination and application to artificial spin ice

From thermodynamic origins, the concept of entropy has expanded to a range of statistical measures of uncertainty, which may still be thermodynamically significant. However, laboratory measurements of entropy continue to rely on direct measurements of heat. New technologies that can map out myriads of microscopic degrees of freedom suggest direct determination of configurational entropy by counting in systems where it is thermodynamically inaccessible, such as granular and colloidal materials, proteins and lithographically fabricated nanometre-scale arrays. Here, we demonstrate a conditional-probability technique to calculate entropy densities of translation-invariant states on lattices using limited configuration data on small clusters, and apply it to arrays of interacting nanometre-scale magnetic islands (artificial spin ice). Models for statistically disordered systems can be assessed by applying the method to relative entropy densities. For artificial spin ice, this analysis shows that nearest-neighbour correlations drive longer-range ones.Comment: 10 page

Three-dimensional jamming and flows of soft glassy materials

Various disordered dense systems such as foams, gels, emulsions and colloidal suspensions, exhibit a jamming transition from a liquid state (they flow) to a solid state below a yield stress. Their structure, thoroughly studied with powerful means of 3D characterization, exhibits some analogy with that of glasses which led to call them soft glassy materials. However, despite its importance for geophysical and industrial applications, their rheological behavior, and its microscopic origin, is still poorly known, in particular because of its nonlinear nature. Here we show from two original experiments that a simple 3D continuum description of the behaviour of soft glassy materials can be built. We first show that when a flow is imposed in some direction there is no yield resistance to a secondary flow: these systems are always unjammed simultaneously in all directions of space. The 3D jamming criterion appears to be the plasticity criterion encountered in most solids. We also find that they behave as simple liquids in the direction orthogonal to that of the main flow; their viscosity is inversely proportional to the main flow shear rate, as a signature of shear-induced structural relaxation, in close similarity with the structural relaxations driven by temperature and density in other glassy systems.Comment: http://www.nature.com/nmat/journal/v9/n2/abs/nmat2615.htm

Measuring every particle's size from three-dimensional imaging experiments

Often experimentalists study colloidal suspensions that are nominally monodisperse. In reality these samples have a polydispersity of 4-10%. At the level of an individual particle, the consequences of this polydispersity are unknown as it is difficult to measure an individual particle size from microscopy. We propose a general method to estimate individual particle radii within a moderately concentrated colloidal suspension observed with confocal microscopy. We confirm the validity of our method by numerical simulations of four major systems: random close packing, colloidal gels, nominally monodisperse dense samples, and nominally binary dense samples. We then apply our method to experimental data, and demonstrate the utility of this method with results from four case studies. In the first, we demonstrate that we can recover the full particle size distribution {\it in situ}. In the second, we show that accounting for particle size leads to more accurate structural information in a random close packed sample. In the third, we show that crystal nucleation occurs in locally monodisperse regions. In the fourth, we show that particle mobility in a dense sample is correlated to the local volume fraction.Comment: 7 pages, 5 figure

Direct imaging of structural disordering and heterogeneous dynamics of fullerene molecular liquid

Structural rearrangements govern the various properties of disordered systems and visualization of these dynamical processes can provide critical information on structural deformation and phase transformation of the systems. However, direct imaging of individual atoms or molecules in a disordered state is quite challenging. Here, we prepare a model molecular system of C70 molecules on graphene and directly visualize the structural and dynamical evolution using aberration-corrected transmission electron microscopy. E-beam irradiation stimulates dynamics of fullerene molecules, which results in the first-order like structural transformation from the molecular crystal to molecular liquid. The real-time tracking of individual molecules using an automatic molecular identification process elucidates the relaxation behavior of a stretched exponential functional form. Moreover, the directly observed heterogeneous dynamics bear similarity to the dynamical heterogeneity in supercooled liquids near the glass transition. Fullerenes on graphene can serve as a new model system, which allows investigation of molecular dynamics in disordered phases

Quantitative imaging of concentrated suspensions under flow

We review recent advances in imaging the flow of concentrated suspensions, focussing on the use of confocal microscopy to obtain time-resolved information on the single-particle level in these systems. After motivating the need for quantitative (confocal) imaging in suspension rheology, we briefly describe the particles, sample environments, microscopy tools and analysis algorithms needed to perform this kind of experiments. The second part of the review focusses on microscopic aspects of the flow of concentrated model hard-sphere-like suspensions, and the relation to non-linear rheological phenomena such as yielding, shear localization, wall slip and shear-induced ordering. Both Brownian and non-Brownian systems will be described. We show how quantitative imaging can improve our understanding of the connection between microscopic dynamics and bulk flow.Comment: Review on imaging hard-sphere suspensions, incl summary of methodology. Submitted for special volume 'High Solid Dispersions' ed. M. Cloitre, Vol. xx of 'Advances and Polymer Science' (Springer, Berlin, 2009); 22 pages, 16 fig

Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition

Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700