Chip Multithreaded Consistency Model
Institute of Scientific and Technical Information of China (English)
Zu-Song Li; Dan-Dan Huan; Wei-Wu Hu; Zhi-Min Tang
2008-01-01
Multithreaded technique is the developing trend of high performance processor. Memory consistency model is essential to the correctness, performance and complexity of multithreaded processor. The chip multithreaded consistency model adapting to multithreaded processor is proposed in this paper. The restriction imposed on memory event ordering by chip multithreaded consistency is presented and formalized. With the idea of critical cycle built by Wei-Wu Hu, we prove that the proposed chip multithreaded consistency model satisfies the criterion of correct execution of sequential consistency model. Chip multithreaded consistency model provides a way of achieving high performance compared with sequential consistency model and ensures the compatibility of software that the execution result in multithreaded processor is the same as the execution result in uniprocessor. The implementation strategy of chip multithreaded consistency model in Godson-2 SMT processor is also proposed. Godson-2 SMT processor supports chip multithreaded consistency model correctly by exception scheme based on the sequential memory access queue of each thread.
Consistent model driven architecture
Niepostyn, Stanisław J.
2015-09-01
The goal of the MDA is to produce software systems from abstract models in a way where human interaction is restricted to a minimum. These abstract models are based on the UML language. However, the semantics of UML models is defined in a natural language. Subsequently the verification of consistency of these diagrams is needed in order to identify errors in requirements at the early stage of the development process. The verification of consistency is difficult due to a semi-formal nature of UML diagrams. We propose automatic verification of consistency of the series of UML diagrams originating from abstract models implemented with our consistency rules. This Consistent Model Driven Architecture approach enables us to generate automatically complete workflow applications from consistent and complete models developed from abstract models (e.g. Business Context Diagram). Therefore, our method can be used to check practicability (feasibility) of software architecture models.
Self-consistent triaxial models
Sanders, Jason L
2015-01-01
We present self-consistent triaxial stellar systems that have analytic distribution functions (DFs) expressed in terms of the actions. These provide triaxial density profiles with cores or cusps at the centre. They are the first self-consistent triaxial models with analytic DFs suitable for modelling giant ellipticals and dark haloes. Specifically, we study triaxial models that reproduce the Hernquist profile from Williams & Evans (2015), as well as flattened isochrones of the form proposed by Binney (2014). We explore the kinematics and orbital structure of these models in some detail. The models typically become more radially anisotropic on moving outwards, have velocity ellipsoids aligned in Cartesian coordinates in the centre and aligned in spherical polar coordinates in the outer parts. In projection, the ellipticity of the isophotes and the position angle of the major axis of our models generally changes with radius. So, a natural application is to elliptical galaxies that exhibit isophote twisting....
DEFF Research Database (Denmark)
Günther-Pomorski, Thomas; Nylander, Tommy; Cardenas Gomez, Marite
2014-01-01
The high complexity of biological membranes has motivated the development and application of a wide range of model membrane systems to study biochemical and biophysical aspects of membranes in situ under well defined conditions. The aim is to provide fundamental understanding of processes...... controlled by membrane structure, permeability and curvature as well as membrane proteins by using a wide range of biochemical, biophysical and microscopic techniques. This review gives an overview of some currently used model biomembrane systems. We will also discuss some key membrane protein properties...... that are relevant for protein-membrane interactions in terms of protein structure and how it is affected by membrane composition, phase behavior and curvature....
Consistent ranking of volatility models
DEFF Research Database (Denmark)
Hansen, Peter Reinhard; Lunde, Asger
2006-01-01
We show that the empirical ranking of volatility models can be inconsistent for the true ranking if the evaluation is based on a proxy for the population measure of volatility. For example, the substitution of a squared return for the conditional variance in the evaluation of ARCH-type models can...
Consistent ranking of volatility models
DEFF Research Database (Denmark)
Hansen, Peter Reinhard; Lunde, Asger
2006-01-01
result in an inferior model being chosen as "best" with a probability that converges to one as the sample size increases. We document the practical relevance of this problem in an empirical application and by simulation experiments. Our results provide an additional argument for using the realized...... variance in out-of-sample evaluations rather than the squared return. We derive the theoretical results in a general framework that is not specific to the comparison of volatility models. Similar problems can arise in comparisons of forecasting models whenever the predicted variable is a latent variable.......We show that the empirical ranking of volatility models can be inconsistent for the true ranking if the evaluation is based on a proxy for the population measure of volatility. For example, the substitution of a squared return for the conditional variance in the evaluation of ARCH-type models can...
Mathematical modelling of membrane separation
DEFF Research Database (Denmark)
Vinther, Frank
This thesis concerns mathematical modelling of membrane separation. The thesis consists of introductory theory on membrane separation, equations of motion, and properties of dextran, which will be the solute species throughout the thesis. Furthermore, the thesis consist of three separate mathemat......This thesis concerns mathematical modelling of membrane separation. The thesis consists of introductory theory on membrane separation, equations of motion, and properties of dextran, which will be the solute species throughout the thesis. Furthermore, the thesis consist of three separate....... It is found that the probability of entering the pore is highest when the largest of the radii in the ellipse is equal to half the radius of the pore, in case of molecules with circular radius less than the pore radius. The results are directly related to the macroscopic distribution coefficient...
From biological membranes to biomimetic model membranes
Directory of Open Access Journals (Sweden)
Eeman, M.
2010-01-01
Full Text Available Biological membranes play an essential role in the cellular protection as well as in the control and the transport of nutrients. Many mechanisms such as molecular recognition, enzymatic catalysis, cellular adhesion and membrane fusion take place into the biological membranes. In 1972, Singer et al. provided a membrane model, called fluid mosaic model, in which each leaflet of the bilayer is formed by a homogeneous environment of lipids in a fluid state including globular assembling of proteins and glycoproteins. Since its conception in 1972, many developments were brought to this model in terms of composition and molecular organization. The main development of the fluid mosaic model was made by Simons et al. (1997 and Brown et al. (1997 who suggested that membrane lipids are organized into lateral microdomains (or lipid rafts with a specific composition and a molecular dynamic that are different to the composition and the dynamic of the surrounding liquid crystalline phase. The discovery of a phase separation in the plane of the membrane has induced an explosion in the research efforts related to the biology of cell membranes but also in the development of new technologies for the study of these biological systems. Due to the high complexity of biological membranes and in order to investigate the biological processes that occur on the membrane surface or within the membrane lipid bilayer, a large number of studies are performed using biomimicking model membranes. This paper aims at revisiting the fundamental properties of biological membranes in terms of membrane composition, membrane dynamic and molecular organization, as well as at describing the most common biomimicking models that are frequently used for investigating biological processes such as membrane fusion, membrane trafficking, pore formation as well as membrane interactions at a molecular level.
Modeling and Testing Legacy Data Consistency Requirements
DEFF Research Database (Denmark)
Nytun, J. P.; Jensen, Christian Søndergaard
2003-01-01
An increasing number of data sources are available on the Internet, many of which offer semantically overlapping data, but based on different schemas, or models. While it is often of interest to integrate such data sources, the lack of consistency among them makes this integration difficult....... This paper addresses the need for new techniques that enable the modeling and consistency checking for legacy data sources. Specifically, the paper contributes to the development of a framework that enables consistency testing of data coming from different types of data sources. The vehicle is UML and its...... accompanying XMI. The paper presents techniques for modeling consistency requirements using OCL and other UML modeling elements: it studies how models that describe the required consistencies among instances of legacy models can be designed in standard UML tools that support XMI. The paper also considers...
A Framework of Memory Consistency Models
Institute of Scientific and Technical Information of China (English)
胡伟武; 施巍松; 等
1998-01-01
Previous descriptions of memory consistency models in shared-memory multiprocessor systems are mainly expressed as constraints on the memory access event ordering and hence are hardware-centric.This paper presents a framework of memory consistency models which describes the memory consistency model on the behavior level.Based on the understanding that the behavior of an execution is determined by the execution order of conflicting accesses,a memory consistency model is defined as an interprocessor synchronization mechanism which orders the execution of operations from different processors.Synchronization order of an execution under certain consistency model is also defined.The synchronization order,together with the program order determines the behavior of an execution.This paper also presents criteria for correct program and correct implementation of consistency models.Regarding an implementation of a consistency model as certain memory event ordering constraints,this paper provides a method to prove the correctness of consistency model implementations,and the correctness of the lock-based cache coherence protocol is proved with this method.
A self-consistent Maltsev pulse model
Buneman, O.
1985-04-01
A self-consistent model for an electron pulse propagating through a plasma is presented. In this model, the charge imbalance between plasma ions, plasma electrons and pulse electrons creates the travelling potential well in which the pulse electrons are trapped.
The membrane skeleton of a unicellular organism consists of bridged, articulating strips
1985-01-01
In this paper we show that a membrane skeleton associated with the plasma membrane of the unicellular organism Euglena consists of approximately 40 individual S-shaped strips that overlap along their lateral margins. The region of strip overlap is occupied by a set of microtubule-associated bridges and microtubule-independent bridges. Both cell form and plasma membrane organization are dependent on the integrity of this membrane skeleton. Removal of the membrane skeleton with a low-molar base...
Self-Consistent Asset Pricing Models
Malevergne, Y
2006-01-01
We discuss the foundations of factor or regression models in the light of the self-consistency condition that the market portfolio (and more generally the risk factors) is (are) constituted of the assets whose returns it is (they are) supposed to explain. As already reported in several articles, self-consistency implies correlations between the return disturbances. As a consequence, the alpha's and beta's of the factor model are unobservable. Self-consistency leads to renormalized beta's with zero effective alpha's, which are observable with standard OLS regressions. Analytical derivations and numerical simulations show that, for arbitrary choices of the proxy which are different from the true market portfolio, a modified linear regression holds with a non-zero value $\\alpha_i$ at the origin between an asset $i$'s return and the proxy's return. Self-consistency also introduces ``orthogonality'' and ``normality'' conditions linking the beta's, alpha's (as well as the residuals) and the weights of the proxy por...
Entropy-based consistent model driven architecture
Niepostyn, Stanisław Jerzy
2016-09-01
A description of software architecture is a plan of the IT system construction, therefore any architecture gaps affect the overall success of an entire project. The definitions mostly describe software architecture as a set of views which are mutually unrelated, hence potentially inconsistent. Software architecture completeness is also often described in an ambiguous way. As a result most methods of IT systems building comprise many gaps and ambiguities, thus presenting obstacles for software building automation. In this article the consistency and completeness of software architecture are mathematically defined based on calculation of entropy of the architecture description. Following this approach, in this paper we also propose our method of automatic verification of consistency and completeness of the software architecture development method presented in our previous article as Consistent Model Driven Architecture (CMDA). The proposed FBS (Functionality-Behaviour-Structure) entropy-based metric applied in our CMDA approach enables IT architects to decide whether the modelling process is complete and consistent. With this metric, software architects could assess the readiness of undergoing modelling work for the start of IT system building. It even allows them to assess objectively whether the designed software architecture of the IT system could be implemented at all. The overall benefit of such an approach is that it facilitates the preparation of complete and consistent software architecture more effectively as well as it enables assessing and monitoring of the ongoing modelling development status. We demonstrate this with a few industry examples of IT system designs.
Application of self-consistent field theory to self-assembled bilayer membranes
Zhang, Ping-Wen; Shi, An-Chang
2015-12-01
Bilayer membranes self-assembled from amphiphilic molecules such as lipids, surfactants, and block copolymers are ubiquitous in biological and physiochemical systems. The shape and structure of bilayer membranes depend crucially on their mechanical properties such as surface tension, bending moduli, and line tension. Understanding how the molecular properties of the amphiphiles determine the structure and mechanics of the self-assembled bilayers requires a molecularly detailed theoretical framework. The self-consistent field theory provides such a theoretical framework, which is capable of accurately predicting the mechanical parameters of self-assembled bilayer membranes. In this mini review we summarize the formulation of the self-consistent field theory, as exemplified by a model system composed of flexible amphiphilic chains dissolved in hydrophilic polymeric solvents, and its application to the study of self-assembled bilayer membranes. Project supported by the National Natural Science Foundation of China (Grant Nos. 11421101 and 21274005) and the Natural Sciences and Engineering Research Council (NSERC) of Canada.
Self-consistent model of fermions
Yershov, V N
2002-01-01
We discuss a composite model of fermions based on three-flavoured preons. We show that the opposite character of the Coulomb and strong interactions between these preons lead to formation of complex structures reproducing three generations of quarks and leptons with all their quantum numbers and masses. The model is self-consistent (it doesn't use input parameters). Nevertheless, the masses of the generated structures match the experimental values.
Consistent Stochastic Modelling of Meteocean Design Parameters
DEFF Research Database (Denmark)
Sørensen, John Dalsgaard; Sterndorff, M. J.
2000-01-01
Consistent stochastic models of metocean design parameters and their directional dependencies are essential for reliability assessment of offshore structures. In this paper a stochastic model for the annual maximum values of the significant wave height, and the associated wind velocity, current...... velocity, and water level is presented. The stochastic model includes statistical uncertainty and dependency between the four stochastic variables. Further, a new stochastic model for annual maximum directional significant wave heights is presented. The model includes dependency between the maximum wave...... height from neighboring directional sectors. Numerical examples are presented where the models are calibrated using the Maximum Likelihood method to data from the central part of the North Sea. The calibration of the directional distributions is made such that the stochastic model for the omnidirectional...
Developing consistent pronunciation models for phonemic variants
CSIR Research Space (South Africa)
Davel, M
2006-09-01
Full Text Available from a lexicon containing variants. In this paper we (the authors) address both these issues by creating ‘pseudo-phonemes’ associated with sets of ‘generation restriction rules’ to model those pronunciations that are consistently realised as two or more...
Are there consistent models giving observable NSI ?
Martinez, Enrique Fernandez
2013-01-01
While the existing direct bounds on neutrino NSI are rather weak, order 10(−)(1) for propagation and 10(−)(2) for production and detection, the close connection between these interactions and new NSI affecting the better-constrained charged letpon sector through gauge invariance make these bounds hard to saturate in realistic models. Indeed, Standard Model extensions leading to neutrino NSI typically imply constraints at the 10(−)(3) level. The question of whether consistent models leading to observable neutrino NSI naturally arises and was discussed in a dedicated session at NUFACT 11. Here we summarize that discussion.
Thermodynamically consistent model calibration in chemical kinetics
Directory of Open Access Journals (Sweden)
Goutsias John
2011-05-01
Full Text Available Abstract Background The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function. Results We introduce a thermodynamically consistent model calibration (TCMC method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from http://www.cis.jhu.edu/~goutsias/CSS lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database. Conclusions TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new
Consistent quadrupole-octupole collective model
Dobrowolski, A.; Mazurek, K.; Góźdź, A.
2016-11-01
Within this work we present a consistent approach to quadrupole-octupole collective vibrations coupled with the rotational motion. A realistic collective Hamiltonian with variable mass-parameter tensor and potential obtained through the macroscopic-microscopic Strutinsky-like method with particle-number-projected BCS (Bardeen-Cooper-Schrieffer) approach in full vibrational and rotational, nine-dimensional collective space is diagonalized in the basis of projected harmonic oscillator eigensolutions. This orthogonal basis of zero-, one-, two-, and three-phonon oscillator-like functions in vibrational part, coupled with the corresponding Wigner function is, in addition, symmetrized with respect to the so-called symmetrization group, appropriate to the collective space of the model. In the present model it is D4 group acting in the body-fixed frame. This symmetrization procedure is applied in order to provide the uniqueness of the Hamiltonian eigensolutions with respect to the laboratory coordinate system. The symmetrization is obtained using the projection onto the irreducible representation technique. The model generates the quadrupole ground-state spectrum as well as the lowest negative-parity spectrum in 156Gd nucleus. The interband and intraband B (E 1 ) and B (E 2 ) reduced transition probabilities are also calculated within those bands and compared with the recent experimental results for this nucleus. Such a collective approach is helpful in searching for the fingerprints of the possible high-rank symmetries (e.g., octahedral and tetrahedral) in nuclear collective bands.
Modeling branching pore structures in membrane filters
Sanaei, Pejman; Cummings, Linda J.
2016-11-01
Membrane filters are in widespread industrial use, and mathematical models to predict their efficacy are potentially very useful, as such models can suggest design modifications to improve filter performance and lifetime. Many models have been proposed to describe particle capture by membrane filters and the associated fluid dynamics, but most such models are based on a very simple structure in which the pores of the membrane are assumed to be simple circularly-cylindrical tubes spanning the depth of the membrane. Real membranes used in applications usually have much more complex geometry, with interconnected pores which may branch and bifurcate. Pores are also typically larger on the upstream side of the membrane than on the downstream side. We present an idealized mathematical model, in which a membrane consists of a series of bifurcating pores, which decrease in size as the membrane is traversed. Feed solution is forced through the membrane by applied pressure, and particles are removed from the feed either by sieving, or by particle adsorption within pores (which shrinks them). Thus the membrane's permeability decreases as the filtration progresses, ultimately falling to zero. We discuss how filtration efficiency depends on the characteristics of the branching structure. Partial support from NSF DMS 1261596 is gratefully acknowledged.
Bergshoeff, E.; Sezgin, E.; Townsend, P.K.
1988-01-01
Several alternative actions for a bosonic membrane have recently been proposed. We show that a linearly realized locally world-volume-supersymmetric (spinning membrane) extension of any of these actions implies an analogous extension of the standard Dirac membrane action. We further show that a
Consistent estimators in random censorship semiparametric models
Institute of Scientific and Technical Information of China (English)
王启华
1996-01-01
For the fixed design regression modelwhen Y, are randomly censored on the right, the estimators of unknown parameter and regression function g from censored observations are defined in the two cases .where the censored distribution is known and unknown, respectively. Moreover, the sufficient conditions under which these estimators are strongly consistent and pth (p>2) mean consistent are also established.
Pressure-Balance Consistency in Magnetospheric Modelling
Institute of Scientific and Technical Information of China (English)
肖永登; 陈出新
2003-01-01
There have been many magnetic field models for geophysical and astrophysical bodies.These theoretical or empirical models represent the reality very well in some cases,but in other cases they may be far from reality.We argue that these models will become more reasonable if they are modified by some coordinate transformations.In order to demonstrate the transformation,we use this method to resolve the "pressure-balance inconsistency"problem that occurs when plasma transports from the outer plasma sheet of the Earth into the inner plasma sheet.
