Electrophoresis simulated with the cage model for reptation

The cage model for polymer reptation is extended to simulate DC electrophoresis. The drift velocity v of a polymer with length L in an electric field with strength E shows three different regions: if the strength of field is small, the drift velocity scales as E/L; for slightly larger strengths, it scales as E^2, independent of length; for high fields, but still E much smaller than 1, the drift velocity decreases exponentially to zero. The behaviour of the first two regions are in agreement with earlier reports on simulations of the Duke-Rubinstein model and with experimental work on DNA polymers in agarose gel.Comment: 14 pages, 9 pictures, 2 table

Evaluation of the Diurnal Cycle in the Atmospheric Boundary Layer Over Land as Represented by a Variety of Single-Column Models: The Second GABLS Experiment

We present the main results from the second model intercomparison within the GEWEX (Global Energy andWater cycle EXperiment) Atmospheric Boundary Layer Study (GABLS). The target is to examine the diurnal cycle over land in today’s numerical weather prediction and climate models for operational and research purposes. The set-up of the case is based on observations taken during the Cooperative Atmosphere-Surface Exchange Study-1999 (CASES-99), which was held in Kansas, USA in the early autumn with a strong diurnal cycle with no clouds present. The models are forced with a constant geostrophic wind, prescribed surface temperature and large-scale divergence. Results from 30 different model simulations and one large-eddy simulation (LES) are analyzed and compared with observations. Even though the surface temperature is prescribed, the models give variable near-surface air temperatures. This, in turn, gives rise to differences in low-level stability affecting the turbulence and the turbulent heat fluxes. The increase in modelled upward sensible heat flux during the morning transition is typically too weak and the growth of the convective boundary layer before noon is too slow. This is related to weak modelled nearsurface winds during the morning hours. The agreement between the models, the LES and observations is the best during the late afternoon. From this intercomparison study, we find that modelling the diurnal cycle is still a big challenge. For the convective part of the diurnal cycle, some of the first-order schemes perform somewhat better while the turbulent kinetic energy (TKE) schemes tend to be slightly better during nighttime conditions. Finer vertical resolution tends to improve results to some extent, but is certainly not the solution to all the deficiencies identifie

Why is it so difficult to represent stably stratified conditions in numerical weather prediction (NWP) models?

In the 1990s, scientists at European Centre for Medium-Range Weather Forecasts (ECMWF) suggested that artificially enhancing turbulent diffusion in stable conditions improves the representation of two important aspects of weather forecasts, i.e., near-surface temperatures and synoptic cyclones. Since then, this practice has often been used for tuning the large-scale performance of operational numerical weather prediction (NWP) models, although it is widely recognized to be detrimental for an accurate representation of stable boundary layers. Here we investigate why, 20 years on, such a compromise is still needed in the ECMWF model. We find that reduced turbulent diffusion in stable conditions improves the representation of winds in stable boundary layers, but it deteriorates the large-scale flow and the near-surface temperatures. This suggests that enhanced diffusion is still needed to compensate for errors caused by other poorly represented processes. Among these, we identify the orographic drag, which influences the large-scale flow in a similar way to the turbulence closure for stable conditions, and the strength of the land-atmosphere coupling, which partially controls the near-surface temperatures. We also take a closer look at the relationship between the turbulence closure in stable conditions and the large-scale flow, which was not investigated in detail with a global NWP model. We demonstrate that the turbulent diffusion in stable conditions affects the large-scale flow by modulating not only the strength of synoptic cyclones and anticyclones, but also the amplitude of the planetary-scale standing waves

Bio-Based Aromatic Polyesters Reversibly Crosslinked via the Diels–Alder Reaction

Diphenolic acid is functionalized with furfuryl amine and subsequently incorporated in a (partly) bio-based polyester through interfacial polycondensation with terepthalic chloride. The furan groups present in the resulting polyester are able to form a thermoreversible covalent network with different bismaleimide moieties via the Diels–Alder (DA) reaction. Our analysis of the polymer network by1H-NMR clearly shows the formation of both possible stereoisomers (endo and exo) from the Diels–Alder coordination of furan and maleimide. Furthermore, it was found that these isomers can be reversibly interchanged at temperatures below the reported retro Diels–Alder reaction temperature, a phenomenon often claimed but, until present, never directly observed, for thermally reversible polymeric systems. Finally, a proof of principle for reversibility and recyclability is shown

