1,198 research outputs found
A formal verification framework and associated tools for enterprise modeling : application to UEML
The aim of this paper is to propose and apply a verification and validation approach to Enterprise Modeling that enables the user to improve the relevance and correctness, the suitability and coherence of a model by using properties specification and formal proof of properties
Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch
The bacterial flagellar switch that controls the direction of flagellar rotation during chemotaxis has a highly cooperative response. This has previously been understood in terms of the classic two-state, concerted model of allosteric regulation. Here, we used high-resolution optical microscopy to observe switching of single motors and uncover the stochastic multistate nature of the switch. Our observations are in detailed quantitative agreement with a recent general model of allosteric cooperativity that exhibits conformational spread—the stochastic growth and shrinkage of domains of adjacent subunits sharing a particular conformational state. We expect that conformational spread will be important in explaining cooperativity in other large signaling complexes
Self-diffusion in a triple-defect A-B binary system : Monte Carlo simulation
In this comprehensive and detailed study, vacancy-mediated self-diffusion of A- and B-elements in triple-defect B2-ordered ASB1-S binaries is simulated by means of a kinetic Monte Carlo (KMC) algorithm involving atomic jumps to nearest-neighbour (nn) and next-nearest-neighbour (nnn) vacancies. The systems are modelled with an Ising-type Hamiltonian with nn and nnn pair interactions completed with migration barriers dependent on local configurations. Self-diffusion is simulated at equilibrium and temperature-dependent vacancy concentrations are generated by means of a Semi Grand Canonical MC (SGCMC) code. The KMC simulations reproduced the phenomena observed experimentally in Ni-Al intermetallics being typical representatives of the 'triple-defect' binaries. In particular, they yielded the characteristic ‘V’-shapes of the isothermal concentration dependencies of A- and B-atom diffusivities, as well as the strong enhancement of the B-atom diffusivity in B-rich systems. The atomistic origins of the phenomenon, as well as other features of the simulated self-diffusion such as temperature and composition dependences of tracer correlation factors and activation energies are analyzed in depth in terms of a number of nanoscopic parameters that are able to be tuned and monitored exclusively with atomistic simulations. The roles of equilibrium and kinetic factors in the generation of the observed features are clearly distinguished and elucidated
Thermodynamic activation energy for self-diffusion and order-order relaxation in intermetallic compounds
Requirements modelling and formal analysis using graph operations
The increasing complexity of enterprise systems requires a more advanced
analysis of the representation of services expected than is currently possible.
Consequently, the specification stage, which could be facilitated by formal
verification, becomes very important to the system life-cycle. This paper presents
a formal modelling approach, which may be used in order to better represent
the reality of the system and to verify the awaited or existing system’s properties,
taking into account the environmental characteristics. For that, we firstly propose
a formalization process based upon properties specification, and secondly we
use Conceptual Graphs operations to develop reasoning mechanisms of verifying
requirements statements. The graphic visualization of these reasoning enables us
to correctly capture the system specifications by making it easier to determine if
desired properties hold. It is applied to the field of Enterprise modelling
Glutathione-S-transferase subtypes α and π as a tool to predict and monitor graft failure or regeneration in a pilot study of living donor liver transplantation
<p>Abstract</p> <p>Objective</p> <p>Glutathione-S-Transferase (GST) subtype α and π are differentially expressed in adult liver tissue. Objective of the study was if GST α and p may serve as predictive markers for liver surgery, especially transplantations.</p> <p>Methods</p> <p>13 patients receiving living donor liver transplantation (LDLT) and their corresponding donors were analyzed for standard serum parameters (ALT, AST, gGT, bilirubin) as well as GST-α and -π before LDLT and daily for 10 days after LDLT. Patients (R) and donors (D) were grouped according to graft loss (R1/D1) or positive outcome (R2/D2) and above named serum parameters were compared between the groups.</p> <p>Results</p> <p>R1 showed significantly increased GST-α and significantly lower GST-π levels than R2 patients or the donors. There was a positive correlation between GST-α and ALT, AST as well as bilirubin and a negative correlation to γGT. However, γGT correlated positively with GST-π. Graft failure was associated with combined low GST-π levels in donors and their recipients before living donor liver transplantation.</p> <p>Conclusion</p> <p>Our data suggest that high GST-α serum levels reflect ongoing liver damage while GST-P indicates the capacity and process of liver regeneration. Additionally, GST-π may be useful as marker for optimizing donor and recipient pairs in living donor liver transplantation.</p