Consistent Partial Least Squares Path Modeling
Dijkstra, Theo K.; Henseler, Jörg
2015-01-01
This paper resumes the discussion in information systems research on the use of partial least squares (PLS) path modeling and shows that the inconsistency of PLS path coefficient estimates in the case of reflective measurement can have adverse consequences for hypothesis testing. To remedy this, the
Diffusion through thin membranes: Modeling across scales
Aho, Vesa; Mattila, Keijo; Kühn, Thomas; Kekäläinen, Pekka; Pulkkinen, Otto; Minussi, Roberta Brondani; Vihinen-Ranta, Maija; Timonen, Jussi
2016-04-01
From macroscopic to microscopic scales it is demonstrated that diffusion through membranes can be modeled using specific boundary conditions across them. The membranes are here considered thin in comparison to the overall size of the system. In a macroscopic scale the membrane is introduced as a transmission boundary condition, which enables an effective modeling of systems that involve multiple scales. In a mesoscopic scale, a numerical lattice-Boltzmann scheme with a partial-bounceback condition at the membrane is proposed and analyzed. It is shown that this mesoscopic approach provides a consistent approximation of the transmission boundary condition. Furthermore, analysis of the mesoscopic scheme gives rise to an expression for the permeability of a thin membrane as a function of a mesoscopic transmission parameter. In a microscopic model, the mean waiting time for a passage of a particle through the membrane is in accordance with this permeability. Numerical results computed with the mesoscopic scheme are then compared successfully with analytical solutions derived in a macroscopic scale, and the membrane model introduced here is used to simulate diffusive transport between the cell nucleus and cytoplasm through the nuclear envelope in a realistic cell model based on fluorescence microscopy data. By comparing the simulated fluorophore transport to the experimental one, we determine the permeability of the nuclear envelope of HeLa cells to enhanced yellow fluorescent protein.
Modelling of proteins in membranes
DEFF Research Database (Denmark)
Sperotto, Maria Maddalena; May, S.; Baumgaertner, A.
2006-01-01
This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly...... affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among others, the following phenomena are discussed: interactions of interfacially adsorbed peptides, pore-forming amphipathic peptides, adsorption of charged proteins onto...... oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins....
Modelling of proteins in membranes
DEFF Research Database (Denmark)
Sperotto, Maria Maddalena; May, S.; Baumgaertner, A.
2006-01-01
This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly ...
Tracking membrane protein association in model membranes.
Directory of Open Access Journals (Sweden)
Myriam Reffay
Full Text Available Membrane proteins are essential in the exchange processes of cells. In spite of great breakthrough in soluble proteins studies, membrane proteins structures, functions and interactions are still a challenge because of the difficulties related to their hydrophobic properties. Most of the experiments are performed with detergent-solubilized membrane proteins. However widely used micellar systems are far from the biological two-dimensions membrane. The development of new biomimetic membrane systems is fundamental to tackle this issue.We present an original approach that combines the Fluorescence Recovery After fringe Pattern Photobleaching technique and the use of a versatile sponge phase that makes it possible to extract crucial informations about interactions between membrane proteins embedded in the bilayers of a sponge phase. The clear advantage lies in the ability to adjust at will the spacing between two adjacent bilayers. When the membranes are far apart, the only possible interactions occur laterally between proteins embedded within the same bilayer, whereas when membranes get closer to each other, interactions between proteins embedded in facing membranes may occur as well.After validating our approach on the streptavidin-biotinylated peptide complex, we study the interactions between two membrane proteins, MexA and OprM, from a Pseudomonas aeruginosa efflux pump. The mode of interaction, the size of the protein complex and its potential stoichiometry are determined. In particular, we demonstrate that: MexA is effectively embedded in the bilayer; MexA and OprM do not interact laterally but can form a complex if they are embedded in opposite bilayers; the population of bound proteins is at its maximum for bilayers separated by a distance of about 200 A, which is the periplasmic thickness of Pseudomonas aeruginosa. We also show that the MexA-OprM association is enhanced when the position and orientation of the protein is restricted by the
Geometry of Membrane Sigma Models
Vysoky, Jan
2015-01-01
String theory still remains one of the promising candidates for a unification of the theory of gravity and quantum field theory. One of its essential parts is relativistic description of moving multi-dimensional objects called membranes (or p-branes) in a curved spacetime. On the classical field theory level, they are described by an action functional extremalising the volume of a manifold swept by a propagating membrane. This and related field theories are collectively called membrane sigma models. Differential geometry is an important mathematical tool in the study of string theory. It turns out that string and membrane backgrounds can be conveniently described using objects defined on a direct sum of tangent and cotangent bundles of the spacetime manifold. Mathematical field studying such object is called generalized geometry. Its integral part is the theory of Leibniz algebroids, vector bundles with a Leibniz algebra bracket on its module of smooth sections. Special cases of Leibniz algebroids are better ...
CONSISTENCY OF LS ESTIMATOR IN SIMPLE LINEAR EV REGRESSION MODELS
Institute of Scientific and Technical Information of China (English)
Liu Jixue; Chen Xiru
2005-01-01
Consistency of LS estimate of simple linear EV model is studied. It is shown that under some common assumptions of the model, both weak and strong consistency of the estimate are equivalent but it is not so for quadratic-mean consistency.
Modeling electrically active viscoelastic membranes.
Directory of Open Access Journals (Sweden)
Sitikantha Roy
Full Text Available The membrane protein prestin is native to the cochlear outer hair cell that is crucial to the ear's amplification and frequency selectivity throughout the whole acoustic frequency range. The outer hair cell exhibits interrelated dimensional changes, force generation, and electric charge transfer. Cells transfected with prestin acquire unique active properties similar to those in the native cell that have also been useful in understanding the process. Here we propose a model describing the major electromechanical features of such active membranes. The model derived from thermodynamic principles is in the form of integral relationships between the history of voltage and membrane resultants as independent variables and the charge density and strains as dependent variables. The proposed model is applied to the analysis of an active force produced by the outer hair cell in response to a harmonic electric field. Our analysis reveals the mechanism of the outer hair cell active (isometric force having an almost constant amplitude and phase up to 80 kHz. We found that the frequency-invariance of the force is a result of interplay between the electrical filtering associated with prestin and power law viscoelasticity of the surrounding membrane. Paradoxically, the membrane viscoelasticity boosts the force balancing the electrical filtering effect. We also consider various modes of electromechanical coupling in membrane with prestin associated with mechanical perturbations in the cell. We consider pressure or strains applied step-wise or at a constant rate and compute the time course of the resulting electric charge. The results obtained here are important for the analysis of electromechanical properties of membranes, cells, and biological materials as well as for a better understanding of the mechanism of hearing and the role of the protein prestin in this mechanism.
Triangle-hinge models for unoriented membranes
Fukuma, Masafumi; Sugishita, Sotaro; Umeda, Naoya
2016-07-01
Triangle-hinge models [M. Fukuma, S. Sugishita, and N. Umeda, J. High Energy Phys. 1507, 088 (2015)] are introduced to describe worldvolume dynamics of membranes. The Feynman diagrams consist of triangles glued together along hinges and can be restricted to tetrahedral decompositions in a large-N limit. In this paper, after clarifying that all the tetrahedra resulting in the original models are orientable, we define a version of triangle-hinge models that can describe the dynamics of unoriented membranes. By regarding each triangle as representing a propagation of an open membrane of disk topology, we introduce a local worldvolume parity transformation which inverts the orientation of a triangle, and define unoriented triangle-hinge models by gauging the transformation. Unlike two-dimensional cases, this local transformation generally relates a manifold to a nonmanifold, but still is a well-defined manipulation among tetrahedral decompositions. We further show that matter fields can be introduced in the same way as in the original oriented models. In particular, the models will describe unoriented membranes in a target spacetime by taking matter fields to be the target space coordinates.
Giant plasma membrane vesicles: models for understanding membrane organization.
Levental, Kandice R; Levental, Ilya
2015-01-01
The organization of eukaryotic membranes into functional domains continues to fascinate and puzzle cell biologists and biophysicists. The lipid raft hypothesis proposes that collective lipid interactions compartmentalize the membrane into coexisting liquid domains that are central to membrane physiology. This hypothesis has proven controversial because such structures cannot be directly visualized in live cells by light microscopy. The recent observations of liquid-liquid phase separation in biological membranes are an important validation of the raft hypothesis and enable application of the experimental toolbox of membrane physics to a biologically complex phase-separated membrane. This review addresses the role of giant plasma membrane vesicles (GPMVs) in refining the raft hypothesis and expands on the application of GPMVs as an experimental model to answer some of key outstanding problems in membrane biology. Copyright © 2015 Elsevier Inc. All rights reserved.
Interaction of Artepillin C with model membranes.
Pazin, Wallance Moreira; Olivier, Danilo da Silva; Vilanova, Neus; Ramos, Ana Paula; Voets, Ilja Karina; Soares, Ademilson Espencer Egea; Ito, Amando Siuiti
2017-05-01
Green propolis, a mixture of beeswax and resinous compounds processed by Apis mellifera, displays several pharmacological properties. Artepillin C, the major compound in green propolis, consists of two prenylated groups bound to a phenyl group. Several studies have focused on the therapeutic effects of Artepillin C, but there is no evidence that it interacts with amphiphilic aggregates to mimic cell membranes. We have experimentally and computationally examined the interaction between Artepillin C and model membranes composed of dimyristoylphosphatidylcholine (DMPC) because phosphatidylcholine (PC) is one of the most abundant phospholipids in eukaryotic cell membranes. PC is located in both outer and inner leaflets and has been used as a simplified membrane model and a non-specific target to study the action of amphiphilic molecules with therapeutic effects. Experimental results indicated that Artepillin C adsorbed onto the DMPC monolayers. Its presence in the lipid suspension pointed to an increased tendency toward unilamellar vesicles and to decreased bilayer thickness. Artepillin C caused point defects in the lipid structure, which eliminated the ripple phase and the pre-transition in thermotropic chain melting. According to molecular dynamics (MD) simulations, (1) Artepillin C aggregated in the aqueous phase before it entered the bilayer; (2) Artepillin C was oriented along the direction normal to the surface; (3) the negatively charged group on Artepillin C was accommodated in the polar region of the membrane; and (4) thinner regions emerged around the Artepillin C molecules. These results help an understanding of the molecular mechanisms underlying the biological action of propolis.
Logical consistency and sum-constrained linear models
van Perlo -ten Kleij, Frederieke; Steerneman, A.G.M.; Koning, Ruud H.
2006-01-01
A topic that has received quite some attention in the seventies and eighties is logical consistency of sum-constrained linear models. Loosely defined, a sum-constrained model is logically consistent if the restrictions on the parameters and explanatory variables are such that the sum constraint is a
The Self-Consistency Model of Subjective Confidence
Koriat, Asher
2012-01-01
How do people monitor the correctness of their answers? A self-consistency model is proposed for the process underlying confidence judgments and their accuracy. In answering a 2-alternative question, participants are assumed to retrieve a sample of representations of the question and base their confidence on the consistency with which the chosen…
Computational modeling of membrane proteins.
Koehler Leman, Julia; Ulmschneider, Martin B; Gray, Jeffrey J
2015-01-01
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
Model Checking Data Consistency for Cache Coherence Protocols
Institute of Scientific and Technical Information of China (English)
Hong Pan; Hui-Min Lin; Yi Lv
2006-01-01
A method for automatic verification of cache coherence protocols is presented, in which cache coherence protocols are modeled as concurrent value-passing processes, and control and data consistency requirement are described as formulas in first-orderμ-calculus. A model checker is employed to check if the protocol under investigation satisfies the required properties. Using this method a data consistency error has been revealed in a well-known cache coherence protocol.The error has been corrected, and the revised protocol has been shown free from data consistency error for any data domain size, by appealing to data independence technique.
A three-dimensional PEM fuel cell model with consistent treatment of water transport in MEA
Meng, Hua
In this paper, a three-dimensional PEM fuel cell model with a consistent water transport treatment in the membrane electrode assembly (MEA) has been developed. In this new PEM fuel cell model, the conservation equation of the water concentration is solved in the gas channels, gas diffusion layers, and catalyst layers while a conservation equation of the water content is established in the membrane. These two equations are connected using a set of internal boundary conditions based on the thermodynamic phase equilibrium and flux equality at the interface of the membrane and the catalyst layer. The existing fictitious water concentration treatment, which assumes thermodynamic phase equilibrium between the water content in the membrane phase and the water concentration, is applied in the two catalyst layers to consider water transport in the membrane phase. Since all the other conservation equations are still developed and solved in the single-domain framework without resort to interfacial boundary conditions, the present new PEM fuel cell model is termed as a mixed-domain method. Results from this mixed-domain approach have been compared extensively with those from the single-domain method, showing good accuracy in terms of not only cell performances and current distributions but also water content variations in the membrane.
Standard Model Vacuum Stability and Weyl Consistency Conditions
DEFF Research Database (Denmark)
Antipin, Oleg; Gillioz, Marc; Krog, Jens;
2013-01-01
At high energy the standard model possesses conformal symmetry at the classical level. This is reflected at the quantum level by relations between the different beta functions of the model. These relations are known as the Weyl consistency conditions. We show that it is possible to satisfy them...... order by order in perturbation theory, provided that a suitable coupling constant counting scheme is used. As a direct phenomenological application, we study the stability of the standard model vacuum at high energies and compare with previous computations violating the Weyl consistency conditions....
Quantum monadology: a consistent world model for consciousness and physics.
Nakagomi, Teruaki
2003-04-01
The NL world model presented in the previous paper is embodied by use of relativistic quantum mechanics, which reveals the significance of the reduction of quantum states and the relativity principle, and locates consciousness and the concept of flowing time consistently in physics. This model provides a consistent framework to solve apparent incompatibilities between consciousness (as our interior experience) and matter (as described by quantum mechanics and relativity theory). Does matter have an inside? What is the flowing time now? Does physics allow the indeterminism by volition? The problem of quantum measurement is also resolved in this model.
Consistency and Reconciliation Model In Regional Development Planning
Directory of Open Access Journals (Sweden)
Dina Suryawati
2016-10-01
Full Text Available The aim of this study was to identify the problems and determine the conceptual model of regional development planning. Regional development planning is a systemic, complex and unstructured process. Therefore, this study used soft systems methodology to outline unstructured issues with a structured approach. The conceptual models that were successfully constructed in this study are a model of consistency and a model of reconciliation. Regional development planning is a process that is well-integrated with central planning and inter-regional planning documents. Integration and consistency of regional planning documents are very important in order to achieve the development goals that have been set. On the other hand, the process of development planning in the region involves technocratic system, that is, both top-down and bottom-up system of participation. Both must be balanced, do not overlap and do not dominate each other. regional, development, planning, consistency, reconciliation
Model-Consistent Sparse Estimation through the Bootstrap
Bach, Francis
2009-01-01
We consider the least-square linear regression problem with regularization by the $\\ell^1$-norm, a problem usually referred to as the Lasso. In this paper, we first present a detailed asymptotic analysis of model consistency of the Lasso in low-dimensional settings. For various decays of the regularization parameter, we compute asymptotic equivalents of the probability of correct model selection. For a specific rate decay, we show that the Lasso selects all the variables that should enter the model with probability tending to one exponentially fast, while it selects all other variables with strictly positive probability. We show that this property implies that if we run the Lasso for several bootstrapped replications of a given sample, then intersecting the supports of the Lasso bootstrap estimates leads to consistent model selection. This novel variable selection procedure, referred to as the Bolasso, is extended to high-dimensional settings by a provably consistent two-step procedure.
Mesoscopic models of biological membranes
DEFF Research Database (Denmark)
Venturoli, M.; Sperotto, Maria Maddalena; Kranenburg, M.;
2006-01-01
, as model systems to understand the fundamental properties of biomembranes. The properties of lipid bilayers can be studied at different time and length scales. For some properties it is sufficient to envision a membrane as an elastic sheet, while for others it is important to take into account the details...... of the individual atoms. In this review, we focus on an intermediate level, where groups of atoms are lumped into pseudo-particles to arrive at a coarse-grained, or mesoscopic, description of a bilayer, which is subsequently studied using molecular simulation. The aim of this review is to compare various strategies...
Consistency analysis of a nonbirefringent Lorentz-violating planar model
Casana, Rodolfo; Moreira, Roemir P M
2011-01-01
In this work analyze the physical consistency of a nonbirefringent Lorentz-violating planar model via the analysis of the pole structure of its Feynman's propagators. The nonbirefringent planar model, obtained from the dimensional reduction of the CPT-even gauge sector of the standard model extension, is composed of a gauge and a scalar fields, being affected by Lorentz-violating (LIV) coefficients encoded in the symmetric tensor $\\kappa_{\\mu\
Modeling and simulation of membrane process
Staszak, Maciej
2017-06-01
The article presents the different approaches to polymer membrane mathematical modeling. Traditional models based on experimental physicochemical correlations and balance models are presented in the first part. Quantum and molecular mechanics models are presented as they are more popular for polymer membranes in fuel cells. The initial part is enclosed by neural network models which found their use for different types of processes in polymer membranes. The second part is devoted to models of fluid dynamics. The computational fluid dynamics technique can be divided into solving of Navier-Stokes equations and into Boltzmann lattice models. Both approaches are presented focusing on membrane processes.
Multiscale Parameter Regionalization for consistent global water resources modelling
Wanders, Niko; Wood, Eric; Pan, Ming; Samaniego, Luis; Thober, Stephan; Kumar, Rohini; Sutanudjaja, Edwin; van Beek, Rens; Bierkens, Marc F. P.
2017-04-01
Due to an increasing demand for high- and hyper-resolution water resources information, it has become increasingly important to ensure consistency in model simulations across scales. This consistency can be ensured by scale independent parameterization of the land surface processes, even after calibration of the water resource model. Here, we use the Multiscale Parameter Regionalization technique (MPR, Samaniego et al. 2010, WRR) to allow for a novel, spatially consistent, scale independent parameterization of the global water resource model PCR-GLOBWB. The implementation of MPR in PCR-GLOBWB allows for calibration at coarse resolutions and subsequent parameter transfer to the hyper-resolution. In this study, the model was calibrated at 50 km resolution over Europe and validation carried out at resolutions of 50 km, 10 km and 1 km. MPR allows for a direct transfer of the calibrated transfer function parameters across scales and we find that we can maintain consistent land-atmosphere fluxes across scales. Here we focus on the 2003 European drought and show that the new parameterization allows for high-resolution calibrated simulations of water resources during the drought. For example, we find a reduction from 29% to 9.4% in the percentile difference in the annual evaporative flux across scales when compared against default simulations. Soil moisture errors are reduced from 25% to 6.9%, clearly indicating the benefits of the MPR implementation. This new parameterization allows us to show more spatial detail in water resources simulations that are consistent across scales and also allow validation of discharge for smaller catchments, even with calibrations at a coarse 50 km resolution. The implementation of MPR allows for novel high-resolution calibrated simulations of a global water resources model, providing calibrated high-resolution model simulations with transferred parameter sets from coarse resolutions. The applied methodology can be transferred to other
Emergent Dynamics of a Thermodynamically Consistent Particle Model
Ha, Seung-Yeal; Ruggeri, Tommaso
2017-03-01
We present a thermodynamically consistent particle (TCP) model motivated by the theory of multi-temperature mixture of fluids in the case of spatially homogeneous processes. The proposed model incorporates the Cucker-Smale (C-S) type flocking model as its isothermal approximation. However, it is more complex than the C-S model, because the mutual interactions are not only " mechanical" but are also affected by the "temperature effect" as individual particles may exhibit distinct internal energies. We develop a framework for asymptotic weak and strong flocking in the context of the proposed model.