The Effect of Molecular Weight on the (Re)-Processability and Material Properties of Bio-Based, Thermoreversibly Cross-Linked Polyesters

A (partially) bio-based short-chain polyester is prepared through interfacial polycondensation of furan-functionalized diphenolic acid with terephthalic chloride. The furan groups along the backbone of the obtained polyester are able to form a covalent network (PE-fur/Bism) with various ratios of 1,1′-(methylenedi-4,1-phenylene)bismaleimide via the thermoreversible Diels–Alder (DA) reaction. Several techniques have been employed to characterize the polyester network, including 1H-NMR, gel permeation chromatography (GPC), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and dynamic mechanical thermal analysis (DMTA). The polyester base polymer displays a glass transition temperature of 115 °C, whereas the temperatures at which the retro-Diels–Alder (rDA) reaction takes place lie above 130 °C for the various polyester/bismaleimide networks. Excellent thermoreversibility and recyclability of the polyester resin have been shown through DSC and DMTA measurements

Exploring strategies for coupled 4D-Var data assimilation using an idealised atmosphere-ocean model

Operational forecasting centres are currently developing data assimilation systems for coupled atmosphere-ocean models. Strongly coupled assimilation, in which a single assimilation system is applied to a coupled model, presents significant technical and scientific challenges. Hence weakly coupled assimilation systems are being developed as a first step, in which the coupled model is used to compare the current state estimate with observations, but corrections to the atmosphere and ocean initial conditions are then calculated independently. In this paper we provide a comprehensive description of the different coupled assimilation methodologies in the context of four dimensional variational assimilation (4D-Var) and use an idealised framework to assess the expected benefits of moving towards coupled data assimilation. We implement an incremental 4D-Var system within an idealised single column atmosphere-ocean model. The system has the capability to run both strongly and weakly coupled assimilations as well as uncoupled atmosphere or ocean only assimilations, thus allowing a systematic comparison of the different strategies for treating the coupled data assimilation problem. We present results from a series of identical twin experiments devised to investigate the behaviour and sensitivities of the different approaches. Overall, our study demonstrates the potential benefits that may be expected from coupled data assimilation. When compared to uncoupled initialisation, coupled assimilation is able to produce more balanced initial analysis fields, thus reducing initialisation shock and its impact on the subsequent forecast. Single observation experiments demonstrate how coupled assimilation systems are able to pass information between the atmosphere and ocean and therefore use near-surface data to greater effect. We show that much of this benefit may also be gained from a weakly coupled assimilation system, but that this can be sensitive to the parameters used in the assimilation

Impacts of orography on large-scale atmospheric circulation

Some of the largest and most persistent circulation errors in global numerical weather prediction and climate models are attributable to the inadequate representation of the impacts of orography on the atmospheric flow. Existing parametrization approaches attempting to account for unresolved orographic processes, such as turbulent form drag, low-level flow blocking or mountain waves, have been successful to some extent. They capture the basic impacts of the unresolved orography on atmospheric circulation in a qualitatively correct way and have led to significant progress in both numerical weather prediction and climate modelling. These approaches, however, have apparent limitations and inadequacies due to poor observational evidence, insufficient fundamental knowledge and an ambiguous separation between resolved and unresolved orographic scales and between different orographic processes. Numerical weather prediction and climate modelling has advanced to a stage where these inadequacies have become critical and hamper progress by limiting predictive skill on a wide range of spatial and temporal scales. More physically-based approaches are needed to quantify the relative importance of apparently disparate orographic processes and to account for their combined effects in a rational and accurate way in numerical models. We argue that, thanks to recent advances, significant progress can be made by combining theoretical approaches with observations, inverse modelling techniques and high-resolution and idealized numerical simulations

Upregulation of Epac-1 in Hepatic Stellate Cells by Prostaglandin E-2 in Liver Fibrosis Is Associated with Reduced Fibrogenesiss