Protocol for Biospecimen Collection and Analysis within the BACPAC Research Program
The Biospecimen Collection and Processing Working Group of the NIH HEAL Initiative BACPAC Research Program was charged with identifying molecular biomarkers of interest to chronic low back pain (cLBP). Having identified biomarkers of interest, the Working Group worked with the New York University Grossman School of Medicine, Center for Biospecimen Research and Development-funded by the Early Phase Pain Investigation Clinical Network Data Coordinating Center-to harmonize consortium-wide and site-specific efforts for biospecimen collection and analysis. Biospecimen collected are saliva, blood (whole, plasma, serum), urine, stool, and spine tissue (paraspinal muscle, ligamentum flavum, vertebral bone, facet cartilage, disc endplate, annulus fibrosus, or nucleus pulposus). The omics data acquisition and analyses derived from the biospecimen include genomics and epigenetics from DNA, proteomics from protein, transcriptomics from RNA, and microbiomics from 16S rRNA. These analyses contribute to the overarching goal of BACPAC to phenotype cLBP and will guide future efforts for precision medicine treatment
(Meta-)stable reconstructions of the diamond(111) surface: interplay between diamond- and graphite-like bonding
Off-lattice Grand Canonical Monte Carlo simulations of the clean diamond
(111) surface, based on the effective many-body Brenner potential, yield the
Pandey reconstruction in agreement with \emph{ab-initio}
calculations and predict the existence of new meta-stable states, very near in
energy, with all surface atoms in three-fold graphite-like bonding. We believe
that the long-standing debate on the structural and electronic properties of
this surface could be solved by considering this type of carbon-specific
configurations.Comment: 4 pages + 4 figures, Phys. Rev. B Rapid Comm., in press (15Apr00).
For many additional details (animations, xyz files) see electronic supplement
to this paper at http://www.sci.kun.nl/tvs/carbon/meta.htm
The {\eta}'-carbon potential at low meson momenta
The production of mesons in coincidence with forward-going
protons has been studied in photon-induced reactions on C and on a
liquid hydrogen (LH) target for incoming photon energies of 1.3-2.6 GeV at
the electron accelerator ELSA. The mesons have been identified
via the decay
registered with the CBELSA/TAPS detector system. Coincident protons have been
identified in the MiniTAPS BaF array at polar angles of . Under these kinematic constraints the
mesons are produced with relatively low kinetic energy (
150 MeV) since the coincident protons take over most of the momentum of the
incident-photon beam. For the C-target this allows the determination of the
real part of the -carbon potential at low meson momenta by
comparing with collision model calculations of the kinetic energy
distribution and excitation function. Fitting the latter data for
mesons going backwards in the center-of-mass system yields a potential depth of
V = (44 16(stat)15(syst)) MeV, consistent with earlier
determinations of the potential depth in inclusive measurements for average
momenta of 1.1 GeV/. Within the experimental
uncertainties, there is no indication of a momentum dependence of the
-carbon potential. The LH data, taken as a reference to check
the data analysis and the model calculations, provide differential and integral
cross sections in good agreement with previous results for
photoproduction off the free proton.Comment: 9 pages, 13 figures. arXiv admin note: text overlap with
arXiv:1608.0607
Conformational Spread in the Flagellar Motor Switch: A Model Study
The reliable response to weak biological signals requires that they be amplified with fidelity. In E. coli, the flagellar motors that control swimming can switch direction in response to very small changes in the concentration of the signaling protein CheY-P, but how this works is not well understood. A recently proposed allosteric model based on cooperative conformational spread in a ring of identical protomers seems promising as it is able to qualitatively reproduce switching, locked state behavior and Hill coefficient values measured for the rotary motor. In this paper we undertook a comprehensive simulation study to analyze the behavior of this model in detail and made predictions on three experimentally observable quantities: switch time distribution, locked state interval distribution, Hill coefficient of the switch response. We parameterized the model using experimental measurements, finding excellent agreement with published data on motor behavior. Analysis of the simulated switching dynamics revealed a mechanism for chemotactic ultrasensitivity, in which cooperativity is indispensable for realizing both coherent switching and effective amplification. These results showed how cells can combine elements of analog and digital control to produce switches that are simultaneously sensitive and reliable
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