Dynamic modeling of ultrafiltration membranes for whey separation processes
Saltık, M.B.; Özkan, Leyla; Jacobs, Marc; Padt, van der Albert
2017-01-01
In this paper, we present a control relevant rigorous dynamic model for an ultrafiltration membrane unit in a whey separation process. The model consists of a set of differential algebraic equations and is developed for online model based applications such as model based control and process monitori
Viscoelastic models with consistent hypoelasticity for fluids undergoing finite deformations
Altmeyer, Guillaume; Rouhaud, Emmanuelle; Panicaud, Benoit; Roos, Arjen; Kerner, Richard; Wang, Mingchuan
2015-08-01
Constitutive models of viscoelastic fluids are written with rate-form equations when considering finite deformations. Trying to extend the approach used to model these effects from an infinitesimal deformation to a finite transformation framework, one has to ensure that the tensors and their rates are indifferent with respect to the change of observer and to the superposition with rigid body motions. Frame-indifference problems can be solved with the use of an objective stress transport, but the choice of such an operator is not obvious and the use of certain transports usually leads to physically inconsistent formulation of hypoelasticity. The aim of this paper is to present a consistent formulation of hypoelasticity and to combine it with a viscosity model to construct a consistent viscoelastic model. In particular, the hypoelastic model is reversible.
Bolasso: model consistent Lasso estimation through the bootstrap
Bach, Francis
2008-01-01
We consider the least-square linear regression problem with regularization by the l1-norm, a problem usually referred to as the Lasso. In this paper, we present a detailed asymptotic analysis of model consistency of the Lasso. For various decays of the regularization parameter, we compute asymptotic equivalents of the probability of correct model selection (i.e., variable selection). For a specific rate decay, we show that the Lasso selects all the variables that should enter the model with probability tending to one exponentially fast, while it selects all other variables with strictly positive probability. We show that this property implies that if we run the Lasso for several bootstrapped replications of a given sample, then intersecting the supports of the Lasso bootstrap estimates leads to consistent model selection. This novel variable selection algorithm, referred to as the Bolasso, is compared favorably to other linear regression methods on synthetic data and datasets from the UCI machine learning rep...
Matar, Gerald K.
2017-06-21
Finding efficient biofouling control strategies requires a better understanding of the microbial ecology of membrane biofilm communities in membrane bioreactors (MBRs). Studies that characterized the membrane biofilm communities in lab-and pilot-scale MBRs are numerous, yet similar studies in full-scale MBRs are limited. Also, most of these studies have characterized the mature biofilm communities with very few studies addressing early biofilm communities. In this study, five full-scale MBRs located in Seattle (Washington, U.S.A.) were selected to address two questions concerning membrane biofilm communities (early and mature): (i) Is the assembly of biofilm communities (early and mature) the result of random immigration of species from the source community (i.e. activated sludge)? and (ii) Is there a core membrane biofilm community in full-scale MBRs? Membrane biofilm (early and mature) and activated sludge (AS) samples were collected from the five MBRs, and 16S rRNA gene sequencing was applied to investigate the bacterial communities of AS and membrane biofilms (early and mature). Alpha and beta diversity measures revealed clear differences in the bacterial community structure between the AS and biofilm (early and mature) samples in the five full-scale MBRs. These differences were mainly due to the presence of large number of unique but rare operational taxonomic units (∼13% of total reads in each MBR) in each sample. In contrast, a high percentage (∼87% of total reads in each MBR) of sequence reads was shared between AS and biofilm samples in each MBR, and these shared sequence reads mainly belong to the dominant taxa in these samples. Despite the large fraction of shared sequence reads between AS and biofilm samples, simulated biofilm communities from random sampling of the respective AS community revealed that biofilm communities differed significantly from the random assemblages (P < 0.001 for each MBR), indicating that the biofilm communities (early
Detection and quantification of flow consistency in business process models
DEFF Research Database (Denmark)
Burattin, Andrea; Bernstein, Vered; Neurauter, Manuel
2017-01-01
Business process models abstract complex business processes by representing them as graphical models. Their layout, as determined by the modeler, may have an effect when these models are used. However, this effect is currently not fully understood. In order to systematically study this effect......, a basic set of measurable key visual features is proposed, depicting the layout properties that are meaningful to the human user. The aim of this research is thus twofold: first, to empirically identify key visual features of business process models which are perceived as meaningful to the user and second......, to show how such features can be quantified into computational metrics, which are applicable to business process models. We focus on one particular feature, consistency of flow direction, and show the challenges that arise when transforming it into a precise metric. We propose three different metrics...
A consistent transported PDF model for treating differential molecular diffusion
Wang, Haifeng; Zhang, Pei
2016-11-01
Differential molecular diffusion is a fundamentally significant phenomenon in all multi-component turbulent reacting or non-reacting flows caused by the different rates of molecular diffusion of energy and species concentrations. In the transported probability density function (PDF) method, the differential molecular diffusion can be treated by using a mean drift model developed by McDermott and Pope. This model correctly accounts for the differential molecular diffusion in the scalar mean transport and yields a correct DNS limit of the scalar variance production. The model, however, misses the molecular diffusion term in the scalar variance transport equation, which yields an inconsistent prediction of the scalar variance in the transported PDF method. In this work, a new model is introduced to remedy this problem that can yield a consistent scalar variance prediction. The model formulation along with its numerical implementation is discussed, and the model validation is conducted in a turbulent mixing layer problem.
Simplified Models for Dark Matter Face their Consistent Completions
Energy Technology Data Exchange (ETDEWEB)
Goncalves, Dorival [Pittsburgh U.; Machado, Pedro N. [Madrid, IFT; No, Jose Miguel [Sussex U.
2016-11-14
Simplified dark matter models have been recently advocated as a powerful tool to exploit the complementarity between dark matter direct detection, indirect detection and LHC experimental probes. Focusing on pseudoscalar mediators between the dark and visible sectors, we show that the simplified dark matter model phenomenology departs significantly from that of consistent ${SU(2)_{\\mathrm{L}} \\times U(1)_{\\mathrm{Y}}}$ gauge invariant completions. We discuss the key physics simplified models fail to capture, and its impact on LHC searches. Notably, we show that resonant mono-Z searches provide competitive sensitivities to standard mono-jet analyses at $13$ TeV LHC.
Simplified Models for Dark Matter Face their Consistent Completions
Goncalves, Dorival; No, Jose Miguel
2016-01-01
Simplified dark matter models have been recently advocated as a powerful tool to exploit the complementarity between dark matter direct detection, indirect detection and LHC experimental probes. Focusing on pseudoscalar mediators between the dark and visible sectors, we show that the simplified dark matter model phenomenology departs significantly from that of consistent ${SU(2)_{\\mathrm{L}} \\times U(1)_{\\mathrm{Y}}}$ gauge invariant completions. We discuss the key physics simplified models fail to capture, and its impact on LHC searches. Notably, we show that resonant mono-Z searches provide competitive sensitivities to standard mono-jet analyses at $13$ TeV LHC.
Towards consistent nuclear models and comprehensive nuclear data evaluations
Energy Technology Data Exchange (ETDEWEB)
Bouland, O [Los Alamos National Laboratory; Hale, G M [Los Alamos National Laboratory; Lynn, J E [Los Alamos National Laboratory; Talou, P [Los Alamos National Laboratory; Bernard, D [FRANCE; Litaize, O [FRANCE; Noguere, G [FRANCE; De Saint Jean, C [FRANCE; Serot, O [FRANCE
2010-01-01
The essence of this paper is to enlighten the consistency achieved nowadays in nuclear data and uncertainties assessments in terms of compound nucleus reaction theory from neutron separation energy to continuum. Making the continuity of theories used in resolved (R-matrix theory), unresolved resonance (average R-matrix theory) and continuum (optical model) rangcs by the generalization of the so-called SPRT method, consistent average parameters are extracted from observed measurements and associated covariances are therefore calculated over the whole energy range. This paper recalls, in particular, recent advances on fission cross section calculations and is willing to suggest some hints for future developments.
A Consistent Pricing Model for Index Options and Volatility Derivatives
DEFF Research Database (Denmark)
Cont, Rama; Kokholm, Thomas
options on the underlying asset. The model has the convenient feature of decoupling the vanilla skews from spot/volatility correlations and allowing for different conditional correlations in large and small spot/volatility moves. We show that our model can simultaneously fit prices of European options......We propose and study a flexible modeling framework for the joint dynamics of an index and a set of forward variance swap rates written on this index, allowing options on forward variance swaps and options on the underlying index to be priced consistently. Our model reproduces various empirically...... on S&P 500 across strikes and maturities as well as options on the VIX volatility index. The calibration of the model is done in two steps, first by matching VIX option prices and then by matching prices of options on the underlying....
A Consistent Pricing Model for Index Options and Volatility Derivatives
DEFF Research Database (Denmark)
Kokholm, Thomas
on the underlying asset. The model has the convenient feature of decoupling the vanilla skews from spot/volatility correlations and allowing for different conditional correlations in large and small spot/volatility moves. We show that our model can simultaneously fit prices of European options on S&P 500 across......We propose and study a flexible modeling framework for the joint dynamics of an index and a set of forward variance swap rates written on this index, allowing options on forward variance swaps and options on the underlying index to be priced consistently. Our model reproduces various empirically...... strikes and maturities as well as options on the VIX volatility index. The calibration of the model is done in two steps, first by matching VIX option prices and then by matching prices of options on the underlying....
Consistency Across Standards or Standards in a New Business Model
Russo, Dane M.
2010-01-01
Presentation topics include: standards in a changing business model, the new National Space Policy is driving change, a new paradigm for human spaceflight, consistency across standards, the purpose of standards, danger of over-prescriptive standards, a balance is needed (between prescriptive and general standards), enabling versus inhibiting, characteristics of success-oriented standards, characteristics of success-oriented standards, and conclusions. Additional slides include NASA Procedural Requirements 8705.2B identifies human rating standards and requirements, draft health and medical standards for human rating, what's been done, government oversight models, examples of consistency from anthropometry, examples of inconsistency from air quality and appendices of government and non-governmental human factors standards.
Interaction of Defensins with Model Cell Membranes
Sanders, Lori K.; Schmidt, Nathan W.; Yang, Lihua; Mishra, Abhijit; Gordon, Vernita D.; Selsted, Michael E.; Wong, Gerard C. L.
2009-03-01
Antimicrobial peptides (AMPs) comprise a key component of innate immunity for a wide range of multicellular organisms. For many AMPs, activity comes from their ability to selectively disrupt and lyse bacterial cell membranes. There are a number of proposed models for this action, but the detailed molecular mechanism of selective membrane permeation remains unclear. Theta defensins are circularized peptides with a high degree of selectivity. We investigate the interaction of model bacterial and eukaryotic cell membranes with theta defensins RTD-1, BTD-7, and compare them to protegrin PG-1, a prototypical AMP, using synchrotron small angle x-ray scattering (SAXS). The relationship between membrane composition and peptide induced changes in membrane curvature and topology is examined. By comparing the membrane phase behavior induced by these different peptides we will discuss the importance of amino acid composition and placement on membrane rearrangement.
A detailed self-consistent vertical Milky Way disc model
Directory of Open Access Journals (Sweden)
Gao S.
2012-02-01
Full Text Available We present a self-consistent vertical disc model of thin and thick disc in the solar vicinity. The model is optimized to fit the local kinematics of main sequence stars by varying the star formation history and the dynamical heating function. The star formation history and the dynamical heating function are not uniquely determined by the local kinematics alone. For four different pairs of input functions we calculate star count predictions at high galactic latitude as a function of colour. The comparison with North Galactic Pole data of SDSS/SEGUE leads to significant constraints of the local star formation history.
Radio data and synchrotron emission in consistent cosmic ray models
Bringmann, Torsten; Lineros, Roberto A
2011-01-01
We consider the propagation of electrons in phenomenological two-zone diffusion models compatible with cosmic-ray nuclear data and compute the diffuse synchrotron emission resulting from their interaction with galactic magnetic fields. We find models in agreement not only with cosmic ray data but also with radio surveys at essentially all frequencies. Requiring such a globally consistent description strongly disfavors both a very large (L>15 kpc) and small (L<1 kpc) effective size of the diffusive halo. This has profound implications for, e.g., indirect dark matter searches.
A Consistent Pricing Model for Index Options and Volatility Derivatives
DEFF Research Database (Denmark)
Kokholm, Thomas
We propose a flexible modeling framework for the joint dynamics of an index and a set of forward variance swap rates written on this index. Our model reproduces various empirically observed properties of variance swap dynamics and enables volatility derivatives and options on the underlying index...... to be priced consistently, while allowing for jumps in volatility and returns. An affine specification using Lévy processes as building blocks leads to analytically tractable pricing formulas for volatility derivatives, such as VIX options, as well as efficient numerical methods for pricing of European options...
A Consistent Pricing Model for Index Options and Volatility Derivatives
DEFF Research Database (Denmark)
Cont, Rama; Kokholm, Thomas
2013-01-01
We propose a flexible modeling framework for the joint dynamics of an index and a set of forward variance swap rates written on this index. Our model reproduces various empirically observed properties of variance swap dynamics and enables volatility derivatives and options on the underlying index...... to be priced consistently, while allowing for jumps in volatility and returns. An affine specification using Lévy processes as building blocks leads to analytically tractable pricing formulas for volatility derivatives, such as VIX options, as well as efficient numerical methods for pricing of European options...
Self consistent modeling of accretion columns in accretion powered pulsars
Falkner, Sebastian; Schwarm, Fritz-Walter; Wolff, Michael Thomas; Becker, Peter A.; Wilms, Joern
2016-04-01
We combine three physical models to self-consistently derive the observed flux and pulse profiles of neutron stars' accretion columns. From the thermal and bulk Comptonization model by Becker & Wolff (2006) we obtain seed photon continua produced in the dense inner regions of the accretion column. In a thin outer layer these seed continua are imprinted with cyclotron resonant scattering features calculated using Monte Carlo simulations. The observed phase and energy dependent flux corresponding to these emission profiles is then calculated, taking relativistic light bending into account. We present simulated pulse profiles and the predicted dependency of the observable X-ray spectrum as a function of pulse phase.
A Consistent Pricing Model for Index Options and Volatility Derivatives
DEFF Research Database (Denmark)
Kokholm, Thomas
We propose a flexible modeling framework for the joint dynamics of an index and a set of forward variance swap rates written on this index. Our model reproduces various empirically observed properties of variance swap dynamics and enables volatility derivatives and options on the underlying index...... to be priced consistently, while allowing for jumps in volatility and returns. An affine specification using Lévy processes as building blocks leads to analytically tractable pricing formulas for volatility derivatives, such as VIX options, as well as efficient numerical methods for pricing of European options...
A consistent collinear triad approximation for operational wave models
Salmon, J. E.; Smit, P. B.; Janssen, T. T.; Holthuijsen, L. H.
2016-08-01
In shallow water, the spectral evolution associated with energy transfers due to three-wave (or triad) interactions is important for the prediction of nearshore wave propagation and wave-driven dynamics. The numerical evaluation of these nonlinear interactions involves the evaluation of a weighted convolution integral in both frequency and directional space for each frequency-direction component in the wave field. For reasons of efficiency, operational wave models often rely on a so-called collinear approximation that assumes that energy is only exchanged between wave components travelling in the same direction (collinear propagation) to eliminate the directional convolution. In this work, we show that the collinear approximation as presently implemented in operational models is inconsistent. This causes energy transfers to become unbounded in the limit of unidirectional waves (narrow aperture), and results in the underestimation of energy transfers in short-crested wave conditions. We propose a modification to the collinear approximation to remove this inconsistency and to make it physically more realistic. Through comparison with laboratory observations and results from Monte Carlo simulations, we demonstrate that the proposed modified collinear model is consistent, remains bounded, smoothly converges to the unidirectional limit, and is numerically more robust. Our results show that the modifications proposed here result in a consistent collinear approximation, which remains bounded and can provide an efficient approximation to model nonlinear triad effects in operational wave models.
Warped 5D Standard Model Consistent with EWPT
Cabrer, Joan A; Quiros, Mariano
2011-01-01
For a 5D Standard Model propagating in an AdS background with an IR localized Higgs, compatibility of bulk KK gauge modes with EWPT yields a phenomenologically unappealing KK spectrum (m > 12.5 TeV) and leads to a "little hierarchy problem". For a bulk Higgs the solution to the hierarchy problem reduces the previous bound only by sqrt(3). As a way out, models with an enhanced bulk gauge symmetry SU(2)_R x U(1)_(B-L) were proposed. In this note we describe a much simpler (5D Standard) Model, where introduction of an enlarged gauge symmetry is no longer required. It is based on a warped gravitational background which departs from AdS at the IR brane and a bulk propagating Higgs. The model is consistent with EWPT for a range of KK masses within the LHC reach.
Consistent regularization and renormalization in models with inhomogeneous phases
Adhikari, Prabal
2016-01-01
In many models in condensed matter physics and high-energy physics, one finds inhomogeneous phases at high density and low temperature. These phases are characterized by a spatially dependent condensate or order parameter. A proper calculation requires that one takes the vacuum fluctuations of the model into account. These fluctuations are ultraviolet divergent and must be regularized. We discuss different consistent ways of regularizing and renormalizing quantum fluctuations, focusing on a symmetric energy cutoff scheme and dimensional regularization. We apply these techniques calculating the vacuum energy in the NJL model in 1+1 dimensions in the large-$N_c$ limit and the 3+1 dimensional quark-meson model in the mean-field approximation both for a one-dimensional chiral-density wave.
Consistent regularization and renormalization in models with inhomogeneous phases
Adhikari, Prabal; Andersen, Jens O.
2017-02-01
In many models in condensed matter and high-energy physics, one finds inhomogeneous phases at high density and low temperature. These phases are characterized by a spatially dependent condensate or order parameter. A proper calculation requires that one takes the vacuum fluctuations of the model into account. These fluctuations are ultraviolet divergent and must be regularized. We discuss different ways of consistently regularizing and renormalizing quantum fluctuations, focusing on momentum cutoff, symmetric energy cutoff, and dimensional regularization. We apply these techniques calculating the vacuum energy in the Nambu-Jona-Lasinio model in 1 +1 dimensions in the large-Nc limit and in the 3 +1 dimensional quark-meson model in the mean-field approximation both for a one-dimensional chiral-density wave.
Self-consistent triaxial de Zeeuw-Carollo Models
Thakur, Parijat; Das, Mousumi; Chakraborty, D K; Ann, H B
2007-01-01
We use the usual method of Schwarzschild to construct self-consistent solutions for the triaxial de Zeeuw & Carollo (1996) models with central density cusps. ZC96 models are triaxial generalisations of spherical $\\gamma$-models of Dehnen whose densities vary as $r^{-\\gamma}$ near the center and $r^{-4}$ at large radii and hence, possess a central density core for $\\gamma=0$ and cusps for $\\gamma > 0$. We consider four triaxial models from ZC96, two prolate triaxials: $(p, q) = (0.65, 0.60)$ with $\\gamma = 1.0$ and 1.5, and two oblate triaxials: $(p, q) = (0.95, 0.60)$ with $\\gamma = 1.0$ and 1.5. We compute 4500 orbits in each model for time periods of $10^{5} T_{D}$. We find that a large fraction of the orbits in each model are stochastic by means of their nonzero Liapunov exponents. The stochastic orbits in each model can sustain regular shapes for $\\sim 10^{3} T_{D}$ or longer, which suggests that they diffuse slowly through their allowed phase-space. Except for the oblate triaxial models with $\\gamma ...