Exchange protein activated by cAMP (Epac-1) is an important signaling mechanism for cAMP-mediated effects, yet factors that change Epac-1 levels are unknown. Such factors are relevant because it has been postulated that Epac-1 directly affects fibrogenesis. Prostaglandin E-2 (PGE(2)) is a well-known cAMP activator, and we therefore studied the effects of this cyclo-oxygenase product on Epac-1 expression and on fibrogenesis within the liver. Liver fibrosis was induced by 8 weeks carbon tetrachloride (CCL4) administration to mice. In the last 2 weeks, mice received vehicle, PGE(2), the cyclo-oxygenase-2 inhibitor niflumic acid (NFA), or PGE(2) coupled to cell-specific carriers to hepatocytes, Kupffer cells, or hepatic stellate cells (HSC). Results showed antifibrotic effects of PGE(2) and profibrotic effects of NFA in CCL4 mice. Western blot analysis revealed reduced Epac-1 protein expression in fibrotic livers of mice and humans compared with healthy livers. PGE(2) administration to fibrotic mice completely restored intrahepatic Epac-1 levels and also led to reduced Rho kinase activity, a downstream target of Epac-1. Cell-specific delivery of PGE(2) to either hepatocytes, Kupffer cells, or HSC identified the latter cell as the key player in the observed effects on Epac-1 and Rho kinase. No significant alterations in protein kinase A expressions were found. In primary isolated HSC, PGE(2) elicited Rap1 translocation reflecting Epac-1 activation, and Epac-1 agonists attenuated platelet-derived growth factor-induced proliferation and migration of these cells. These studies demonstrate that PGE(2) enhances Epac-1 activity in HSC, which is associated with significant changes in (myo)fibroblast activities in vitro and in vivo. Therefore, Epac-1 is a potential target for antifibrotic drugs.</p

Phosphate Groups in the Lipid A Moiety Determine the Effects of LPS on Hepatic Stellate Cells:A Role for LPS-Dephosphorylating Activity in Liver Fibrosis

Alkaline phosphatase (AP) activity is highly upregulated in plasma during liver diseases. Previously, we demonstrated that AP is able to detoxify lipopolysaccharide (LPS) by dephosphorylating its lipid A moiety. Because a role of gut-derived LPS in liver fibrogenesis has become evident, we now examined the relevance of phosphate groups in the lipid A moiety in this process. The effects of mono-phosphoryl and di-phosphoryl lipid A (MPLA and DPLA, respectively) were studied in vitro and LPS-dephosphorylating activity was studied in normal and fibrotic mouse and human livers. The effects of intestinal AP were studied in mice with CCL4-induced liver fibrosis. DPLA strongly stimulated fibrogenic and inflammatory activities in primary rat hepatic stellate cells (rHSCs) and RAW264.7 macrophages with similar potency as full length LPS. However, MPLA did not affect any of the parameters. LPS-dephosphorylating activity was found in mouse and human livers and was strongly increased during fibrogenesis. Treatment of fibrotic mice with intravenous intestinal-AP significantly attenuated intrahepatic desmin+- and αSMA+ -HSC and CD68+- macrophage accumulation. In conclusion, the lack of biological activity of MPLA, contrasting with the profound activities of DPLA, shows the relevance of LPS-dephosphorylating activity. The upregulation of LPS-dephosphorylating activity in fibrotic livers and the protective effects of exogenous AP during fibrogenesis indicate an important physiological role of intestinal-derived AP during liver fibrosis

HOW RELIABLE IS IN SITU SATURATION MONITORING (ISSM) USING X-RAY?

ABSTRACT In core flooding studies, where fluids are injected to mobilize hydrocarbons, X-ray measurements are often used to monitor the hydrocarbon saturations in the core. This is done as a function of the position in the core and as a function of time. The goal is to understand how effective the injected fluids can displace the hydrocarbons, and to measure how much hydrocarbons are left behind in the core. The calculation of in place saturations from X-ray, however, is not straightforward, and it is often unclear what the uncertainties in the calculated saturations are. In this paper, we compare calculated saturations from X-ray with saturations from direct measurement of produced hydrocarbon volumes from the core. The direct measurement is obtained using a novel apparatus which measures the production of oil using a balance under a back pressure. We show that differences between the two methods can be quite substantial and we discuss what may be the reasons causing these differences. The paper ends with a discussion on how we can improve the use of in situ saturation monitoring for unsteady state experiments