Adsorption of chain molecules in pores with crystalline walls: a density functional approach

A microscopic density functional theory of adsorption of chain molecules on the attractive solid surfaces of crystalline symmetry is developed. The proposed approach is based on the expansions of one-particle functions into two-dimensional Fourier series. Illustrative calculations for dimers, 8- and 16-mers adsorbed on a (100) fcc crystal surface indicate the effect of the periodicity of the adsorbing potential on the structure of the adsorbed layer and thermodynamics of adsorption.Розвинуто мiкроскопiчну теорiю функцiоналу густини для вивчення адсорбцiї ланцюгових молекул на притягальних твердих поверхнях кристалiчної симетрiї. Запропонований пiдхiд ґрунтується на розкладах одночастинкових функцiй у двовимiрнi ряди Фур’є. Для iлюстрацiї проведено обчислення для димерiв, 8- i 16-мерiв, що адсорбованi на кристалiчнiй поверхнi (100) fcc, якi демонструють вплив перiодичностi адсорбуючого потенцiалу на структуру адсорбованого шару i термодинамiку адсорбцiї

Phase separation of an asymmetric binary fluid mixture confined in a nanoscopic slit pore: Molecular-dynamics simulations

As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones interactions for the carbon dioxide molecules. In previous work, it has been shown that this model reproduces the real phase diagram reasonable well, and also the initial stages of spinodal decomposition in the bulk following a sudden expansion of the system could be studied. Using the parallelized simulation package ESPResSo on a multiprocessor supercomputer, phase separation of thin fluid films confined between parallel walls that are repulsive for both types of molecules are simulated in a rather large system (1356 x 1356 x 67.8 A^3, corresponding to about 3.2 million atoms). Following the sudden system expansion, a complicated interplay between phase separation in the directions perpendicular and parallel to the walls is found: in the early stages the hexadecane molecules accumulate mostly in the center of the slit pore, but as the coarsening of the structure in the parallel direction proceeds, the inhomogeneity in the perpendicular direction gets much reduced. Studying then the structure factors and correlation functions at fixed distances from the wall, the densities are essentially not conserved at these distances, and hence the behavior differs strongly from spinodal decomposition in the bulk. Some of the characteristic lengths show a nonmonotonic variation with time, and simple coarsening described by power-law growth is only observed if the domain sizes are much larger than the film thickness.Comment: accepted for publication in PR

Monte Carlo Methods for Estimating Interfacial Free Energies and Line Tensions

Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal growth, etc.). This article reviews two methods to estimate both interfacial free energies and line tensions by Monte Carlo simulations of simple models, (e.g. the Ising model, a symmetrical binary Lennard-Jones fluid exhibiting a miscibility gap, and a simple Lennard-Jones fluid). One method is based on thermodynamic integration. This method is useful to study flat and inclined interfaces for Ising lattices, allowing also the estimation of line tensions of three-phase contact lines, when the interfaces meet walls (where "surface fields" may act). A generalization to off-lattice systems is described as well. The second method is based on the sampling of the order parameter distribution of the system throughout the two-phase coexistence region of the model. Both the interface free energies of flat interfaces and of (spherical or cylindrical) droplets (or bubbles) can be estimated, including also systems with walls, where sphere-cap shaped wall-attached droplets occur. The curvature-dependence of the interfacial free energy is discussed, and estimates for the line tensions are compared to results from the thermodynamic integration method. Basic limitations of all these methods are critically discussed, and an outlook on other approaches is given

Pseudomonas aeruginosa Pili and Flagella Mediate Distinct Binding and Signaling Events at the Apical and Basolateral Surface of Airway Epithelium