Are paleoclimate model ensembles consistent with the MARGO data synthesis?
Directory of Open Access Journals (Sweden)
J. C. Hargreaves
2011-03-01
Full Text Available We investigate the consistency of various ensembles of model simulations with the Multiproxy Approach for the Reconstruction of the Glacial Ocean Surface (MARGO sea surface temperature data synthesis. We discover that while two multi-model ensembles, created through the Paleoclimate Model Intercomparison Projects (PMIP and PMIP2, pass our simple tests of reliability, an ensemble based on parameter variation in a single model does not perform so well. We show that accounting for observational uncertainty in the MARGO database is of prime importance for correctly evaluating the ensembles. Perhaps surprisingly, the inclusion of a coupled dynamical ocean (compared to the use of a slab ocean does not appear to cause a wider spread in the sea surface temperature anomalies, but rather causes systematic changes with more heat transported north in the Atlantic. There is weak evidence that the sea surface temperature data may be more consistent with meridional overturning in the North Atlantic being similar for the LGM and the present day, however, the small size of the PMIP2 ensemble prevents any statistically significant results from being obtained.
Are paleoclimate model ensembles consistent with the MARGO data synthesis?
Directory of Open Access Journals (Sweden)
J. C. Hargreaves
2011-08-01
Full Text Available We investigate the consistency of various ensembles of climate model simulations with the Multiproxy Approach for the Reconstruction of the Glacial Ocean Surface (MARGO sea surface temperature data synthesis. We discover that while two multi-model ensembles, created through the Paleoclimate Model Intercomparison Projects (PMIP and PMIP2, pass our simple tests of reliability, an ensemble based on parameter variation in a single model does not perform so well. We show that accounting for observational uncertainty in the MARGO database is of prime importance for correctly evaluating the ensembles. Perhaps surprisingly, the inclusion of a coupled dynamical ocean (compared to the use of a slab ocean does not appear to cause a wider spread in the sea surface temperature anomalies, but rather causes systematic changes with more heat transported north in the Atlantic. There is weak evidence that the sea surface temperature data may be more consistent with meridional overturning in the North Atlantic being similar for the LGM and the present day. However, the small size of the PMIP2 ensemble prevents any statistically significant results from being obtained.
Consistency analysis of a nonbirefringent Lorentz-violating planar model
Energy Technology Data Exchange (ETDEWEB)
Casana, Rodolfo; Ferreira, Manoel M.; Moreira, Roemir P.M. [Universidade Federal do Maranhao (UFMA), Departamento de Fisica, Sao Luis, MA (Brazil)
2012-07-15
In this work analyze the physical consistency of a nonbirefringent Lorentz-violating planar model via the analysis of the pole structure of its Feynman propagators. The nonbirefringent planar model, obtained from the dimensional reduction of the CPT-even gauge sector of the standard model extension, is composed of a gauge and a scalar fields, being affected by Lorentz-violating (LIV) coefficients encoded in the symmetric tensor {kappa}{sub {mu}{nu}}. The propagator of the gauge field is explicitly evaluated and expressed in terms of linear independent symmetric tensors, presenting only one physical mode. The same holds for the scalar propagator. A consistency analysis is performed based on the poles of the propagators. The isotropic parity-even sector is stable, causal and unitary mode for 0{<=}{kappa}{sub 00}<1. On the other hand, the anisotropic sector is stable and unitary but in general noncausal. Finally, it is shown that this planar model interacting with a {lambda}{phi}{sup 4}-Higgs field supports compact-like vortex configurations. (orig.)
Consistency analysis of a nonbirefringent Lorentz-violating planar model
Casana, Rodolfo; Ferreira, Manoel M.; Moreira, Roemir P. M.
2012-07-01
In this work analyze the physical consistency of a nonbirefringent Lorentz-violating planar model via the analysis of the pole structure of its Feynman propagators. The nonbirefringent planar model, obtained from the dimensional reduction of the CPT-even gauge sector of the standard model extension, is composed of a gauge and a scalar fields, being affected by Lorentz-violating (LIV) coefficients encoded in the symmetric tensor κ μν . The propagator of the gauge field is explicitly evaluated and expressed in terms of linear independent symmetric tensors, presenting only one physical mode. The same holds for the scalar propagator. A consistency analysis is performed based on the poles of the propagators. The isotropic parity-even sector is stable, causal and unitary mode for 0≤ κ 00<1. On the other hand, the anisotropic sector is stable and unitary but in general noncausal. Finally, it is shown that this planar model interacting with a λ| φ|4-Higgs field supports compactlike vortex configurations.
Burlatsky, S F; O'Neill, J; Atrazhev, V V; Varyukhin, A N; Dmitriev, D V; Erikhman, N S
2013-01-01
Under typical PEM fuel cell operating conditions, part of membrane electrode assembly is subjected to humidity cycling due to variation of inlet gas RH and/or flow rate. Cyclic membrane hydration/dehydration would cause cyclic swelling/shrinking of the unconstrained membrane. In a constrained membrane, it causes cyclic stress resulting in mechanical failure in the area adjacent to the gas inlet. A mathematical modeling framework for prediction of the lifetime of a PEM FC membrane subjected to hydration cycling is developed in this paper. The model predicts membrane lifetime as a function of RH cycling amplitude and membrane mechanical properties. The modeling framework consists of three model components: a fuel cell RH distribution model, a hydration/dehydration induced stress model that predicts stress distribution in the membrane, and a damage accrual model that predicts membrane life-time. Short descriptions of the model components along with overall framework are presented in the paper. The model was used...
Macroscopic Modeling of Polymer-Electrolyte Membranes
Energy Technology Data Exchange (ETDEWEB)
Weber, A.Z.; Newman, J.
2007-04-01
In this chapter, the various approaches for the macroscopic modeling of transport phenomena in polymer-electrolyte membranes are discussed. This includes general background and modeling methodologies, as well as exploration of the governing equations and some membrane-related topic of interest.
Self-Consistent Modeling of Reionization in Cosmological Hydrodynamical Simulations
Oñorbe, Jose; Lukić, Zarija
2016-01-01
The ultraviolet background (UVB) emitted by quasars and galaxies governs the ionization and thermal state of the intergalactic medium (IGM), regulates the formation of high-redshift galaxies, and is thus a key quantity for modeling cosmic reionization. The vast majority of cosmological hydrodynamical simulations implement the UVB via a set of spatially uniform photoionization and photoheating rates derived from UVB synthesis models. We show that simulations using canonical UVB rates reionize, and perhaps more importantly, spuriously heat the IGM, much earlier z ~ 15 than they should. This problem arises because at z > 6, where observational constraints are non-existent, the UVB amplitude is far too high. We introduce a new methodology to remedy this issue, and generate self-consistent photoionization and photoheating rates to model any chosen reionization history. Following this approach, we run a suite of hydrodynamical simulations of different reionization scenarios, and explore the impact of the timing of ...
Consistent Static Models of Local Thermospheric Composition Profiles
Picone, J M; Drob, D P
2016-01-01
The authors investigate the ideal, nondriven multifluid equations of motion to identify consistent (i.e., truly stationary), mechanically static models for composition profiles within the thermosphere. These physically faithful functions are necessary to define the parametric core of future empirical atmospheric models and climatologies. Based on the strength of interspecies coupling, the thermosphere has three altitude regions: (1) the lower thermosphere (herein z ~200 km), in which the species flows are approximately uncoupled; and (3) a transition region in between, where the effective species particle mass and the effective species vertical flow interpolate between the solutions for the upper and lower thermosphere. We place this view in the context of current terminology within the community, i.e., a fully mixed (lower) region and an upper region in diffusive equilibrium (DE). The latter condition, DE, currently used in empirical composition models, does not represent a truly static composition profile ...
Thermodynamically consistent model of brittle oil shales under overpressure
Izvekov, Oleg
2016-04-01
The concept of dual porosity is a common way for simulation of oil shale production. In the frame of this concept the porous fractured media is considered as superposition of two permeable continua with mass exchange. As a rule the concept doesn't take into account such as the well-known phenomenon as slip along natural fractures, overpressure in low permeability matrix and so on. Overpressure can lead to development of secondary fractures in low permeability matrix in the process of drilling and pressure reduction during production. In this work a new thermodynamically consistent model which generalizes the model of dual porosity is proposed. Particularities of the model are as follows. The set of natural fractures is considered as permeable continuum. Damage mechanics is applied to simulation of secondary fractures development in low permeability matrix. Slip along natural fractures is simulated in the frame of plasticity theory with Drucker-Prager criterion.
A minimal model of self-consistent partial synchrony
Clusella, Pau; Politi, Antonio; Rosenblum, Michael
2016-09-01
We show that self-consistent partial synchrony in globally coupled oscillatory ensembles is a general phenomenon. We analyze in detail appearance and stability properties of this state in possibly the simplest setup of a biharmonic Kuramoto-Daido phase model as well as demonstrate the effect in limit-cycle relaxational Rayleigh oscillators. Such a regime extends the notion of splay state from a uniform distribution of phases to an oscillating one. Suitable collective observables such as the Kuramoto order parameter allow detecting the presence of an inhomogeneous distribution. The characteristic and most peculiar property of self-consistent partial synchrony is the difference between the frequency of single units and that of the macroscopic field.
Short Polymer Modeling using Self-Consistent Integral Equation Method
Kim, Yeongyoon; Park, So Jung; Kim, Jaeup
2014-03-01
Self-consistent field theory (SCFT) is an excellent mean field theoretical tool for predicting the morphologies of polymer based materials. In the standard SCFT, the polymer is modeled as a Gaussian chain which is suitable for a polymer of high molecular weight, but not necessarily for a polymer of low molecular weight. In order to overcome this limitation, Matsen and coworkers have recently developed SCFT of discrete polymer chains in which one polymer is modeled as finite number of beads joined by freely jointed bonds of fixed length. In their model, the diffusion equation of the canonical SCFT is replaced by an iterative integral equation, and the full spectral method is used for the production of the phase diagram of short block copolymers. In this study, for the finite length chain problem, we apply pseudospectral method which is the most efficient numerical scheme to solve the iterative integral equation. We use this new numerical method to investigate two different types of polymer bonds: spring-beads model and freely-jointed chain model. By comparing these results with those of the Gaussian chain model, the influences on the morphologies of diblock copolymer melts due to the chain length and the type of bonds are examined. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (no. 2012R1A1A2043633).
Self consistent tight binding model for dissociable water
Lin, You; Wynveen, Aaron; Halley, J. W.; Curtiss, L. A.; Redfern, P. C.
2012-05-01
We report results of development of a self consistent tight binding model for water. The model explicitly describes the electrons of the liquid self consistently, allows dissociation of the water and permits fast direct dynamics molecular dynamics calculations of the fluid properties. It is parameterized by fitting to first principles calculations on water monomers, dimers, and trimers. We report calculated radial distribution functions of the bulk liquid, a phase diagram and structure of solvated protons within the model as well as ac conductivity of a system of 96 water molecules of which one is dissociated. Structural properties and the phase diagram are in good agreement with experiment and first principles calculations. The estimated DC conductivity of a computational sample containing a dissociated water molecule was an order of magnitude larger than that reported from experiment though the calculated ratio of proton to hydroxyl contributions to the conductivity is very close to the experimental value. The conductivity results suggest a Grotthuss-like mechanism for the proton component of the conductivity.
Mean-field theory and self-consistent dynamo modeling
Energy Technology Data Exchange (ETDEWEB)
Yoshizawa, Akira; Yokoi, Nobumitsu [Tokyo Univ. (Japan). Inst. of Industrial Science; Itoh, Sanae-I [Kyushu Univ., Fukuoka (Japan). Research Inst. for Applied Mechanics; Itoh, Kimitaka [National Inst. for Fusion Science, Toki, Gifu (Japan)
2001-12-01
Mean-field theory of dynamo is discussed with emphasis on the statistical formulation of turbulence effects on the magnetohydrodynamic equations and the construction of a self-consistent dynamo model. The dynamo mechanism is sought in the combination of the turbulent residual-helicity and cross-helicity effects. On the basis of this mechanism, discussions are made on the generation of planetary magnetic fields such as geomagnetic field and sunspots and on the occurrence of flow by magnetic fields in planetary and fusion phenomena. (author)
Consistency of the tachyon warm inflationary universe models
Energy Technology Data Exchange (ETDEWEB)
Zhang, Xiao-Min; Zhu, Jian-Yang, E-mail: zhangxm@mail.bnu.edu.cn, E-mail: zhujy@bnu.edu.cn [Department of Physics, Beijing Normal University, Beijing 100875 (China)
2014-02-01
This study concerns the consistency of the tachyon warm inflationary models. A linear stability analysis is performed to find the slow-roll conditions, characterized by the potential slow-roll (PSR) parameters, for the existence of a tachyon warm inflationary attractor in the system. The PSR parameters in the tachyon warm inflationary models are redefined. Two cases, an exponential potential and an inverse power-law potential, are studied, when the dissipative coefficient Γ = Γ{sub 0} and Γ = Γ(φ), respectively. A crucial condition is obtained for a tachyon warm inflationary model characterized by the Hubble slow-roll (HSR) parameter ε{sub H}, and the condition is extendable to some other inflationary models as well. A proper number of e-folds is obtained in both cases of the tachyon warm inflation, in contrast to existing works. It is also found that a constant dissipative coefficient (Γ = Γ{sub 0}) is usually not a suitable assumption for a warm inflationary model.
A self-consistent spin-diffusion model for micromagnetics
Abert, Claas
2016-12-17
We propose a three-dimensional micromagnetic model that dynamically solves the Landau-Lifshitz-Gilbert equation coupled to the full spin-diffusion equation. In contrast to previous methods, we solve for the magnetization dynamics and the electric potential in a self-consistent fashion. This treatment allows for an accurate description of magnetization dependent resistance changes. Moreover, the presented algorithm describes both spin accumulation due to smooth magnetization transitions and due to material interfaces as in multilayer structures. The model and its finite-element implementation are validated by current driven motion of a magnetic vortex structure. In a second experiment, the resistivity of a magnetic multilayer structure in dependence of the tilting angle of the magnetization in the different layers is investigated. Both examples show good agreement with reference simulations and experiments respectively.
Tethered bimolecular lipid membranes - A novel model membrane platform
Energy Technology Data Exchange (ETDEWEB)
Knoll, Wolfgang; Koeper, Ingo; Naumann, Renate; Sinner, Eva-Kathrin [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)
2008-10-01
stabilization of lipid bilayers, i.e., the protein-tethered membrane. Our efforts in experimentally characterizing the resulting membrane functions and correlating the data with the structural details of the bilayer architectures are complemented by theoretical studies modeling the electrical and electrochemical response of functional tethered lipid bilayer membranes by extended SPICE simulations. (author)
Modelling and simulation of affinity membrane adsorption.
Boi, Cristiana; Dimartino, Simone; Sarti, Giulio C
2007-08-24
A mathematical model for the adsorption of biomolecules on affinity membranes is presented. The model considers convection, diffusion and adsorption kinetics on the membrane module as well as the influence of dead end volumes and lag times; an analysis of flow distribution on the whole system is also included. The parameters used in the simulations were obtained from equilibrium and dynamic experimental data measured for the adsorption of human IgG on A2P-Sartoepoxy affinity membranes. The identification of a bi-Langmuir kinetic mechanisms for the experimental system investigated was paramount for a correct process description and the simulated breakthrough curves were in good agreement with the experimental data. The proposed model provides a new insight into the phenomena involved in the adsorption on affinity membranes and it is a valuable tool to assess the use of membrane adsorbers in large scale processes.
Modeling anisotropic elasticity of fluid membranes
Ramakrishnan, N; Ipsen, John H; 10.1002/mats.201100002
2011-01-01
The biological membrane, which compartmentalizes the cell and its organelles, exhibit wide variety of macroscopic shapes of varying morphology and topology. A systematic understanding of the relation of membrane shapes to composition, external field, environmental conditions etc. have important biological relevance. Here we review the triangulated surface model, used in the macroscopic simulation of membranes and the associated Monte Carlo (DTMC) methods. New techniques to calculate surface quantifiers, that will facilitate the study of additional in-plane orientational degrees of freedom, has been introduced. The mere presence of a polar and nematic fields in the ordered phase drives the ground state conformations of the membrane to a cylinder and tetrahedron respectively.
Classical and Quantum Consistency of the DGP Model
Nicolis, A; Nicolis, Alberto; Rattazzi, Riccardo
2004-01-01
We study the Dvali-Gabadadze-Porrati model by the method of the boundary effective action. The truncation of this action to the bending mode \\pi consistently describes physics in a wide range of regimes both at the classical and at the quantum level. The Vainshtein effect, which restores agreement with precise tests of general relativity, follows straightforwardly. We give a simple and general proof of stability, i.e. absence of ghosts in the fluctuations, valid for most of the relevant cases, like for instance the spherical source in asymptotically flat space. However we confirm that around certain interesting self-accelerating cosmological solutions there is a ghost. We consider the issue of quantum corrections. Around flat space \\pi becomes strongly coupled below a macroscopic length of 1000 km, thus impairing the predictivity of the model. Indeed the tower of higher dimensional operators which is expected by a generic UV completion of the model limits predictivity at even larger length scales. We outline ...
Cholesterol transport in model membranes
Garg, Sumit; Porcar, Lionel; Butler, Paul; Perez-Salas, Ursula
2010-03-01
Physiological processes distribute cholesterol unevenly within the cell. The levels of cholesterol are maintained by intracellular transport and a disruption in the cell's ability to keep these normal levels will lead to disease. Exchange rates of cholesterol are generally studied in model systems using labeled lipid vesicles. Initially donor vesicles have all the cholesterol and acceptor vesicles are devoid of it. They are mixed and after some time the vesicles are separated and cholesterol is traced in each vesicle. The studies performed up to date have significant scatter indicating that the methodologies are not consistent. The present work shows in-situ Time-Resolved SANS studies of cholesterol exchange rates in unsaturated PC lipid vesicles. Molecular dynamics simulations were done to investigate the energetic and kinetic behavior of cholesterol in this system. This synergistic approach will provide insight into our efforts to understand cholesterol traffic.
Consistent constraints on the Standard Model Effective Field Theory
Berthier, Laure
2015-01-01
We develop the global constraint picture in the (linear) effective field theory generalisation of the Standard Model, incorporating data from detectors that operated at PEP, PETRA, TRISTAN, SpS, Tevatron, SLAC, LEPI and LEP II, as well as low energy precision data. We fit one hundred observables. We develop a theory error metric for this effective field theory, which is required when constraints on parameters at leading order in the power counting are to be pushed to the percent level, or beyond, unless the cut off scale is assumed to be large, $\\Lambda \\gtrsim \\, 3 \\, {\\rm TeV}$. We more consistently incorporate theoretical errors in this work, avoiding this assumption, and as a direct consequence bounds on some leading parameters are relaxed. We show how an $\\rm S,T$ analysis is modified by the theory errors we include as an illustrative example.
