Lattice Boltzmann simulations of drying suspensions of soft particles.

The ordering of particles in the drying process of a colloidal suspension is crucial in determining the properties of the resulting film. For example, microscopic inhomogeneities can lead to the formation of cracks and defects that can deteriorate the quality of the film considerably. This type of problem is inherently multiscale and here we study it numerically, using our recently developed method for the simulation of soft polymeric capsules in multicomponent fluids. We focus on the effect of the particle softness on the film microstructure during the drying phase and how it relates to the formation of defects. We quantify the order of the particles by measuring both the Voronoi entropy and the isotropic order parameter. Surprisingly, both observables exhibit a non-monotonic behaviour when the softness of the particles is increased. We further investigate the correlation between the interparticle interaction and the change in the microstructure during the evaporation phase. We observe that the rigid particles form chain-like structures that tend to scatter into small clusters when the particle softness is increased. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.

The importance of chemical potential in the determination of water slip in nanochannels.

We investigate the slip properties of water confined in graphite-like nanochannels by non-equilibrium molecular dynamics simulations, with the aim of identifying and analyze separately the influence of different physical quantities on the slip length. In a system under confinement but connected to a reservoir of fluid, the chemical potential is the natural control parameter: we show that two nanochannels characterized by the same macroscopic contact angle--but a different microscopic surface potential--do not exhibit the same slip length unless the chemical potential of water in the two channels is matched. Some methodological issues related to the preparation of samples for the comparative analysis in confined geometries are also discussed.

Dielectric and terahertz spectroscopy of polarizable and nonpolarizable water models: a comparative study.

Using extensive classical molecular dynamics simulations, we compute the dielectric and far-infrared spectra of nine popular water models, including polarizable and nonpolarizable ones. We analyze the dielectric spectra using a two-relaxation model that allows one to extract the characteristic time of both the main dielectric relaxation and the fast relaxation. The use of a Cole-Cole functional form permits also quantitative assessment of the absence of deviations from the Debye form of the main dielectric peak. In the THz region of the spectrum, we compute the infrared absorbance caused by molecular libration, which appears to be qualitatively different for three main groups of molecular models. The complexity of the librational band is further investigated by decomposing the spectrum into the contributions of water fractions with a different number of hydrogen-bonded neighbors.

Population ecology of heterotypic tumour cell cultures.

OBJECTIVES: Here, we propose a population ecology perspective to describe dynamic interplay between human leukaemia and cervical cancer cells growing together in the same environment. MATERIALS AND METHODS: MOLT-3 (human T-lymphoblastic leukaemia) and HeLa (human cervical adenocarcinoma) cells were grown together or alone. Living cells were measured using flow cytometry, by counting propidium iodide-negative cells either CD5(+) (MOLT-3) or CD55(+) (HeLa). We developed a mathematical model to take into account possible interactions between cells and among cells and their environmental niches. Model equations were then fitted to growth data. RESULTS: Ecological interactions that require direct cell contact and indirect mechanisms acting on cell niches, successfully modelled cell population growth. Predicted heterotypic adhesion between the two different cell types was demonstrated experimentally. CONCLUSIONS: Theoretical ecology can be assayed using human cells and, most importantly, it can provide a conceptual framework to describe and understand evolution of mixed tumour cell populations.

Communication: Kinetic and pairing contributions in the dielectric spectra of electrolyte solutions.

In the late 1970s, Hubbard and Onsager predicted that adding salt to a polar solution would result in a reduced dielectric permittivity that arises from the unexpected tendency of solvent dipoles to align opposite to the applied field. Here we develop a novel non-equilibrium molecular dynamics simulation approach to determine this decrement accurately. Using a thermodynamic consistent all-atom force field we show that for an aqueous solution containing sodium chloride around 4.8 mol/l, this effect accounts for 12% of the total dielectric permittivity. The dielectric decrement can be strikingly different if a less accurate force field for the ions is used. Using the widespread GROMOS parameters, we observe in fact an increment of the dielectric permittivity rather than a decrement, caused by ion pairing and introduced by a too low dispersion force.

Metabolic scaling in solid tumours.

Tumour metabolism is an outstanding topic of cancer research, as it determines the growth rate and the global activity of tumours. Recently, by combining the diffusion of oxygen, nutrients, and metabolites in the extracellular environment, and the internal motions that mix live and dead cells, we derived a growth law of solid tumours which is linked to parameters at the cellular level. Here we use this growth law to obtain a metabolic scaling law for solid tumours, which is obeyed by tumours of different histotypes both in vitro and in vivo, and we display its relation with the fractal dimension of the distribution of live cells in the tumour mass. The scaling behaviour is related to measurable parameters, with potential applications in the clinical practice.

Production and characterisation of monoclonal antibodies for the quantification of potentially allergenic xylanase from Aspergillus niger.

