Impact of surface roughness on diffusion of confined fluids

Using event-driven molecular dynamics simulations, we quantify how the self diffusivity of confined hard-sphere fluids depends on the nature of the confining boundaries. We explore systems with featureless confining boundaries that treat particle-boundary collisions in different ways and also various types of physically (i.e., geometrically) rough boundaries. We show that, for moderately dense fluids, the ratio of the self diffusivity of a rough wall system to that of an appropriate smooth-wall reference system is a linear function of the reciprocal wall separation, with the slope depending on the nature of the roughness. We also discuss some simple practical ways to use this information to predict confined hard-sphere fluid behavior in different rough-wall systems

Orientational correlations in confined DNA

We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.Comment: Revised version including supplemental material, 7 pages, 8 figure

Cooperative Origin of Low-Density Domains in Liquid Water

We study the size of clusters formed by water molecules possessing large enough tetrahedrality with respect to their nearest neighbors. Using Monte Carlo simulation of the SPC/E model of water, together with a geometric analysis based on Voronoi tessellation, we find that regions of lower density than the bulk are formed by accretion of molecules into clusters exceeding a minimum size. Clusters are predominantly linear objects and become less compact as they grow until they reach a size beyond which further accretion is not accompanied by a density decrease. The results suggest that the formation of "ice-like" regions in liquid water is cooperative.Comment: 16 pages, 6 figure

Quantitative Imaging of B1 Cyclin Expression Across the Cell Cycle Using Green Fluorescent Protein Tagging and Epifluorescence

In this article, we report the number of cyclin B1 proteins tagged with enhanced green fluorescent protein (eGFP) in fixed U‐2 OS cells across the cell cycle. We use a quantitative analysis of epifluorescence to determine the number of eGFP molecules in a nondestructive way, and integrated over the cell we find 104 to 105 molecules. Based on the measured number of eGFP tagged cyclin B1 proteins, knowledge of cyclin B1 dynamics through the cell cycle, and the cell morphology, we identify the stages of cells in the cell cycle

Relationship between Structure, Entropy and Diffusivity in Water and Water-like Liquids

Anomalous behaviour of the excess entropy ($S_e$) and the associated scaling relationship with diffusivity are compared in liquids with very different underlying interactions but similar water-like anomalies: water (SPC/E and TIP3P models), tetrahedral ionic melts (SiO$_2$ and BeF$_2$) and a fluid with core-softened, two-scale ramp (2SRP) interactions. We demonstrate the presence of an excess entropy anomaly in the two water models. Using length and energy scales appropriate for onset of anomalous behaviour, the density range of the excess entropy anomaly is shown to be much narrower in water than in ionic melts or the 2SRP fluid. While the reduced diffusivities ($D^*$) conform to the excess entropy scaling relation, $D^* =A\exp (\alpha S_e)$ for all the systems (Y. Rosenfeld, Phys. Rev. A {\bf 1977}, {\it 15}, 2545), the exponential scaling parameter, $\alpha$, shows a small isochore-dependence in the case of water. Replacing $S_e$ by pair correlation-based approximants accentuates the isochore-dependence of the diffusivity scaling. Isochores with similar diffusivity scaling parameters are shown to have the temperature dependence of the corresponding entropic contribution. The relationship between diffusivity, excess entropy and pair correlation approximants to the excess entropy are very similar in all the tetrahedral liquids.Comment: 24 pages, 4 figures, to be published in Journal of Physical Chemistry

Chemical Constituents from Bombacopsis glabra (Pasq.) A. Robyns: Complete ¹H and 13C NMR Assignments and X Ray Structure of 5-Hydroxy-3,6,7,8,4'-pentamethoxyflavone

The flavone 5-hydroxy-3,6,7,8,4'-pentamethoxyflavone (1) and the triterpenes lupenone, 9,19-cyclolanost-23-ene-3beta,25-diol (2), (24R)-9,19-cyclolanost-25-ene-3beta,24-diol (3) and (24S)-9,19-cyclolanost-25-ene-3beta,24-diol (4) were isolated from the hexane extract of the stem bark of Bombacopsis glabra (Bombacaceae). The structures were determined by 13C and ¹H NMR (1D and 2D) and mass spectrometry, and by comparison with literature data for triterpenes. The structure of the flavone 1 was unambiguously confirmed by a X-ray diffraction study. The five substances were isolated for the first time from Bombacaceae species

Enhancing the immunogenicity of tumour lysate-loaded dendritic cell vaccines by conjugation to virus-like particles