Creation of Consistent Burn Wounds: A Rat Model
Directory of Open Access Journals (Sweden)
Elijah Zhengyang Cai
2014-07-01
Full Text Available Background Burn infliction techniques are poorly described in rat models. An accurate study can only be achieved with wounds that are uniform in size and depth. We describe a simple reproducible method for creating consistent burn wounds in rats. Methods Ten male Sprague-Dawley rats were anesthetized and dorsum shaved. A 100 g cylindrical stainless-steel rod (1 cm diameter was heated to 100℃ in boiling water. Temperature was monitored using a thermocouple. We performed two consecutive toe-pinch tests on different limbs to assess the depth of sedation. Burn infliction was limited to the loin. The skin was pulled upwards, away from the underlying viscera, creating a flat surface. The rod rested on its own weight for 5, 10, and 20 seconds at three different sites on each rat. Wounds were evaluated for size, morphology and depth. Results Average wound size was 0.9957 cm2 (standard deviation [SD] 0.1845 (n=30. Wounds created with duration of 5 seconds were pale, with an indistinct margin of erythema. Wounds of 10 and 20 seconds were well-defined, uniformly brown with a rim of erythema. Average depths of tissue damage were 1.30 mm (SD 0.424, 2.35 mm (SD 0.071, and 2.60 mm (SD 0.283 for duration of 5, 10, 20 seconds respectively. Burn duration of 5 seconds resulted in full-thickness damage. Burn duration of 10 seconds and 20 seconds resulted in full-thickness damage, involving subjacent skeletal muscle. Conclusions This is a simple reproducible method for creating burn wounds consistent in size and depth in a rat burn model.
A self-consistent dynamo model for fully convective stars
Yadav, Rakesh Kumar; Christensen, Ulrich; Morin, Julien; Gastine, Thomas; Reiners, Ansgar; Poppenhaeger, Katja; Wolk, Scott J.
2016-01-01
The tachocline region inside the Sun, where the rigidly rotating radiative core meets the differentially rotating convection zone, is thought to be crucial for generating the Sun's magnetic field. Low-mass fully convective stars do not possess a tachocline and were originally expected to generate only weak small-scale magnetic fields. Observations, however, have painted a different picture of magnetism in rapidly-rotating fully convective stars: (1) Zeeman broadening measurements revealed average surface field of several kiloGauss (kG), which is similar to the typical field strength found in sunspots. (2) Zeeman-Doppler-Imaging (ZDI) technique discovered large-scale magnetic fields with a morphology often similar to the Earth's dipole-dominated field. (3) Comparison of Zeeman broadening and ZDI results showed that more than 80% of the magnetic flux resides at small scales. So far, theoretical and computer simulation efforts have not been able to reproduce these features simultaneously. Here we present a self-consistent global model of magnetic field generation in low-mass fully convective stars. A distributed dynamo working in the model spontaneously produces a dipole-dominated surface magnetic field of the observed strength. The interaction of this field with the turbulent convection in outer layers shreds it, producing small-scale fields that carry most of the magnetic flux. The ZDI technique applied to synthetic spectropolarimetric data based on our model recovers most of the large-scale field. Our model simultaneously reproduces the morphology and magnitude of the large-scale field as well as the magnitude of the small-scale field observed on low-mass fully convective stars.
Linking lipid architecture to bilayer structure and mechanics using self-consistent field modelling
Energy Technology Data Exchange (ETDEWEB)
Pera, H.; Kleijn, J. M.; Leermakers, F. A. M., E-mail: Frans.leermakers@wur.nl [Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6307 HB Wageningen (Netherlands)
2014-02-14
To understand how lipid architecture determines the lipid bilayer structure and its mechanics, we implement a molecularly detailed model that uses the self-consistent field theory. This numerical model accurately predicts parameters such as Helfrichs mean and Gaussian bending modulus k{sub c} and k{sup ¯} and the preferred monolayer curvature J{sub 0}{sup m}, and also delivers structural membrane properties like the core thickness, and head group position and orientation. We studied how these mechanical parameters vary with system variations, such as lipid tail length, membrane composition, and those parameters that control the lipid tail and head group solvent quality. For the membrane composition, negatively charged phosphatidylglycerol (PG) or zwitterionic, phosphatidylcholine (PC), and -ethanolamine (PE) lipids were used. In line with experimental findings, we find that the values of k{sub c} and the area compression modulus k{sub A} are always positive. They respond similarly to parameters that affect the core thickness, but differently to parameters that affect the head group properties. We found that the trends for k{sup ¯} and J{sub 0}{sup m} can be rationalised by the concept of Israelachivili's surfactant packing parameter, and that both k{sup ¯} and J{sub 0}{sup m} change sign with relevant parameter changes. Although typically k{sup ¯}<0, membranes can form stable cubic phases when the Gaussian bending modulus becomes positive, which occurs with membranes composed of PC lipids with long tails. Similarly, negative monolayer curvatures appear when a small head group such as PE is combined with long lipid tails, which hints towards the stability of inverse hexagonal phases at the cost of the bilayer topology. To prevent the destabilisation of bilayers, PG lipids can be mixed into these PC or PE lipid membranes. Progressive loading of bilayers with PG lipids lead to highly charged membranes, resulting in J{sub 0}{sup m}≫0, especially at low ionic
Ngatchou, Annita
2010-01-01
Pheochromocytoma is a tumor of the adrenal gland which originates from chromaffin cells and is characterized by the secretion of excessive amounts of neurotransmitter which lead to high blood pressure and palpitations. Pheochromocytoma contain membrane bound granules that store neurotransmitter. The release of these stored molecules into the extracellular space occurs by fusion of the granule membrane with the cell plasma membrane, a process called exocytosis. The molecular mechanism of this membrane fusion is not well understood. It is proposed that the so called SNARE proteins [1] are the pillar of vesicle fusion as their cleavage by clostridial toxin notably, Botulinum neurotoxin and Tetanus toxin abrogate the secretion of neurotransmitter [2]. Here, I describe how physical principles are applied to a biological cell to explore the role of the vesicle SNARE protein synaptobrevin-2 in easing granule fusion. The data presented here suggest a paradigm according to which the movement of the C-terminal of synaptobrevin-2 disrupts the lipid bilayer to form a fusion pore through which molecules can exit.
Pluralistic and stochastic gene regulation: examples, models and consistent theory.
Salas, Elisa N; Shu, Jiang; Cserhati, Matyas F; Weeks, Donald P; Ladunga, Istvan
2016-06-01
We present a theory of pluralistic and stochastic gene regulation. To bridge the gap between empirical studies and mathematical models, we integrate pre-existing observations with our meta-analyses of the ENCODE ChIP-Seq experiments. Earlier evidence includes fluctuations in levels, location, activity, and binding of transcription factors, variable DNA motifs, and bursts in gene expression. Stochastic regulation is also indicated by frequently subdued effects of knockout mutants of regulators, their evolutionary losses/gains and massive rewiring of regulatory sites. We report wide-spread pluralistic regulation in ≈800 000 tightly co-expressed pairs of diverse human genes. Typically, half of ≈50 observed regulators bind to both genes reproducibly, twice more than in independently expressed gene pairs. We also examine the largest set of co-expressed genes, which code for cytoplasmic ribosomal proteins. Numerous regulatory complexes are highly significant enriched in ribosomal genes compared to highly expressed non-ribosomal genes. We could not find any DNA-associated, strict sense master regulator. Despite major fluctuations in transcription factor binding, our machine learning model accurately predicted transcript levels using binding sites of 20+ regulators. Our pluralistic and stochastic theory is consistent with partially random binding patterns, redundancy, stochastic regulator binding, burst-like expression, degeneracy of binding motifs and massive regulatory rewiring during evolution.
Consistency of modified MLE in EV model with replicated observations
Institute of Scientific and Technical Information of China (English)
ZHANG; Sanguo
2001-01-01
［1］Kendall, M., Stuart, A., The Advanced Theory of Statistics, Vol. 2, New York: Charles Griffin, 1979.［2］Anderson, T. W., Estimating linear statistical relationships, Ann. Statist., 1984, 12: 1.［3］Cui Hengjian, Asymptotic normality of M-estimates in the EV model, Sys. Sci. and Math. Sci., 1997, 10(3): 225.［4］Madansky, A., The fitting of straight lines when both variables are subject to error, JASA, 1959, 54: 173.［5］Villegas, C., Maximum likelihood estimations of a linear functional relationship, Ann. Math. Statist., 1961, 32(4): 1048.［6］Stout, W. F., Almost Sure Convergence, New York: Academic Press, 1974.［7］Petrov, V. V., Sums of Independent Random Variables, New York: Springer-Verlag, 1975.［8］Lai, T. L., Robbins, H., Wei, C. Z., Strong consistency of least squares estimates in multiple regression, J. Multivariate Anal., 1979, 9: 343.［9］Chen Xiru, On limiting properties of U-statistics and von-Mises statistics, Scientia Sinica (in Chinese), 1980, (6): 522.
Dynamic Consistency between Value and Coordination Models - Research Issues.
Bodenstaff, L.; Wombacher, Andreas; Reichert, M.U.; meersman, R; Tari, Z; herrero, p
Inter-organizational business cooperations can be described from different viewpoints each fulfilling a specific purpose. Since all viewpoints describe the same system they must not contradict each other, thus, must be consistent. Consistency can be checked based on common semantic concepts of the
Understanding transport in model water desalination membranes
Chan, Edwin
Polyamide based thin film composites represent the the state-of-the-art nanofiltration and reverse osmosis membranes used in water desalination. The performance of these membranes is enabled by the ultrathin (~100 nm) crosslinked polyamide film in facilitating the selective transport of water over salt ions. While these materials have been refined over the last several decades, understanding the relationships between polyamide structure and membrane performance remains a challenge because of the complex and heterogeneous nature of the polyamide film. In this contribution, we present our approach to addressing this challenge by studying the transport properties of model polyamide membranes synthesized via molecular layer-by-layer (mLbL) assembly. First, we demonstrate that mLbL can successfully construct polyamide membranes with well-defined nanoscale thickness and roughness using a variety of monomer formulations. Next, we present measurement tools for characterizing the network structure and transport of these model polyamide membranes. Specifically, we used X-ray and neutron scattering techniques to characterize their structure as well as a recently-developed indentation based poromechanics approach to extrapolate their water diffusion coefficient. Finally, we illustrate how these measurements can provide insight into the original problem by linking the key polyamide network properties, i.e. water-polyamide interaction parameter and characteristic network mesh size, to the membrane performance.
A proposal for a consistent parametrization of earth models
Forbriger, Thomas; Friederich, Wolfgang
2005-08-01
The current way to parametrize earth models in terms of real-valued seismic velocities and quality factors is incomplete as it does not specify how complex-valued viscoelastic moduli or complex velocities should be computed from them. Various ways to do this can be found in the literature. Depending on the context they may specify (1) the real part of the viscoelastic modulus, (2) the absolute value of the viscoelastic modulus, (3) the real part of complex velocity or (4) the phase velocity of a propagating plane wave. We propose here to exclusively use the first alternative because it is the only one which allows both a flexible choice of elastic parameters and a mathematically rigorous evaluation of the complex-valued viscoelastic moduli. The other definitions only permit an evaluation of viscoelastic moduli if the tabulated quality factors are directly associated with the listed velocities. Ignoring the subtle differences between the three definitions leads to variations in viscoelastic moduli which are second order in 1/Q where Q is a quality factor. This may be the reason why the topic has never been discussed in the literature. In case of shallow seismic media, however, where quality factors may assume values of less than 10, the subtle differences become noticeable in synthetic seismograms. It is then essential to use the same definition in all algorithms to make results comparable. Matters become worse for anisotropic media, which are commonly specified in terms of real elastic moduli and quality factors for effective isotropic moduli. In that case, the complex-valued viscoelastic moduli cannot be determined uniquely. However, interpreting the tabulated constants as the real parts of the complex-valued viscoelastic moduli at least allows a consistent definition, which respects the relative magnitude of the anelastic and anisotropic parts compared to the elastic parts. It should be noted that all these considerations apply to complex-valued viscoelastic
Warling, Odile; Bovy, Christophe; Coïmbra, Carla; Noterdaeme, Timothée; Delwaide, Jean; Louis, Edouard
2014-04-28
The association of primary sclerosing cholangitis (PSC) and autoimmune hepatitis (AIH) is known as an overlap syndrome (OS). OS can also be described in the setting of concomitant presence of AIH and PSC. These diseases can in some cases be associated with ulcerative colitis. In this case report we describe, to our knowledge, the first case in the literature of a young Caucasian male suffering from ulcerative colitis and an overlap syndrome consisting of an association between PSC-AIH, with the concomitant presence of a membranous glomerulonephritis.
Self-consistent modelling of resonant tunnelling structures
DEFF Research Database (Denmark)
Fiig, T.; Jauho, A.P.
1992-01-01
We report a comprehensive study of the effects of self-consistency on the I-V-characteristics of resonant tunnelling structures. The calculational method is based on a simultaneous solution of the effective-mass Schrödinger equation and the Poisson equation, and the current is evaluated with the ......We report a comprehensive study of the effects of self-consistency on the I-V-characteristics of resonant tunnelling structures. The calculational method is based on a simultaneous solution of the effective-mass Schrödinger equation and the Poisson equation, and the current is evaluated...... applied voltages and carrier densities at the emitter-barrier interface. We include the two-dimensional accumulation layer charge and the quantum well charge in our self-consistent scheme. We discuss the evaluation of the current contribution originating from the two-dimensional accumulation layer charges...
Modeling of ion conductivity in Nafion membranes
Institute of Scientific and Technical Information of China (English)
YANG Zhen; PENG Xiaofeng; WANG Buxuan; LEE Duujong; DUAN Yuanyuan
2007-01-01
A theoretical investigation was conducted to describe the ion transport behavior in a Nafion Membrane of proton exchange membrane fuel cells (PEMFC).By analyzing the surface energy configuration of the ionic clusters in a Nafion membrane,an equivalent field intensity,Ee,was introduced to facilitate the analysis of surface resistance against ion conduction in the central region of clusters.An expression was derived for ionic conductivity incorporating the influence of surface resistance.A face-centered cubic (FCC)lattice model for a spatial cluster distribution was used to modify the effect of water content on ionic conductivity in the polymeric matrix,i.e.,the regions between clusters.Compared with the available empirical correlations,the new expression showed much better agreement with the available experimental results,which indicates the rationality to consider the structural influence on ion conduction in water-swollen Nation membranes.
A Consistent Pricing Model for Index Options and Volatility Derivatives
DEFF Research Database (Denmark)
Kokholm, Thomas
on the underlying asset. The model has the convenient feature of decoupling the vanilla skews from spot/volatility correlations and allowing for different conditional correlations in large and small spot/volatility moves. We show that our model can simultaneously fit prices of European options on S&P 500 across......We propose a flexible modeling framework for the joint dynamics of an index and a set of forward variance swap rates written on this index. Our model reproduces various empirically observed properties of variance swap dynamics and enables volatility derivatives and options on the underlying index...
Simulation Model of Membrane Gas Separator Using Aspen Custom Modeler
Energy Technology Data Exchange (ETDEWEB)
Song, Dong-keun [Korea Institute of Machinery and Materials, Daejeon (Korea, Republic of); Shin, Gahui; Yun, Jinwon; Yu, Sangseok [Chungnam Nat’l Univ., Daejeon (Korea, Republic of)
2016-12-15
Membranes are used to separate pure gas from gas mixtures. In this study, three different types of mass transport through a membrane were developed in order to investigate the gas separation capabilities of a membrane. The three different models typically used are a lumped model, a multi-cell model, and a discretization model. Despite the multi-cell model producing similar results to a discretization model, the discretization model was selected for this investigation, due to the cell number dependence of a multi-cell model. The mass transport model was then used to investigate the effects of pressure difference, flow rate, total exposed area, and permeability. The results showed that the pressure difference increased with the stage cut, but the selectivity was a trade-off for the increasing pressure difference. Additionally, even though permeability is an important parameter, the selectivity and stage cut of the membrane converged as permeability increased.
Is the island universe model consistent with observations?
Piao, Yun-Song
2005-01-01
We study the island universe model, in which initially the universe is in a cosmological constant sea, then the local quantum fluctuations violating the null energy condition create the islands of matter, some of which might corresponds to our observable universe. We examine the possibility that the island universe model is regarded as an alternative scenario of the origin of observable universe.
An Extended Model Driven Framework for End-to-End Consistent Model Transformation
Directory of Open Access Journals (Sweden)
Mr. G. Ramesh
2016-08-01
Full Text Available Model Driven Development (MDD results in quick transformation from models to corresponding systems. Forward engineering features of modelling tools can help in generating source code from models. To build a robust system it is important to have consistency checking in the design models and the same between design model and the transformed implementation. Our framework named as Extensible Real Time Software Design Inconsistency Checker (XRTSDIC proposed in our previous papers supports consistency checking in design models. This paper focuses on automatic model transformation. An algorithm and defined transformation rules for model transformation from UML class diagram to ERD and SQL are being proposed. The model transformation bestows many advantages such as reducing cost of development, improving quality, enhancing productivity and leveraging customer satisfaction. Proposed framework has been enhanced to ensure that the transformed implementations conform to their model counterparts besides checking end-to-end consistency.
Consistent Evolution of Software Artifacts and Non-Functional Models
2014-11-14
Ruscio D., Pierantonio A., Arcelli D., Eramo R., Trubiani C., Tucci M. Dipartimento di Ingegneria e Scienze dell’Informazione e Matematica ...Models (SRMs), and ( ii ) antipattern solutions as Target Role Models (TRMs). Hence, SRM-TRM pairs represent new instruments in the hands of developers to...helps to identify the antipatterns that more heavily contribute to the violation of performance requirements [10], and ( ii ) another one aimed at
A Membrane Model from Implicit Elasticity Theory
Freed, A. D.; Liao, J.; Einstein, D. R.
2014-01-01
A Fungean solid is derived for membranous materials as a body defined by isotropic response functions whose mathematical structure is that of a Hookean solid where the elastic constants are replaced by functions of state derived from an implicit, thermodynamic, internal-energy function. The theory utilizes Biot’s (1939) definitions for stress and strain that, in 1-dimension, are the stress/strain measures adopted by Fung (1967) when he postulated what is now known as Fung’s law. Our Fungean membrane model is parameterized against a biaxial data set acquired from a porcine pleural membrane subjected to three, sequential, proportional, planar extensions. These data support an isotropic/deviatoric split in the stress and strain-rate hypothesized by our theory. These data also demonstrate that the material response is highly non-linear but, otherwise, mechanically isotropic. These data are described reasonably well by our otherwise simple, four-parameter, material model. PMID:24282079
Interaction of Mastoparan with Model Membranes
Haloot, Justin
2010-10-01
The use of antimicrobial agents began during the 20th century to reduce the effects of infectious diseases. Since the 1990s, antimicrobial resistance has become an ever-increasing global problem. Our laboratory recently found that small antimicrobial peptides (AMPs) have potent antimicrobial activity against a wide range of Gram-negative and Gram-positive organisms including antibiotic resistant organisms. These AMPs are potential therapeutic agents against the growing problem of antimicrobial resistance. AMPs are small peptides produced by plants, insects and animals. Several hypotheses concede that these peptides cause some type of structural perturbations and increased membrane permeability in bacteria however, how AMPs kill bacteria remains unclear. The goal of this study was to design an assay that would allow us to evaluate and monitor the pore forming ability of an AMP, Mastoparan, on model membrane structures called liposomes. Development of this model will facilitate the study of how mastoparan and related AMPs interact with the bacterial membrane.