Pseudomonas aeruginosa, an important opportunistic pathogen of man, exploits numerous factors for initial attachment to the host, an event required to establish bacterial infection. In this paper, we rigorously explore the role of two major bacterial adhesins, type IV pili (Tfp) and flagella, in bacterial adherence to distinct host receptors at the apical (AP) and basolateral (BL) surfaces of polarized lung epithelial cells and induction of subsequent host signaling and pathogenic events. Using an isogenic mutant of P. aeruginosa that lacks flagella or utilizing beads coated with purified Tfp, we establish that Tfp are necessary and sufficient for maximal binding to host N-glycans at the AP surface of polarized epithelium. In contrast, experiments utilizing a P. aeruginosa isogenic mutant that lacks Tfp or using beads coated with purified flagella demonstrate that flagella are necessary and sufficient for maximal binding to heparan sulfate (HS) chains of heparan sulfate proteoglycans (HSPGs) at the BL surface of polarized epithelium. Using two different cell-free systems, we demonstrate that Tfp-coated beads show highest binding affinity to complex N-glycan chains coated onto plastic plates and preferentially aggregate with beads coated with N-glycans, but not with single sugars or HS. In contrast, flagella-coated beads bind to or aggregate preferentially with HS or HSPGs, but demonstrate little binding to N-glycans. We further show that Tfp-mediated binding to host N-glycans results in activation of phosphatidylinositol 3-kinase (PI3K)/Akt pathway and bacterial entry at the AP surface. At the BL surface, flagella-mediated binding to HS activates the epidermal growth factor receptor (EGFR), adaptor protein Shc, and PI3K/Akt, and induces bacterial entry. Remarkably, flagella-coated beads alone can activate EGFR and Shc. Together, this work provides new insights into the intricate interactions between P. aeruginosa and lung epithelium that may be potentially useful in the development of novel treatments for P. aeruginosa infections

The Evolution of Extracellular Matrix

We present a perspective on the molecular evolution of the extracellular matrix (ECM) in metazoa that draws on research publications and data from sequenced genomes and expressed sequence tag libraries. ECM components do not function in isolation, and the biological ECM system or “adhesome” also depends on posttranslational processing enzymes, cell surface receptors, and extracellular proteases. We focus principally on the adhesome of internal tissues and discuss its origins at the dawn of the metazoa and the expansion of complexity that occurred in the chordate lineage. The analyses demonstrate very high conservation of a core adhesome that apparently evolved in a major wave of innovation in conjunction with the origin of metazoa. Integrin, CD36, and certain domains predate the metazoa, and some ECM-related proteins are identified in choanoflagellates as predicted sequences. Modern deuterostomes and vertebrates have many novelties and elaborations of ECM as a result of domain shuffling, domain innovations and gene family expansions. Knowledge of the evolution of metazoan ECM is important for understanding how it is built as a system, its roles in normal tissues and disease processes, and has relevance for tissue engineering, the development of artificial organs, and the goals of synthetic biology

Bacterial Flagella: Twist and Stick, or Dodge across the Kingdoms

The flagellum organelle is an intricate multiprotein assembly best known for its rotational propulsion of bacteria. However, recent studies have expanded our knowledge of other functions in pathogenic contexts, particularly adherence and immune modulation, e.g., for Salmonella enterica, Campylobacter jejuni, Pseudomonas aeruginosa, and Escherichia coli. Flagella-mediated adherence is important in host colonisation for several plant and animal pathogens, but the specific interactions that promote flagella binding to such diverse host tissues has remained elusive. Recent work has shown that the organelles act like probes that find favourable surface topologies to initiate binding. An emerging theme is that more general properties, such as ionic charge of repetitive binding epitopes and rotational force, allow interactions with plasma membrane components. At the same time, flagellin monomers are important inducers of plant and animal innate immunity: variation in their recognition impacts the course and outcome of infections in hosts from both kingdoms. Bacteria have evolved different strategies to evade or even promote this specific recognition, with some important differences shown for phytopathogens. These studies have provided a wider appreciation of the functions of bacterial flagella in the context of both plant and animal reservoirs

The estimation of chrominum contamination degree of soil and water in the vicinity of tannery waste lagoon near Lubartow (Poland)