Xylanase from Aspergillus niger (ANX) is widely used in bakeries as a processing aid since it stabilises and improves dough quality. An association between allergic symptoms among bakery workers and sensitisation to ANX has been reported, indicating that this enzyme is an occupational allergen. The presence of ANX in dough improvers and semi-finished goods is often hidden due to incomplete and unclear labelling. The quantification of microbial enzymes in these products is necessary and the determination of the actual concentration of ANX in workplaces is therefore essential to assess the occupational risk. To this purpose we have developed and characterised monoclonal antibodies to ANX. The monoclonal antibodies do not show any cross-reaction with other commonly used microbial enzymes, and they allow the detection of ANX in complex mixtures by ELISA inhibition assays down to the concentration limit of approximately 10 µg kg(-1). These mAbs are a valuable tool to detect and quantify ANX and to investigate its allergenic potential in the workplace.

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation.

We present the results of a combined metadynamics-umbrella sampling investigation of the puckered conformers of pyranoses described using the GROMOS 45a4 force field. The free energy landscape of Cremer-Pople puckering coordinates has been calculated for the whole series of α and ß aldohexoses, showing that the current force field parameters fail in reproducing proper puckering free energy differences between chair conformers. We suggest a modification to the GROMOS 45a4 parameter set which improves considerably the agreement of simulation results with theoretical and experimental estimates of puckering free energies. We also report on the experimental measurement of altrose conformer populations by means of NMR spectroscopy, which show good agreement with the predictions of current theoretical models.

Ensemble inequivalence in single-molecule experiments.

In bulk systems the calculation of the main thermodynamic quantities leads to the same expectation values in the thermodynamic limit, regardless of the choice of the statistical ensemble. Single linear molecules can be still regarded as statistical systems, where the thermodynamic limit is represented by infinitely long chains. The question of equivalence between different ensembles is not at all obvious and has been addressed in the literature, with sometimes contradicting conclusions. We address this problem by studying the scaling properties of the ensemble difference for two different chain models as a function of the degree of polymerization. By characterizing the scaling behavior of the difference between the isotensional (Gibbs) and isometric (Helmholtz) ensembles in the transition from the low-stretching to the high-stretching regime, we show that ensemble equivalence cannot be reached for macroscopic chains in the low force regime, and we characterize the transition from the inequivalence to the equivalence regime.

On the calculation of puckering free energy surfaces.

Cremer-Pople puckering coordinates appear to be the natural candidate variables to explore the conformational space of cyclic compounds and in literature different parametrizations have been used to this end. However, while every parametrization is equivalent in identifying conformations, it is not obvious that they can also act as proper collective variables for the exploration of the puckered conformations free energy surface. It is shown that only the polar parametrization is fit to produce an unbiased estimate of the free energy landscape. As an example, the case of a six-membered ring, glucuronic acid, is presented, showing the artifacts that are generated when a wrong parametrization is used.

Dominant reaction pathways in high-dimensional systems.

This paper is devoted to the development of a theoretical and computational framework denominated dominant reaction pathways (DRPs) to efficiently sample the statistically significant thermally activated reaction pathways, in multidimensional systems. The DRP approach is consistently derived from the Langevin equation through a systematic expansion in the thermal energy, k(B)T. Its main advantage with respect to existing simulation techniques is that it provides a natural and rigorous framework to perform the path sampling using constant displacement steps, rather than constant time steps. In our previous work, we have shown how to obtain the set of most probable reaction pathways, i.e., the lowest order in the k(B)T expansion. In this work, we show how to compute the corrections to the leading order due to stochastic fluctuations around the most probable trajectories. We also discuss how to obtain predictions for the evolution of arbitrary observables and how to generate conformations, which are representative of the transition state ensemble. We illustrate how our method works in practice by studying the diffusion of a point particle in a two-dimensional funneled external potential.

Aqueous extract of Arbutus unedo inhibits STAT1 activation in human breast cancer cell line MDA-MB-231 and human fibroblasts through SHP2 activation.

Arbutus unedo L. has been for a long time employed in traditional and popular medicine as an astringent, diuretic, urinary anti-septic, and more recently, in the therapy of hypertension and diabetes. Signal transducer and activator of transcription 1 (STAT1) is a fascinating and complex protein with multiple yet contrasting transcriptional functions. Although activation of this nuclear factor is finely regulated in order to control the entire inflammatory process, its hyper-activation or time-spatially erroneous activation may lead to exacerbation of inflammation. The modulation of this nuclear factor, therefore, has recently been considered as a new strategy in the treatment of inflammatory diseases. In this study, we present data showing that the aqueous extract of Arbutus unedo's leaves exerts inhibitory action on interferon-gamma (IFN-gamma) elicited activation of STAT1, both in human breast cancer cell line MDA-MB-231 and in human fibroblasts. This down-regulation of STAT1 is shown to result from a reduced tyrosine phosphorylation of STAT1 protein. Evidence is also presented indicating that the inhibitory effect of this extract may be mediated through enhancement of tyrosine phosphorylation of SHP2 tyrosine phosphatase. The modulation of this nuclear factor turns out into the regulation of the expression of a number of genes involved in the inflammatory response such as inducible nitric oxide synthase (iNOS) and intercellular adhesion molecule-1 (ICAM-1). Taken together, our results suggest that the employment of the Arbutus unedo aqueous extract is promising, at least, as an auxiliary anti-inflammatory treatment of diseases in which STAT1 plays a critical role.