Towards a self-consistent dynamical nuclear model
Roca-Maza, X.; Niu, Y. F.; Colò, G.; Bortignon, P. F.
2017-04-01
Density functional theory (DFT) is a powerful and accurate tool, exploited in nuclear physics to investigate the ground-state and some of the collective properties of nuclei along the whole nuclear chart. Models based on DFT are not, however, suitable for the description of single-particle dynamics in nuclei. Following the field theoretical approach by A Bohr and B R Mottelson to describe nuclear interactions between single-particle and vibrational degrees of freedom, we have taken important steps towards the building of a microscopic dynamic nuclear model. In connection with this, one important issue that needs to be better understood is the renormalization of the effective interaction in the particle-vibration approach. One possible way to renormalize the interaction is by the so-called subtraction method. In this contribution, we will implement the subtraction method in our model for the first time and study its consequences.
Gas Clumping in Self-Consistent Reionisation Models
Finlator, K; Özel, F; Davé, R
2012-01-01
We use a suite of cosmological hydrodynamic simulations including a self-consistent treatment for inhomogeneous reionisation to study the impact of galactic outflows and photoionisation heating on the volume-averaged recombination rate of the intergalactic medium (IGM). By incorporating an evolving ionising escape fraction and a treatment for self-shielding within Lyman limit systems, we have run the first simulations of "photon-starved" reionisation scenarios that simultaneously reproduce observations of the abundance of galaxies, the optical depth to electron scattering of cosmic microwave background photons \\tau, and the effective optical depth to Lyman\\alpha absorption at z=5. We confirm that an ionising background reduces the clumping factor C by more than 50% by smoothing moderately-overdense (\\Delta=1--100) regions. Meanwhile, outflows increase clumping only modestly. The clumping factor of ionised gas is much lower than the overall baryonic clumping factor because the most overdense gas is self-shield...
Modelling plasticity of unsaturated soils in a thermodynamically consistent framework
Coussy, O
2010-01-01
Constitutive equations of unsaturated soils are often derived in a thermodynamically consistent framework through the use a unique 'effective' interstitial pressure. This later is naturally chosen as the space averaged interstitial pressure. However, experimental observations have revealed that two stress state variables were needed to describe the stress-strain-strength behaviour of unsaturated soils. The thermodynamics analysis presented here shows that the most general approach to the behaviour of unsaturated soils actually requires three stress state variables: the suction, which is required to describe the retention properties of the soil and two effective stresses, which are required to describe the soil deformation at water saturation held constant. Actually, it is shown that a simple assumption related to internal deformation leads to the need of a unique effective stress to formulate the stress-strain constitutive equation describing the soil deformation. An elastoplastic framework is then presented ...
Modeling electrokinetic flows by consistent implicit incompressible smoothed particle hydrodynamics
Energy Technology Data Exchange (ETDEWEB)
Pan, Wenxiao; Kim, Kyungjoo; Perego, Mauro; Tartakovsky, Alexandre M.; Parks, Michael L.
2017-04-01
We present an efficient implicit incompressible smoothed particle hydrodynamics (I2SPH) discretization of Navier-Stokes, Poisson-Boltzmann, and advection-diffusion equations subject to Dirichlet or Robin boundary conditions. It is applied to model various two and three dimensional electrokinetic flows in simple or complex geometries. The I2SPH's accuracy and convergence are examined via comparison with analytical solutions, grid-based numerical solutions, or empirical models. The new method provides a framework to explore broader applications of SPH in microfluidics and complex fluids with charged objects, such as colloids and biomolecules, in arbitrary complex geometries.
Consistency Problem with Tracer Advection in the Atmospheric Model GAMIL
Institute of Scientific and Technical Information of China (English)
ZHANG Kai; WAN Hui; WANG Bin; ZHANG Meigen
2008-01-01
The radon transport test,which is a widely used test case for atmospheric transport models,is carried out to evaluate the tracer advection schemes in the Grid-Point Atmospheric Model of IAP-LASG (GAMIL).TWO of the three available schemes in the model are found to be associated with significant biases in the polar regions and in the upper part of the atmosphere,which implies potentially large errors in the simulation of ozone-like tracers.Theoretical analyses show that inconsistency exists between the advection schemes and the discrete continuity equation in the dynamical core of GAMIL and consequently leads to spurious sources and sinks in the tracer transport equation.The impact of this type of inconsistency is demonstrated by idealized tests and identified as the cause of the aforementioned biases.Other potential effects of this inconsistency are also discussed.Results of this study provide some hints for choosing suitable advection schemes in the GAMIL model.At least for the polar-region-concentrated atmospheric components and the closely correlated chemical species,the Flux-Form Semi-Lagrangian advection scheme produces more reasonable simulations of the large-scale transport processes without significantly increasing the computational expense.
Self-consistent Models of Strong Interaction with Chiral Symmetry
Nambu, Y.; Pascual, P.
1963-04-01
Some simple models of (renormalizable) meson-nucleon interaction are examined in which the nucleon mass is entirely due to interaction and the chiral ( gamma {sub 5}) symmetry is "broken'' to become a hidden symmetry. It is found that such a scheme is possible provided that a vector meson is introduced as an elementary field. (auth)
A seismologically consistent compositional model of Earth's core.
Badro, James; Côté, Alexander S; Brodholt, John P
2014-05-27
Earth's core is less dense than iron, and therefore it must contain "light elements," such as S, Si, O, or C. We use ab initio molecular dynamics to calculate the density and bulk sound velocity in liquid metal alloys at the pressure and temperature conditions of Earth's outer core. We compare the velocity and density for any composition in the (Fe-Ni, C, O, Si, S) system to radial seismological models and find a range of compositional models that fit the seismological data. We find no oxygen-free composition that fits the seismological data, and therefore our results indicate that oxygen is always required in the outer core. An oxygen-rich core is a strong indication of high-pressure and high-temperature conditions of core differentiation in a deep magma ocean with an FeO concentration (oxygen fugacity) higher than that of the present-day mantle.
A more consistent intraluminal rhesus monkey model of ischemic stroke
Institute of Scientific and Technical Information of China (English)
Bo Zhao; Fauzia Akbary; Shengli Li; Jing Lu; Feng Ling; Xunming Ji; Guowei Shang; Jian Chen; Xiaokun Geng; Xin Ye; Guoxun Xu; Ju Wang; Jiasheng Zheng; Hongjun Li
2014-01-01
Endovascular surgery is advantageous in experimentally induced ischemic stroke because it causes fewer cranial traumatic lesions than invasive surgery and can closely mimic the pathophysiol-ogy in stroke patients. However, the outcomes are highly variable, which limits the accuracy of evaluations of ischemic stroke studies. In this study, eight healthy adult rhesus monkeys were randomized into two groups with four monkeys in each group:middle cerebral artery occlusion at origin segment (M1) and middle cerebral artery occlusion at M2 segment. The blood lfow in the middle cerebral artery was blocked completely for 2 hours using the endovascular microcoil placement technique (1 mm × 10 cm) (undetachable), to establish a model of cerebral ischemia. The microcoil was withdrawn and the middle cerebral artery blood lfow was restored. A revers-ible middle cerebral artery occlusion model was identiifed by hematoxylin-eosin staining, digital subtraction angiography, magnetic resonance angiography, magnetic resonance imaging, and neurological evaluation. The results showed that the middle cerebral artery occlusion model was successfully established in eight adult healthy rhesus monkeys, and ischemic lesions were apparent in the brain tissue of rhesus monkeys at 24 hours after occlusion. The rhesus monkeys had symp-toms of neurological deifcits. Compared with the M1 occlusion group, the M2 occlusion group had lower infarction volume and higher neurological scores. These experimental ifndings indicate that reversible middle cerebral artery occlusion can be produced with the endovascular microcoil technique in rhesus monkeys. The M2 occluded model had less infarction and less neurological impairment, which offers the potential for application in the ifeld of brain injury research.
A more consistent intraluminal rhesus monkey model of ischemic stroke.
Zhao, Bo; Shang, Guowei; Chen, Jian; Geng, Xiaokun; Ye, Xin; Xu, Guoxun; Wang, Ju; Zheng, Jiasheng; Li, Hongjun; Akbary, Fauzia; Li, Shengli; Lu, Jing; Ling, Feng; Ji, Xunming
2014-12-01
Endovascular surgery is advantageous in experimentally induced ischemic stroke because it causes fewer cranial traumatic lesions than invasive surgery and can closely mimic the pathophysiology in stroke patients. However, the outcomes are highly variable, which limits the accuracy of evaluations of ischemic stroke studies. In this study, eight healthy adult rhesus monkeys were randomized into two groups with four monkeys in each group: middle cerebral artery occlusion at origin segment (M1) and middle cerebral artery occlusion at M2 segment. The blood flow in the middle cerebral artery was blocked completely for 2 hours using the endovascular microcoil placement technique (1 mm × 10 cm) (undetachable), to establish a model of cerebral ischemia. The microcoil was withdrawn and the middle cerebral artery blood flow was restored. A reversible middle cerebral artery occlusion model was identified by hematoxylin-eosin staining, digital subtraction angiography, magnetic resonance angiography, magnetic resonance imaging, and neurological evaluation. The results showed that the middle cerebral artery occlusion model was successfully established in eight adult healthy rhesus monkeys, and ischemic lesions were apparent in the brain tissue of rhesus monkeys at 24 hours after occlusion. The rhesus monkeys had symptoms of neurological deficits. Compared with the M1 occlusion group, the M2 occlusion group had lower infarction volume and higher neurological scores. These experimental findings indicate that reversible middle cerebral artery occlusion can be produced with the endovascular microcoil technique in rhesus monkeys. The M2 occluded model had less infarction and less neurological impairment, which offers the potential for application in the field of brain injury research.
Flood damage: a model for consistent, complete and multipurpose scenarios
Menoni, Scira; Molinari, Daniela; Ballio, Francesco; Minucci, Guido; Mejri, Ouejdane; Atun, Funda; Berni, Nicola; Pandolfo, Claudia
2016-12-01
Effective flood risk mitigation requires the impacts of flood events to be much better and more reliably known than is currently the case. Available post-flood damage assessments usually supply only a partial vision of the consequences of the floods as they typically respond to the specific needs of a particular stakeholder. Consequently, they generally focus (i) on particular items at risk, (ii) on a certain time window after the occurrence of the flood, (iii) on a specific scale of analysis or (iv) on the analysis of damage only, without an investigation of damage mechanisms and root causes. This paper responds to the necessity of a more integrated interpretation of flood events as the base to address the variety of needs arising after a disaster. In particular, a model is supplied to develop multipurpose complete event scenarios. The model organizes available information after the event according to five logical axes. This way post-flood damage assessments can be developed that (i) are multisectoral, (ii) consider physical as well as functional and systemic damage, (iii) address the spatial scales that are relevant for the event at stake depending on the type of damage that has to be analyzed, i.e., direct, functional and systemic, (iv) consider the temporal evolution of damage and finally (v) allow damage mechanisms and root causes to be understood. All the above features are key for the multi-usability of resulting flood scenarios. The model allows, on the one hand, the rationalization of efforts currently implemented in ex post damage assessments, also with the objective of better programming financial resources that will be needed for these types of events in the future. On the other hand, integrated interpretations of flood events are fundamental to adapting and optimizing flood mitigation strategies on the basis of thorough forensic investigation of each event, as corroborated by the implementation of the model in a case study.
Deterministic Consistency: A Programming Model for Shared Memory Parallelism
Aviram, Amittai; Ford, Bryan
2009-01-01
The difficulty of developing reliable parallel software is generating interest in deterministic environments, where a given program and input can yield only one possible result. Languages or type systems can enforce determinism in new code, and runtime systems can impose synthetic schedules on legacy parallel code. To parallelize existing serial code, however, we would like a programming model that is naturally deterministic without language restrictions or artificial scheduling. We propose "...
Directory of Open Access Journals (Sweden)
Damian M Cummings
2010-05-01
Full Text Available Since the identification of the gene responsible for HD (Huntington's disease, many genetic mouse models have been generated. Each employs a unique approach for delivery of the mutated gene and has a different CAG repeat length and background strain. The resultant diversity in the genetic context and phenotypes of these models has led to extensive debate regarding the relevance of each model to the human disorder. Here, we compare and contrast the striatal synaptic phenotypes of two models of HD, namely the YAC128 mouse, which carries the full-length huntingtin gene on a yeast artificial chromosome, and the CAG140 KI*** (knock-in mouse, which carries a human/mouse chimaeric gene that is expressed in the context of the mouse genome, with our previously published data obtained from the R6/2 mouse, which is transgenic for exon 1 mutant huntingtin. We show that striatal MSNs (medium-sized spiny neurons in YAC128 and CAG140 KI mice have similar electrophysiological phenotypes to that of the R6/2 mouse. These include a progressive increase in membrane input resistance, a reduction in membrane capacitance, a lower frequency of spontaneous excitatory postsynaptic currents and a greater frequency of spontaneous inhibitory postsynaptic currents in a subpopulation of striatal neurons. Thus, despite differences in the context of the inserted gene between these three models of HD, the primary electrophysiological changes observed in striatal MSNs are consistent. The outcomes suggest that the changes are due to the expression of mutant huntingtin and such alterations can be extended to the human condition.
Directory of Open Access Journals (Sweden)
Damian M Cummings
2010-06-01
Full Text Available Since the identification of the gene responsible for HD (Huntington's disease, many genetic mouse models have been generated. Each employs a unique approach for delivery of the mutated gene and has a different CAG repeat length and background strain. The resultant diversity in the genetic context and phenotypes of these models has led to extensive debate regarding the relevance of each model to the human disorder. Here, we compare and contrast the striatal synaptic phenotypes of two models of HD, namely the YAC128 mouse, which carries the full-length huntingtin gene on a yeast artificial chromosome, and the CAG140 KI (knock-in mouse, which carries a human/mouse chimaeric gene that is expressed in the context of the mouse genome, with our previously published data obtained from the R6/2 mouse, which is transgenic for exon 1 mutant huntingtin. We show that striatal MSNs (medium-sized spiny neurons in YAC128 and CAG140 KI mice have similar electrophysiological phenotypes to that of the R6/2 mouse. These include a progressive increase in membrane input resistance, a reduction in membrane capacitance, a lower frequency of spontaneous excitatory postsynaptic currents and a greater frequency of spontaneous inhibitory postsynaptic currents in a subpopulation of striatal neurons. Thus, despite differences in the context of the inserted gene between these three models of HD, the primary electrophysiological changes observed in striatal MSNs are consistent. The outcomes suggest that the changes are due to the expression of mutant huntingtin and such alterations can be extended to the human condition.
Model-building codes for membrane proteins.
Energy Technology Data Exchange (ETDEWEB)
Shirley, David Noyes; Hunt, Thomas W.; Brown, W. Michael; Schoeniger, Joseph S. (Sandia National Laboratories, Livermore, CA); Slepoy, Alexander; Sale, Kenneth L. (Sandia National Laboratories, Livermore, CA); Young, Malin M. (Sandia National Laboratories, Livermore, CA); Faulon, Jean-Loup Michel; Gray, Genetha Anne (Sandia National Laboratories, Livermore, CA)
2005-01-01
We have developed a novel approach to modeling the transmembrane spanning helical bundles of integral membrane proteins using only a sparse set of distance constraints, such as those derived from MS3-D, dipolar-EPR and FRET experiments. Algorithms have been written for searching the conformational space of membrane protein folds matching the set of distance constraints, which provides initial structures for local conformational searches. Local conformation search is achieved by optimizing these candidates against a custom penalty function that incorporates both measures derived from statistical analysis of solved membrane protein structures and distance constraints obtained from experiments. This results in refined helical bundles to which the interhelical loops and amino acid side-chains are added. Using a set of only 27 distance constraints extracted from the literature, our methods successfully recover the structure of dark-adapted rhodopsin to within 3.2 {angstrom} of the crystal structure.
Modelling Of Manufacturing Processes With Membranes
Crăciunean, Daniel Cristian; Crăciunean, Vasile
2015-07-01
The current objectives to increase the standards of quality and efficiency in manufacturing processes can be achieved only through the best combination of inputs, independent of spatial distance between them. This paper proposes modelling production processes based on membrane structures introduced in [4]. Inspired from biochemistry, membrane computation [4] is based on the concept of membrane represented in its formalism by the mathematical concept of multiset. The manufacturing process is the evolution of a super cell system from its initial state according to the given actions of aggregation. In this paper we consider that the atomic production unit of the process is the action. The actions and the resources on which the actions are produced, are distributed in a virtual network of companies working together. The destination of the output resources is specified by corresponding output events.
Choi, Sung W; Gerencser, Akos A; Ng, Ryan; Flynn, James M; Melov, Simon; Danielson, Steven R; Gibson, Bradford W; Nicholls, David G; Bredesen, Dale E; Brand, Martin D
2012-11-21
Depressed cortical energy supply and impaired synaptic function are predominant associations of Alzheimer's disease (AD). To test the hypothesis that presynaptic bioenergetic deficits are associated with the progression of AD pathogenesis, we compared bioenergetic variables of cortical and hippocampal presynaptic nerve terminals (synaptosomes) from commonly used mouse models with AD-like phenotypes (J20 age 6 months, Tg2576 age 16 months, and APP/PS age 9 and 14 months) to age-matched controls. No consistent bioenergetic deficiencies were detected in synaptosomes from the three models; only APP/PS cortical synaptosomes from 14-month-old mice showed an increase in respiration associated with proton leak. J20 mice were chosen for a highly stringent investigation of mitochondrial function and content. There were no significant differences in the quality of the synaptosomal preparations or the mitochondrial volume fraction. Furthermore, respiratory variables, calcium handling, and membrane potentials of synaptosomes from symptomatic J20 mice under calcium-imposed stress were not consistently impaired. The recovery of marker proteins during synaptosome preparation was the same, ruling out the possibility that the lack of functional bioenergetic defects in synaptosomes from J20 mice was due to the selective loss of damaged synaptosomes during sample preparation. Our results support the conclusion that the intrinsic bioenergetic capacities of presynaptic nerve terminals are maintained in these symptomatic AD mouse models.