Publikacja przedstawia skażenie gleby, wód i roślin przez chrom w okolicy składowiska odpadów garbarskich w Lubartowie. Przez ponad 20 lat odpady z garbarni zawierające duże ilości chromu były składowane w niezabezpieczonym wyrobisku piaskowym, które leży tuż przy rzece Wieprz. Wyniki naszych badań porównane są z wynikami raportów z początku lat 90 dotyczących skażenia chromem okolicy Lubartowa. Przedstawione jest porównanie dwóch metod określania stężenia chromu w glebie. Wyniki pokazują, że okolica składowiska odpadów jest wciąż skażona i wymaga poważnego programu oczyszczenia jej i przywrócenia do stanu przed składowaniem odpadów.The article presents contamination of soil, water and plant with chrominum in the vicinity of tannery waste lagoon in Lubartow. reach in chrominum wastes from the tannery have been gathered for more than 20 years in usealed basin which was situated close to the Wieprz river.results of our investigations are compared with reports on chrominum contamination of the same object but coming from early nineties. Two methods of total chrominum determination in soils are compared. The results show that the area of waste disposal is still contaminated and a serious remediation program is needed

Quality of water in Czajcze and Domysłowskie lakes in different seasons of the year

Celem niniejszej pracy było rozpoznanie zmian jakości wód powierzchniowych jezior Czajczego i Domysłowskiego w okresie od lata 2003 do wiosny 2004.1. 1. W okresie badawczym sierpień 2003 - czerwiec 2004 wody powierzchniowe jezior Czajczego i Domysłowskiego ze względu na wyniki oznaczeń ChZT-Mn były wodami III klasy jakości oceniając wg przepisów urzędowych stosowanych do oceny naturalnych wód powierzchniowych w Polsce. Okresowo (podczas zimy i wiosny) były one wodami IV-V klasy jakości ze względu na wartości stężeń PO43-rozp, zaś oceniając - w oparciu o kryteria trofii - wg wartości stężeń Pog w okresie cyrkulacji wiosennej wód jeziornych wodami politroficznymi. 2.Znaczne zmiany natlenienia wód, poczynając od stanów silnego przetlenienia (późne lato 2003 i późna wiosna 2004) - spowodowanych stosunkowo krótkotrwałym bujnym rozwojem roślinności wodnej - do stanów permanentnego niedotlenienia (około 50÷95% natlenienia), świadczące o przewadze procesów dysymilacyjnych nad asymilacyjnymi w ekosystemach jezior Czajczego i Domysłowskiego - wskazują na znaczną eutrofizację obydwu jezior. 3.Jeżeli chodzi o zasobność wód badanych jezior w substancje mineralne, to w okresie lato 2003÷wiosna 2004 wody powierzchniowe jezior Czajczego i Domysłowskiego w Wolińskim Parku Narodowym były wodami słabo zmineralizowanymi o stężeniach soli mineralnych ulegających niedużym wahaniom sezonowym.Wolin National Park, established as first maritime Park in Poland, besides marine (Pomeranian Bay) and estuarial (Szczecin Lagoon) ecosystems, consists of typical lake ecosystems: Czajcze, Domysłowskie, Rabiąż and Warnowo Lakes, partially belonging to Warnowsko-Kołczewskie Lake District situated in the central part of Wolin Island. Up to now investigations of quality of water in these lakes during all season of the year have not been carried out yet. The aim of this study was to research quality of surface waters of Czajcze and Domysłowskie Lakes between summer 2003 and spring 2004. In arbitrarily appointed time 21 physical and chemical indices of water quality were investigated, selected for defining general status (temperature, pH, dissolved O2 and saturation with O2, solid residue, residue after ignition), trophy (concentrations of NH4+, NO2-, NO3- and dissolved PO43- and total P) and mineralization level (specific electrolytic conductivity, total hardness, concentrations of Ca2+, Mg2+, Cl-, SO42-, total alkalinity, and total concentrations of Fe and Mn) of waters. These data enable to make shorter analysis support to 17 from 46 indicators of quality were determined, basing on official standard of the system for evaluation of inland freshwater quality, which is obligatory in Poland. Especially collected results during period of intense exuberant development of aquatic vegetation and also during down flow of spring water during snow-melt season, in periods whilst lakes are covered with ice determined, that waters of lakes Czajcze and Domysłowskie in researched season were poorly mineralized inland waters. In water ecosystems of both lakes, typical changes of these lakes eutrophication take place particularly, when dissimilation had prevailed over assimilation processes (saturation with O2: 50÷95%) through last part of year