BACKGROUND: Tumour cell lysates are an excellent source of many defined and undefined tumour antigens and have been used clinically in immunotherapeutic regimes but with limited success. METHODS: We conjugated Mel888 melanoma lysates to rabbit haemorrhagic disease virus virus-like particles (VLP), which can act as vehicles to deliver multiple tumour epitopes to dendritic cells (DC) to effectively activate antitumour responses. RESULTS: Virus-like particles did not stimulate the phenotypic maturation of DC although, the conjugation of lysates to VLP (VLP-lysate) did overcome lysate-induced suppression of DC activation. Lysate-conjugated VLP enhanced delivery of antigenic proteins to DC, while the co-delivery of VLP-lysates with OK432 resulted in cross-priming of naïve T cells, with expansion of a MART1(+) population of CD8(+) T cells and generation of a specific cytotoxic response against Mel888 tumour cell targets. The responses generated with VLP-lysate and OK432 were superior to those stimulated by unconjugated lysate with OK432. CONCLUSION: Collectively, these results show that the combination of VLP-lysate with OK432 delivered to DC overcomes the suppressive effects of lysates, and enables priming of naïve T cells with superior ability to specifically kill their target tumour cells

A large-scale experiment to evaluate control of invasive muskrats

The muskrat (Ondatra zibethicus) is an invasive species in Europe. The extensive waterways of the Netherlands provide ideal habitat for muskrats, and a large population established itself after arrival in 1941. A control program was put into effect immediately because muskrat burrowing can compromise the integrity of dikes and, hence, poses a significant public safety risk. The current (2015) annual catch of approximately 89,000 individuals is equivalent to approximately 0.30 muskrats/km of waterway, well above the national objective in spite of decades of effort. The control program is expensive (€35 M annually) and contested by animal rights groups. These factors created the need for a careful evaluation of the full range of control possibilities, from ‘no control’ to ‘extermination.’ As part of this, we experimentally evaluated the validity of a previously published correlation (based on historical data) between catch and effort. We raised or lowered removal effort (2013–2016) in a stratified random sample of 117 5-km × 5-km ‘atlas squares’ from the national grid. We found that catch-per-unit effort (CPUE) decreased after effort was increased, and rose after effort was decreased, by amounts slightly greater than expected based on the correlational data, though confidence intervals enclose zero. As anticipated, CPUE varied consistently and strongly between seasons. The biggest (and unanticipated) effects were those of the catch in the preceding 3 years (‘history’), and surrounding area (‘neighborhood’). Our experiment confirms estimates of intensity of control required to lower muskrat populations. These results will help with more effective allocation of control effort, and better-informed evaluation of the economic costs of various control options

Thermodynamic Behavior of a Model Covalent Material Described by the Environment-Dependent Interatomic Potential

Using molecular dynamics simulations we study the thermodynamic behavior of a single-component covalent material described by the recently proposed Environment-Dependent Interatomic Potential (EDIP). The parameterization of EDIP for silicon exhibits a range of unusual properties typically found in more complex materials, such as the existence of two structurally distinct disordered phases, a density decrease upon melting of the low-temperature amorphous phase, and negative thermal expansion coefficients for both the crystal (at high temperatures) and the amorphous phase (at all temperatures). Structural differences between the two disordered phases also lead to a first-order transition between them, which suggests the existence of a second critical point, as is believed to exist for amorphous forms of frozen water. For EDIP-Si, however, the unusual behavior is associated not only with the open nature of tetrahedral bonding but also with a competition between four-fold (covalent) and five-fold (metallic) coordination. The unusual behavior of the model and its unique ability to simulation the liquid/amorphous transition on molecular-dynamics time scales make it a suitable prototype for fundamental studies of anomalous thermodynamics in disordeered systems.Comment: 48 pages (double-spaced), 13 figure

Expression of divIB of Bacillus subtilis during vegetative growth

Expression of the division initiation gene, divIB, of Bacillus subtilis vegetative growth was examined. lacZ fusion studies and transcription start point mapping have established that a sigma A promoter proximal to divIB is utilized in vivo. The -10 region of this promoter, which is located 93 bp upstream of the start codon, has been defined precisely by site-directed mutagenesis that destroys the promoter. Examination of transcripts by Northern (RNA) blotting has shown that there are at least two transcripts for divIB. The established proximal promoter was found to give rise to a very minor transcript which could not be convincingly demonstrated in wild-type cells but which became apparent upon insertion of a plasmid into the chromosome just upstream of this promoter. The major transcript for divIB originated from a site several kb upstream of the gene and is probably the same as the long polycistronic message also traversing the murD-spoVE-murG genes that was identified previously by others (A.D. Henriques, H. de Lencastre, and P.J. Piggot, Biochimie 74:735-748, 1992). Transcription from the proximal promoter alone, in an upstream-deletion mutant strain, provided sufficient DivIB for normal growth and division as well as sporulation