Consistency problems for Heath-Jarrow-Morton interest rate models
Filipović, Damir
2001-01-01
The book is written for a reader with knowledge in mathematical finance (in particular interest rate theory) and elementary stochastic analysis, such as provided by Revuz and Yor (Continuous Martingales and Brownian Motion, Springer 1991). It gives a short introduction both to interest rate theory and to stochastic equations in infinite dimension. The main topic is the Heath-Jarrow-Morton (HJM) methodology for the modelling of interest rates. Experts in SDE in infinite dimension with interest in applications will find here the rigorous derivation of the popular "Musiela equation" (referred to in the book as HJMM equation). The convenient interpretation of the classical HJM set-up (with all the no-arbitrage considerations) within the semigroup framework of Da Prato and Zabczyk (Stochastic Equations in Infinite Dimensions) is provided. One of the principal objectives of the author is the characterization of finite-dimensional invariant manifolds, an issue that turns out to be vital for applications. Finally, ge...
Gazit, Ehud; La Rocca, Paolo; Sansom, Mark S. P.; Shai, Yechiel
1998-10-01
The aim of this study was to elucidate the mechanism of membrane insertion and the structural organization of pores formed by Bacillus thuringiensis δ -endotoxin. We determined the relative affinities for membranes of peptides corresponding to the seven helices that compose the toxin pore-forming domain, their modes of membrane interaction, their structures within membranes, and their orientations relative to the membrane normal. In addition, we used resonance energy transfer measurements of all possible combinatorial pairs of membrane-bound helices to map the network of interactions between helices in their membrane-bound state. The interaction of the helices with the bilayer membrane was also probed by a Monte Carlo simulation protocol to determine lowest-energy orientations. Our results are consistent with a situation in which helices α 4 and α 5 insert into the membrane as a helical hairpin in an antiparallel manner, while the other helices lie on the membrane surface like the ribs of an umbrella (the ``umbrella model''). Our results also support the suggestion that α 7 may serve as a binding sensor to initiate the structural rearrangement of the pore-forming domain.
The antimicrobial peptide aurein 1.2 disrupts model membranes via the carpet mechanism.
Fernandez, David I; Le Brun, Anton P; Whitwell, Thomas C; Sani, Marc-Antoine; James, Michael; Separovic, Frances
2012-12-05
The membrane interactions of the antimicrobial peptide aurein 1.2 were studied using a range of biophysical techniques to determine the location and the mechanism of action in DMPC (dimyristoylphosphatidylcholine) and DMPC/DMPG (dimyristoylphosphatidylglycerol) model membranes that mimic characteristics of eukaryotic and prokaryotic membranes, respectively. Neutron reflectometry and solid-state NMR revealed subtle changes in membrane structure caused by the peptide. Quartz crystal microbalance with dissipation, vesicle dye leakage and atomic force microscopy measurements were used to investigate the global mode of peptide interaction. Aurein 1.2 displayed an enhanced interaction with the anionic DMPC/DMPG membrane while exhibiting primarily a surface interaction with both types of model membranes, which led to bilayer disruption and membrane lysis. The antimicrobial peptide interaction is consistent with the carpet mechanism for aurein 1.2 with discrete structural changes depending on the type of phospholipid membrane.
Self-Segregation of Myelin Membrane Lipids in Model Membranes
Yurlova, Larisa; Kahya, Nicoletta; Aggarwal, Shweta; Kaiser, Hermann-Josef; Chiantia, Salvatore; Bakhti, Mostafa; Pewzner-Jung, Yael; Ben-David, Oshrit; Futerman, Anthony H.; Bruegger, Britta; Simons, Mikael
2011-01-01
Rapid conduction of nerve impulses requires coating of axons by myelin sheaths, which are multilamellar, lipid-rich membranes produced by oligodendrocytes in the central nervous system. To act as an insulator, myelin has to form a stable and firm membrane structure. In this study, we have analyzed t
Aggregated wind power plant models consisting of IEC wind turbine models
DEFF Research Database (Denmark)
Altin, Müfit; Göksu, Ömer; Hansen, Anca Daniela
2015-01-01
turbines, parameters and models to represent each individual wind turbine in detail makes it necessary to develop aggregated wind power plant models considering the simulation time for power system stability studies. In this paper, aggregated wind power plant models consisting of the IEC 61400-27 variable...
The model of stress distribution in polymer electrolyte membrane
Atrazhev, Vadim V; Dmitriev, Dmitry V; Erikhman, Nikolay S; Sultanov, Vadim I; Patterson, Timothy; Burlatsky, Sergei F
2014-01-01
An analytical model of mechanical stress in a polymer electrolyte membrane (PEM) of a hydrogen/air fuel cell with porous Water Transfer Plates (WTP) is developed in this work. The model considers a mechanical stress in the membrane is a result of the cell load cycling under constant oxygen utilization. The load cycling causes the cycling of the inlet gas flow rate, which results in the membrane hydration/dehydration close to the gas inlet. Hydration/dehydration of the membrane leads to membrane swelling/shrinking, which causes mechanical stress in the constrained membrane. Mechanical stress results in through-plane crack formation. Thereby, the mechanical stress in the membrane causes mechanical failure of the membrane, limiting fuel cell lifetime. The model predicts the stress in the membrane as a function of the cell geometry, membrane material properties and operation conditions. The model was applied for stress calculation in GORE-SELECT.
Koldsø, Heidi; Reddy, Tyler; Fowler, Philip W; Duncan, Anna L; Sansom, Mark S P
2016-09-01
The cytoskeleton underlying cell membranes may influence the dynamic organization of proteins and lipids within the bilayer by immobilizing certain transmembrane (TM) proteins and forming corrals within the membrane. Here, we present coarse-grained resolution simulations of a biologically realistic membrane model of asymmetrically organized lipids and TM proteins. We determine the effects of a model of cytoskeletal immobilization of selected membrane proteins using long time scale coarse-grained molecular dynamics simulations. By introducing compartments with varying degrees of restraints within the membrane models, we are able to reveal how compartmentalization caused by cytoskeletal immobilization leads to reduced and anomalous diffusional mobility of both proteins and lipids. This in turn results in a reduced rate of protein dimerization within the membrane and of hopping of membrane proteins between compartments. These simulations provide a molecular realization of hierarchical models often invoked to explain single-molecule imaging studies of membrane proteins.
Tumaneng, Paul W.; Pandit, Sagar A.; Zhao, Guijun; Scott, H. L.
2011-03-01
The connection between membrane inhomogeneity and the structural basis of lipid rafts has sparked interest in the lateral organization of model lipid bilayers of two and three components. In an effort to investigate anisotropic lipid distribution in mixed bilayers, a self-consistent mean-field theoretical model is applied to palmitoyloleoylphosphatidylcholine (POPC)-palmitoyl sphingomyelin (PSM)-cholesterol mixtures. The compositional dependence of lateral organization in these mixtures is mapped onto a ternary plot. The model utilizes molecular dynamics simulations to estimate interaction parameters and to construct chain conformation libraries. We find that at some concentration ratios the bilayers separate spatially into regions of higher and lower chain order coinciding with areas enriched with PSM and POPC, respectively. To examine the effect of the asymmetric chain structure of POPC on bilayer lateral inhomogeneity, we consider POPC-lipid interactions with and without angular dependence. Results are compared with experimental data and with results from a similar model for mixtures of dioleoylphosphatidylcholine, steroyl sphingomyelin, and cholesterol.
Stability of Model Membranes in Extreme Environments
Namani, Trishool; Deamer, David W.
2008-08-01
The first forms of cellular life required a source of amphiphilic compounds capable of assembling into stable boundary structures. Membranes composed of fatty acids have been proposed as model systems of primitive membranes, but their bilayer structure is stable only within a narrow pH range and low ionic strength. They are particularly sensitive to aggregating effects of divalent cations (Mg+2, Ca+2, Fe+2) that would be present in Archaean sea water. Here we report that mixtures of alkyl amines and fatty acids form vesicles at strongly basic and acidic pH ranges which are resistant to the effects of divalent cations up to 0.1 M. Vesicles formed by mixtures of decylamine and decanoic acid (1:1 mole ratio) are relatively permeable to pyranine, a fluorescent anionic dye, but permeability could be reduced by adding 2 mol% of a polycyclic aromatic hydrocarbon such as pyrene. Permeability to the dye was also reduced by increasing the chain length of the amphiphiles. For instance, 1:1 mole ratio mixtures of dodecylamine and dodecanoic acid were able to retain pyranine dye during and following gel filtration. We conclude that primitive cell membranes were likely to be composed of mixtures of amphiphilic and hydrophobic molecules that manifested increased stability over pure fatty acid membranes.
Phase behaviors and membrane properties of model liposomes: Temperature effect
Wu, Hsing-Lun; Sheng, Yu-Jane; Tsao, Heng-Kwong
2014-09-01
The phase behaviors and membrane properties of small unilamellar vesicles have been explored at different temperatures by dissipative particle dynamics simulations. The vesicles spontaneously formed by model lipids exhibit pre-transition from gel to ripple phase and main transition from ripple to liquid phase. The vesicle shape exhibits the faceted feature at low temperature, becomes more sphere-like with increasing temperature, but loses its sphericity at high temperature. As the temperature rises, the vesicle size grows but the membrane thickness declines. The main transition (Tm) can be identified by the inflection point. The membrane structural characteristics are analyzed. The inner and outer leaflets are asymmetric. The length of the lipid tail and area density of the lipid head in both leaflets decrease with increasing temperature. However, the mean lipid volume grows at low temperature but declines at high temperature. The membrane mechanical properties are also investigated. The water permeability grows exponentially with increasing T but the membrane tension peaks at Tm. Both the bending and stretching moduli have their minima near Tm. Those results are consistent with the experimental observations, indicating that the main signatures associated with phase transition are clearly observed in small unilamellar vesicles.
Consistency in Estimation and Model Selection of Dynamic Panel Data Models with Fixed Effects
Directory of Open Access Journals (Sweden)
Guangjie Li
2015-07-01
Full Text Available We examine the relationship between consistent parameter estimation and model selection for autoregressive panel data models with fixed effects. We find that the transformation of fixed effects proposed by Lancaster (2002 does not necessarily lead to consistent estimation of common parameters when some true exogenous regressors are excluded. We propose a data dependent way to specify the prior of the autoregressive coefficient and argue for comparing different model specifications before parameter estimation. Model selection properties of Bayes factors and Bayesian information criterion (BIC are investigated. When model uncertainty is substantial, we recommend the use of Bayesian Model Averaging to obtain point estimators with lower root mean squared errors (RMSE. We also study the implications of different levels of inclusion probabilities by simulations.
A general model for membrane-based separation processes
DEFF Research Database (Denmark)
Soni, Vipasha; Abildskov, Jens; Jonsson, Gunnar Eigil;
2009-01-01
behaviour will play an important role. In this paper, modelling of membrane-based processes for separation of gas and liquid mixtures are considered. Two general models, one for membrane-based liquid separation processes (with phase change) and another for membrane-based gas separation are presented...
Mathematical and Computational Modeling of Polymer Exchange Membrane Fuel Cells
Ulusoy, Sehribani
In this thesis a comprehensive review of fuel cell modeling has been given and based on the review, a general mathematical fuel cell model has been developed in order to understand the physical phenomena governing the fuel cell behavior and in order to contribute to the efforts investigating the optimum performance at different operating conditions as well as with different physical parameters. The steady state, isothermal model presented here accounts for the combined effects of mass and species transfer, momentum conservation, electrical current distribution through the gas channels, the electrodes and the membrane, and the electrochemical kinetics of the reactions in the anode and cathode catalyst layers. One of the important features of the model is that it proposes a simpler modified pseudo-homogeneous/agglomerate catalyst layer model which takes the advantage of the simplicity of pseudo-homogenous modeling while taking into account the effects of the agglomerates in the catalyst layer by using experimental geometric parameters published. The computation of the general mathematical model can be accomplished in 3D, 2D and 1D with the proper assumptions. Mainly, there are two computational domains considered in this thesis. The first modeling domain is a 2D Membrane Electrode Assembly (MEA) model including the modified agglomerate/pseudo-homogeneous catalyst layer modeling with consistent treatment of water transport in the MEA while the second domain presents a 3D model with different flow filed designs: straight, stepped and tapered. COMSOL Multiphysics along with Batteries and Fuel Cell Module have been used for 2D & 3D model computations while ANSYS FLUENT PEMFC Module has been used for only 3D two-phase computation. Both models have been validated with experimental data. With 2D MEA model, the effects of temperature and water content of the membrane as well as the equivalent weight of the membrane on the performance have been addressed. 3D COMSOL simulation
Modeling of membrane processes for air revitalization and water recovery
Lange, Kevin E.; Foerg, Sandra L.; Dall-Bauman, Liese A.
1992-01-01
Gas-separation and reverse-osmosis membrane models are being developed in conjunction with membrane testing at NASA JSC. The completed gas-separation membrane model extracts effective component permeabilities from multicomponent test data, and predicts the effects of flow configuration, operating conditions, and membrane dimensions on module performance. Variable feed- and permeate-side pressures are considered. The model has been applied to test data for hollow-fiber membrane modules with simulated cabin-air feeds. Results are presented for a membrane designed for air drying applications. Extracted permeabilities are used to predict the effect of operating conditions on water enrichment in the permeate. A first-order reverse-osmosis model has been applied to test data for spiral wound membrane modules with a simulated hygiene water feed. The model estimates an effective local component rejection coefficient under pseudosteady-state conditions. Results are used to define requirements for a detailed reverse-osmosis model.
Moreno Chaparro, Nicolas
2015-06-30
We introduce a framework for model reduction of polymer chain models for dissipative particle dynamics (DPD) simulations, where the properties governing the phase equilibria such as the characteristic size of the chain, compressibility, density, and temperature are preserved. The proposed methodology reduces the number of degrees of freedom required in traditional DPD representations to model equilibrium properties of systems with complex molecules (e.g., linear polymers). Based on geometrical considerations we explicitly account for the correlation between beads in fine-grained DPD models and consistently represent the effect of these correlations in a reduced model, in a practical and simple fashion via power laws and the consistent scaling of the simulation parameters. In order to satisfy the geometrical constraints in the reduced model we introduce bond-angle potentials that account for the changes in the chain free energy after the model reduction. Following this coarse-graining process we represent high molecular weight DPD chains (i.e., ≥200≥200 beads per chain) with a significant reduction in the number of particles required (i.e., ≥20≥20 times the original system). We show that our methodology has potential applications modeling systems of high molecular weight molecules at large scales, such as diblock copolymer and DNA.
A new k-epsilon model consistent with Monin-Obukhov similarity theory
DEFF Research Database (Denmark)
van der Laan, Paul; Kelly, Mark C.; Sørensen, Niels N.
2016-01-01
A new k-" model is introduced that is consistent with Monin–Obukhov similarity theory (MOST). The proposed k-" model is compared with another k-" model that was developed in an attempt to maintain inlet profiles compatible with MOST. It is shown that the previous k-" model is not consistent with ...
A simplified stock-flow consistent post-Keynesian growth model
dos Santos, Claudio H.; Zezza, Gennaro
2005-01-01
A Simplified Stock-Flow Consistent Post-Keynesian Growth Model Claudio H. Dos Santos* and Gennaro Zezza** Abstract: Despite being arguably the most rigorous form of structuralist/post-Keynesian macroeconomics, stock-flow consistent models are quite often complex and difficult to deal with. This paper presents a model that, despite retaining the methodological advantages of the stock-flow consistent method, is intuitive enough to be taught at an undergraduate level. Moreover, the model can eas...
Guinot, Vincent
2017-09-01
The Integral Porosity and Dual Integral Porosity two-dimensional shallow water models have been proposed recently as efficient upscaled models for urban floods. Very little is known so far about their consistency and wave propagation properties. Simple numerical experiments show that both models are unusually sensitive to the computational grid. In the present paper, a two-dimensional consistency and characteristic analysis is carried out for these two models. The following results are obtained: (i) the models are almost insensitive to grid design when the porosity is isotropic, (ii) anisotropic porosity fields induce an artificial polarization of the mass/momentum fluxes along preferential directions when triangular meshes are used and (iii) extra first-order derivatives appear in the governing equations when regular, quadrangular cells are used. The hyperbolic system is thus mesh-dependent, and with it the wave propagation properties of the model solutions. Criteria are derived to make the solution less mesh-dependent, but it is not certain that these criteria can be satisfied at all computational points when real-world situations are dealt with.
Study of Raft Domains in Model Membrane of DPPC/PE/Cholesterol
Lor, Chai; Hirst, Linda
2010-10-01
Raft domains in bilayer membrane are thought to play an important role in many cell functions such as cell signaling or trans-membrane protein activation. Here we use a model membrane consisting of DPPC/PE/cholesterol to examine the structure of membrane rafts and phase interactions. In particular we are interested in lipids containing the highly polyunsaturated fatty acid DHA. We use both atomic force microscopy (AFM) and fluorescence microscopy to obtain information on the structural properties of raft regions and track cholesterol. As expected, we find phase separation of raft regions between saturated and unsaturated lipids. Moreover, we find that the roughness of the domains change with varying cholesterol concentration possibly due to overpacking. This model study provides further understanding of the role of cholesterol in bilayer membrane leading towards a better knowledge of cell membranes.
Atomic force microscopy of model lipid membranes.
Morandat, Sandrine; Azouzi, Slim; Beauvais, Estelle; Mastouri, Amira; El Kirat, Karim
2013-02-01
Supported lipid bilayers (SLBs) are biomimetic model systems that are now widely used to address the biophysical and biochemical properties of biological membranes. Two main methods are usually employed to form SLBs: the transfer of two successive monolayers by Langmuir-Blodgett or Langmuir-Schaefer techniques, and the fusion of preformed lipid vesicles. The transfer of lipid films on flat solid substrates offers the possibility to apply a wide range of surface analytical techniques that are very sensitive. Among them, atomic force microscopy (AFM) has opened new opportunities for determining the nanoscale organization of SLBs under physiological conditions. In this review, we first focus on the different protocols generally employed to prepare SLBs. Then, we describe AFM studies on the nanoscale lateral organization and mechanical properties of SLBs. Lastly, we survey recent developments in the AFM monitoring of bilayer alteration, remodeling, or digestion, by incubation with exogenous agents such as drugs, proteins, peptides, and nanoparticles.
Fishkind, Donniell E; Tang, Minh; Vogelstein, Joshua T; Priebe, Carey E
2012-01-01
A stochastic block model consists of a random partition of n vertices into blocks 1,2,...,K for which, conditioned on the partition, every pair of vertices has probability of adjacency entirely determined by the block membership of the two vertices. (The model parameters are K, the distribution of the random partition, and a communication probability matrix M in [0,1]^(K x K) listing the adjacency probabilities associated with all pairs of blocks.) Suppose a realization of the n x n vertex adjacency matrix is observed, but the underlying partition of the vertices into blocks is not observed; the main inferential task is to correctly partition the vertices into the blocks with only a negligible number of vertices misassigned. For this inferential task, Rohe et al. (2011) prove the consistency of spectral partitioning applied to the normalized Laplacian, and Sussman et al. (2011) extend this to prove consistency of spectral partitioning directly on the adjacency matrix; both procedures assume that K and rankM a...
DEFF Research Database (Denmark)
Kock, Anders Bredahl
2015-01-01
the tuning parameter by Bayesian Information Criterion (BIC) results in consistent model selection. However, it is also shown that the adaptive Lasso has no power against shrinking alternatives of the form c/T if it is tuned to perform consistent model selection. We show that if the adaptive Lasso is tuned...