Quantitative protein dynamics from dominant folding pathways.

We develop a theoretical approach to the protein-folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps are removed, and simulating the entire reaction in atomistic details using existing computers becomes feasible. We discuss how to determine the most probable folding pathway, identify configurations representative of the transition state, and compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine dipeptide, within an all-atom model based on the empiric GROMOS96 force field.

Inhomogeneity effects on the structure and dynamics of water at the surface of a membrane: a computer simulation study.

The authors report the structural and dynamical properties of water interacting with the surface of a lipid bilayer. Three regions have been identified, which show different dynamical regimes of water: a region of strong water-solute interaction, a transition region, and the bulk water region. The dynamics of the strong-interacting water is dominated by caging effects, as shown by the analysis of the self-intermediate scattering function, and by the disrupture of water's hydrogen bond network, while the smooth transition to bulk water is traced back to the roughness of the bilayer surface.

Dominant pathways in protein folding.

We present a method to investigate the kinetics of protein folding and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. By writing the solution of the Fokker-Planck equation in terms of a path integral, we derive a Hamilton-Jacobi variational principle from which we are able to compute the most probable pathway of folding. The method is applied to the folding of the Villin headpiece subdomain simulated using a Go model. An initial collapsing phase driven by the initial configuration is followed by a rearrangement phase, in which secondary structures are formed and all computed paths display strong similarities. This completely general method does not require the prior knowledge of any reaction coordinate and is an efficient tool to perform simulations of the entire folding process with available computers.

Dark cells in human oral leukoplakias.

Dark basal keratinocytes, characterized by a strong affinity for basic dyes and by electron density of cytoplasm and nucleus, could be recognized in eleven oral leukoplakias. The percentage of dark cells was higher in the group comprising leukoplakias verrucosa, and erosiva (28% of the basal cells) than in the leukoplakia simplex group (10%). The presence of these cells is a good indicator of the degree of histological dysplasia and correlates well with the preneoplastic potential of these lesions.

Hyperkeratinization and hyperplasia of the forestomach epithelium in vitamin A deficient rats.

Specific pathogen free F-344 rats were kept on a vitamin A deficient diet for 3-5 months. After 3 months on this diet the forestomach epithelium showed a mild atrophy. Stereological cytology showed a marked increase in the volume density of cytoplasmic filament bundles and decrease in the volume density of non-bundled cytoplasmic filaments. The volume fraction of keratohyalin granules increased whereas the volume fraction of membrane coating granules decreased. Some animals maintained for 4-5 months on the hypovitaminic diet exhibited the same mild atrophic forestomach epithelium accompanied by hyperkeratinization. Others showed a marked epithelial atrophy and 4 out of 12 animals revealed a marked hyperplasia with increased 3H thymidine labeling index and several papillomatous proliferations. Although many of these alterations reflect a decrease in proliferation as well as hyperkeratinization, the latter changes were not unlike those produced by known carcinogens, and support the putative important role of vitamin A in both carcinogenesis and chemoprevention.

Rapid screening for chemical carcinogens: transforming activity of selected nitroso compounds detected in a transplacental host-mediated culture system.

The transplacental host-mediated hamster cell culture system was used to test a variety of solvents and chemicals of unknown and known (positive and negative) activity for their ability to induce morphologic transformation of cells and growth in agar. Examination of approximately 13,000 colonies of cells from untreated animals yielded no transformants, thus demonstrating no spontaneous transformation in the system. Similar negative results were obtained after animals were treated with the solvents acetone, ethanol, dimethyl sulfoxide, dimethylformamide, and trioctanoin oil. Several known carcinogens, including benzo[a]pyrene, methylnitrosourethane, urethan, and diethylnitrosamine, were positive for transforming activity. Three pesticides, carbaryl, methomyl, and landrin, and their N-nitroso derivatives were tested. All the nitrosated forms had transforming activity, but only one of the pesticides, landrin, was positive. In all experiments conducted, results of the agar-growth test correlated well with tests for morphologic transformation. The transplacental hamster embryol cell culture system therefore detected transforming activity of N-nitroso compounds and some known carcinogens.