Towards a consistent model of the Galaxy; 2, Derivation of the model
Méra, D; Schäffer, R
1998-01-01
We use the calculations derived in a previous paper (Méra, Chabrier and Schaeffer, 1997), based on observational constraints arising from star counts, microlensing experiments and kinematic properties, to determine the amount of dark matter under the form of stellar and sub-stellar objects in the different parts of the Galaxy. This yields the derivation of different mass-models for the Galaxy. In the light of all the afore-mentioned constraints, we discuss two models that correspond to different conclusions about the nature and the location of the Galactic dark matter. In the first model there is a small amount of dark matter in the disk, and a large fraction of the dark matter in the halo is still undetected and likely to be non-baryonic. The second, less conventional model is consistent with entirely, or at least predominantly baryonic dark matter, under the form of brown dwarfs in the disk and white dwarfs in the dark halo. We derive observational predictions for these two models which should be verifiabl...
A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry.
Directory of Open Access Journals (Sweden)
Satyan Sharma
Full Text Available The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.
Modeling the pharmacodynamics of passive membrane permeability
Swift, Robert V.; Amaro, Rommie E.
2011-11-01
Small molecule permeability through cellular membranes is critical to a better understanding of pharmacodynamics and the drug discovery endeavor. Such permeability may be estimated as a function of the free energy change of barrier crossing by invoking the barrier domain model, which posits that permeation is limited by passage through a single "barrier domain" and assumes diffusivity differences among compounds of similar structure are negligible. Inspired by the work of Rezai and co-workers (JACS 128:14073-14080, 2006), we estimate this free energy change as the difference in implicit solvation free energies in chloroform and water, but extend their model to include solute conformational affects. Using a set of eleven structurally diverse FDA approved compounds and a set of thirteen congeneric molecules, we show that the solvation free energies are dominated by the global minima, which allows solute conformational distributions to be effectively neglected. For the set of tested compounds, the best correlation with experiment is obtained when the implicit chloroform global minimum is used to evaluate the solvation free energy difference.
Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes.
Directory of Open Access Journals (Sweden)
Bartosz Różycki
Full Text Available The formation of vesicles is essential for many biological processes, in particular for the trafficking of membrane proteins within cells. The Endosomal Sorting Complex Required for Transport (ESCRT directs membrane budding away from the cytosol. Unlike other vesicle formation pathways, the ESCRT-mediated budding occurs without a protein coat. Here, we propose a minimal model of ESCRT-induced vesicle budding. Our model is based on recent experimental observations from direct fluorescence microscopy imaging that show ESCRT proteins colocalized only in the neck region of membrane buds. The model, cast in the framework of membrane elasticity theory, reproduces the experimentally observed vesicle morphologies with physically meaningful parameters. In this parameter range, the minimum energy configurations of the membrane are coatless buds with ESCRTs localized in the bud neck, consistent with experiment. The minimum energy configurations agree with those seen in the fluorescence images, with respect to both bud shapes and ESCRT protein localization. On the basis of our model, we identify distinct mechanistic pathways for the ESCRT-mediated budding process. The bud size is determined by membrane material parameters, explaining the narrow yet different bud size distributions in vitro and in vivo. Our membrane elasticity model thus sheds light on the energetics and possible mechanisms of ESCRT-induced membrane budding.
Self-consistent modeling of DEMOs with 1.5D BALDUR integrated predictive modeling code
Wisitsorasak, A.; Somjinda, B.; Promping, J.; Onjun, T.
2017-02-01
Self-consistent simulations of four DEMO designs proposed by teams from China, Europe, India, and Korea are carried out using the BALDUR integrated predictive modeling code in which theory-based models are used, for both core transport and boundary conditions. In these simulations, a combination of the NCLASS neoclassical transport and multimode (MMM95) anomalous transport model is used to compute a core transport. The boundary is taken to be at the top of the pedestal, where the pedestal values are described using a pedestal temperature model based on a combination of magnetic and flow shear stabilization, pedestal width scaling and an infinite- n ballooning pressure gradient model and a pedestal density model based on a line average density. Even though an optimistic scenario is considered, the simulation results suggest that, with the exclusion of ELMs, the fusion gain Q obtained for these reactors is pessimistic compared to their original designs, i.e. 52% for the Chinese design, 63% for the European design, 22% for the Korean design, and 26% for the Indian design. In addition, the predicted bootstrap current fractions are also found to be lower than their original designs, as fractions of their original designs, i.e. 0.49 (China), 0.66 (Europe), and 0.58 (India). Furthermore, in relation to sensitivity, it is found that increasing values of the auxiliary heating power and the electron line average density from their design values yield an enhancement of fusion performance. In addition, inclusion of sawtooth oscillation effects demonstrate positive impacts on the plasma and fusion performance in European, Indian and Korean DEMOs, but degrade the performance in the Chinese DEMO.
Membranous nephropathy: from models to man
Beck, Laurence H.; Salant, David J.
2014-01-01
As recently as 2002, most cases of primary membranous nephropathy (MN), a relatively common cause of nephrotic syndrome in adults, were considered idiopathic. We now recognize that MN is an organ-specific autoimmune disease in which circulating autoantibodies bind to an intrinsic antigen on glomerular podocytes and form deposits of immune complexes in situ in the glomerular capillary walls. Here we define the clinical and pathological features of MN and describe the experimental models that enabled the discovery of the major target antigen, the M-type phospholipase A2 receptor 1 (PLA2R). We review the pathophysiology of experimental MN and compare and contrast it with the human disease. We discuss the diagnostic value of serological testing for anti-PLA2R and tissue staining for the redistributed antigen, and their utility for differentiating between primary and secondary MN, and between recurrent MN after kidney transplant and de novo MN. We end with consideration of how knowledge of the antigen might direct future therapeutic strategies. PMID:24892704
A Symplectic Multi-Particle Tracking Model for Self-Consistent Space-Charge Simulation
Qiang, Ji
2016-01-01
Symplectic tracking is important in accelerator beam dynamics simulation. So far, to the best of our knowledge, there is no self-consistent symplectic space-charge tracking model available in the accelerator community. In this paper, we present a two-dimensional and a three-dimensional symplectic multi-particle spectral model for space-charge tracking simulation. This model includes both the effect from external fields and the effect of self-consistent space-charge fields using a split-operator method. Such a model preserves the phase space structure and shows much less numerical emittance growth than the particle-in-cell model in the illustrative examples.
A CVAR scenario for a standard monetary model using theory-consistent expectations
DEFF Research Database (Denmark)
Juselius, Katarina
2017-01-01
A theory-consistent CVAR scenario describes a set of testable regularities capturing basic assumptions of the theoretical model. Using this concept, the paper considers a standard model for exchange rate determination and shows that all assumptions about the model's shock structure and steady...
Caillon, Lucie; Lequin, Olivier; Khemtémourian, Lucie
2013-09-01
Human islet amyloid polypeptide (IAPP) forms amyloid fibrils in the pancreatic islets of patients suffering from type 2 diabetes mellitus (T2DM). The formation of IAPP fibrils has been shown to cause membrane damage which most likely is responsible for the death of pancreatic islet β-cells during the pathogenesis of T2DM. Several studies have demonstrated a clear interaction between IAPP and lipid membranes. However the effect of different lipid compositions and of various membrane mimetics (including micelles, bicelles, SUV and LUV) on fibril formation kinetics and fibril morphology has not yet systematically been analysed. Here we report that the interaction of IAPP with various membrane models promoted different processes of fibril formation. Our data reveal that in SDS and DPC micelles, IAPP adopts a stable α-helical structure for several days, suggesting that the micelle models may stabilize monomeric or small oligomeric species of IAPP. In contrast, zwitterionic DMPC/DHPC bicelles and DOPC SUV accelerate the fibril formation compared to zwitterionic DOPC LUV, indicating that the size of the membrane model and its curvature influence the fibrillation process. Negatively charged membranes decrease the lag-time of the fibril formation kinetics while phosphatidylethanolamine and cholesterol have an opposite effect, probably due to the modulation of the physical properties of the membrane and/or due to direct interactions with IAPP within the membrane core. Finally, our results show that the modulation of lipid composition influences not only the growth of fibrils at the membrane surface but also the interactions of β-sheet oligomers with membranes.
Spatiotemporal Organization of Spin-Coated Supported Model Membranes
Simonsen, Adam Cohen
All cells of living organisms are separated from their surroundings and organized internally by means of flexible lipid membranes. In fact, there is consensus that the minimal requirements for self-replicating life processes include the following three features: (1) information carriers (DNA, RNA), (2) a metabolic system, and (3) encapsulation in a container structure [1]. Therefore, encapsulation can be regarded as an essential part of life itself. In nature, membranes are highly diverse interfacial structures that compartmentalize cells [2]. While prokaryotic cells only have an outer plasma membrane and a less-well-developed internal membrane structure, eukaryotic cells have a number of internal membranes associated with the organelles and the nucleus. Many of these membrane structures, including the plasma membrane, are complex layered systems, but with the basic structure of a lipid bilayer. Biomembranes contain hundreds of different lipid species in addition to embedded or peripherally associated membrane proteins and connections to scaffolds such as the cytoskeleton. In vitro, lipid bilayers are spontaneously self-organized structures formed by a large group of amphiphilic lipid molecules in aqueous suspensions. Bilayer formation is driven by the entropic properties of the hydrogen bond network in water in combination with the amphiphilic nature of the lipids. The molecular shapes of the lipid constituents play a crucial role in bilayer formation, and only lipids with approximately cylindrical shapes are able to form extended bilayers. The bilayer structure of biomembranes was discovered by Gorter and Grendel in 1925 [3] using monolayer studies of lipid extracts from red blood cells. Later, a number of conceptual models were developed to rationalize the organization of lipids and proteins in biological membranes. One of the most celebrated is the fluid-mosaic model by Singer and Nicolson (1972) [4]. According to this model, the lipid bilayer component of
Development of a Kohn-Sham like potential in the Self-Consistent Atomic Deformation Model
Mehl, M J; Stokes, H T
1996-01-01
This is a brief description of how to derive the local ``atomic'' potentials from the Self-Consistent Atomic Deformation (SCAD) model density function. Particular attention is paid to the spherically averaged case.
Development of a Kohn-Sham like potential in the Self-Consistent Atomic Deformation Model
Mehl, M. J.; Boyer, L. L.; Stokes, H. T.
1996-01-01
This is a brief description of how to derive the local ``atomic'' potentials from the Self-Consistent Atomic Deformation (SCAD) model density function. Particular attention is paid to the spherically averaged case.
Bayesian nonparametric estimation and consistency of mixed multinomial logit choice models
De Blasi, Pierpaolo; Lau, John W; 10.3150/09-BEJ233
2011-01-01
This paper develops nonparametric estimation for discrete choice models based on the mixed multinomial logit (MMNL) model. It has been shown that MMNL models encompass all discrete choice models derived under the assumption of random utility maximization, subject to the identification of an unknown distribution $G$. Noting the mixture model description of the MMNL, we employ a Bayesian nonparametric approach, using nonparametric priors on the unknown mixing distribution $G$, to estimate choice probabilities. We provide an important theoretical support for the use of the proposed methodology by investigating consistency of the posterior distribution for a general nonparametric prior on the mixing distribution. Consistency is defined according to an $L_1$-type distance on the space of choice probabilities and is achieved by extending to a regression model framework a recent approach to strong consistency based on the summability of square roots of prior probabilities. Moving to estimation, slightly different te...
Lee, Junggil
2015-01-10
This paper presents the development of a rigorous theoretical model to predict the transmembrane flux of a flat sheet hydrophobic composite membrane, comprising both an active layer of polytetrafluoroethylene and a scrim-backing support layer of polypropylene, in the direct contact membrane distillation (DCMD) process. An integrated model includes the mass, momentum, species and energy balances for both retentate and permeate flows, coupled with the mass transfer of water vapor through the composite membrane and the heat transfer across the membrane and through the boundary layers adjacent to the membrane surfaces. Experimental results and model predictions for permeate flux and performance ratio are compared and shown to be in good agreement. The permeate flux through the composite layer can be ignored in the consideration of mass transfer pathways at the composite membrane. The effect of the surface porosity and the thickness of active and support layers on the process performance of composite membrane has also been studied. Among these parameters, surface porosity is identified to be the main factor significantly influencing the permeate flux and performance ratio, while the relative influence of the surface porosity on the performance ratio is less than that on flux.
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.
Qi, Yifei; Cheng, Xi; Lee, Jumin; Vermaas, Josh V; Pogorelov, Taras V; Tajkhorshid, Emad; Park, Soohyung; Klauda, Jeffery B; Im, Wonpil
2015-11-17
Slow diffusion of the lipids in conventional all-atom simulations of membrane systems makes it difficult to sample large rearrangements of lipids and protein-lipid interactions. Recently, Tajkhorshid and co-workers developed the highly mobile membrane-mimetic (HMMM) model with accelerated lipid motion by replacing the lipid tails with small organic molecules. The HMMM model provides accelerated lipid diffusion by one to two orders of magnitude, and is particularly useful in studying membrane-protein associations. However, building an HMMM simulation system is not easy, as it requires sophisticated treatment of the lipid tails. In this study, we have developed CHARMM-GUI HMMM Builder (http://www.charmm-gui.org/input/hmmm) to provide users with ready-to-go input files for simulating HMMM membrane systems with/without proteins. Various lipid-only and protein-lipid systems are simulated to validate the qualities of the systems generated by HMMM Builder with focus on the basic properties and advantages of the HMMM model. HMMM Builder supports all lipid types available in CHARMM-GUI and also provides a module to convert back and forth between an HMMM membrane and a full-length membrane. We expect HMMM Builder to be a useful tool in studying membrane systems with enhanced lipid diffusion.
Thermodynamically consistent mesoscopic fluid particle models for a van der Waals fluid
Serrano, Mar; Español, Pep
2000-01-01
The GENERIC structure allows for a unified treatment of different discrete models of hydrodynamics. We first propose a finite volume Lagrangian discretization of the continuum equations of hydrodynamics through the Voronoi tessellation. We then show that a slight modification of these discrete equations has the GENERIC structure. The GENERIC structure ensures thermodynamic consistency and allows for the introduction of correct thermal noise. In this way, we obtain a consistent discrete model ...
Mathematical modelling of dextran filtration through hollow fibre membranes
DEFF Research Database (Denmark)
Vinther, Frank; Pinelo, Manuel; Brøns, Morten
2014-01-01
In this paper we present a mathematical model of an ultrafiltration process. The results of the model are produced using standard numerical techniques with Comsol Multiphysics. The model describes the fluid flow and separation in hollow fibre membranes. The flow of solute and solvent within...... of the solute permeability the concentration dependent viscosity decreases the volumetric flux through the membrane at high pressures. This effect is due to a very high concentration at the membrane surface. The model is related to experimental data. There is a good qualitative and a reasonable quantitative...
An Integrated Framework Advancing Membrane Protein Modeling and Design.
Directory of Open Access Journals (Sweden)
Rebecca F Alford
2015-09-01
Full Text Available Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1 prediction of free energy changes upon mutation; (2 high-resolution structural refinement; (3 protein-protein docking; and (4 assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design.
Taraschi, Theodore F.; Ellingson, John S.; Wu, Alice; Zimmerman, Robert; Rubin, Emanuel
1986-06-01
The structural properties of liver microsomes and erythrocytes obtained from rats that had been chronically administered ethanol were examined by electron spin resonance (ESR) following ethanol withdrawal for 1-10 days. Membranes obtained from control animals exhibited considerable molecular disordering upon the addition of ethanol in vitro (50-100 mM). Conversely, microsomal and erythrocyte membranes from alcoholic animals were resistant to this disordering by ethanol (membrane tolerance). These membrane properties were also apparent in lipid bilayers comprised of either total lipids or phospholipids isolated from the control and alcoholic animals. While several weeks of ethanol administration were required for both erythrocytes and microsomes to develop membrane tolerance, erythrocytes from alcoholic animals were disordered by ethanol in vitro after the animals had been withdrawn from ethanol for only 1 day. The same rapid loss of tolerance was observed in microsomes after 2 days of withdrawal. The same time course for the loss of tolerance was observed in lipid bilayers prepared from the total lipid and phospholipid extracts. No significant differences in the cholesterol/phospholipid ratio were observed between the microsomal or erythrocyte membranes isolated before and after withdrawal. Thus, alterations in the microsomal and erythrocyte phospholipids, and not cholesterol content, were responsible for conveying membrane tolerance. Membrane structural properties can be rapidly adjusted in a mammalian system in response to the withdrawal of the external membrane perturbant ethanol. The withdrawal model, which begins with established membrane tolerance and leads to rapid and complete loss of tolerance, provides a model to analyze the compositional changes responsible for this tolerance to disordering by ethanol.
Adjoint-consistent formulations of slip models for coupled electroosmotic flow systems
Garg, Vikram V
2014-09-27
Background Models based on the Helmholtz `slip\\' approximation are often used for the simulation of electroosmotic flows. The objectives of this paper are to construct adjoint-consistent formulations of such models, and to develop adjoint-based numerical tools for adaptive mesh refinement and parameter sensitivity analysis. Methods We show that the direct formulation of the `slip\\' model is adjoint inconsistent, and leads to an ill-posed adjoint problem. We propose a modified formulation of the coupled `slip\\' model, which is shown to be well-posed, and therefore automatically adjoint-consistent. Results Numerical examples are presented to illustrate the computation and use of the adjoint solution in two-dimensional microfluidics problems. Conclusions An adjoint-consistent formulation for Helmholtz `slip\\' models of electroosmotic flows has been proposed. This formulation provides adjoint solutions that can be reliably used for mesh refinement and sensitivity analysis.
Michaels, Patrick J; Christy, John R; Herman, Chad S; Liljegren, Lucia M; Annan, James D
2013-01-01
Assessing the consistency between short-term global temperature trends in observations and climate model projections is a challenging problem. While climate models capture many processes governing short-term climate fluctuations, they are not expected to simulate the specific timing of these somewhat random phenomena - the occurrence of which may impact the realized trend. Therefore, to assess model performance, we develop distributions of projected temperature trends from a collection of climate models running the IPCC A1B emissions scenario. We evaluate where observed trends of length 5 to 15 years fall within the distribution of model trends of the same length. We find that current trends lie near the lower limits of the model distributions, with cumulative probability-of-occurrence values typically between 5 percent and 20 percent, and probabilities below 5 percent not uncommon. Our results indicate cause for concern regarding the consistency between climate model projections and observed climate behavior...
Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.
Botello-Smith, Wesley M; Liu, Xingping; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray
2013-01-01
Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.
Institute of Scientific and Technical Information of China (English)
Yee LEUNG; WU Kefa; DONG Tianxin
2001-01-01
In this paper, a multivariate linear functional relationship model, where the covariance matrix of the observational errors is not restricted, is considered. The parameter estimation of this model is discussed. The estimators are shown to be a strongly consistent estimation under some mild conditions on the incidental parameters.
Silvis, Maurits H
2015-01-01
Assuming a general constitutive relation for the turbulent stresses in terms of the local large-scale velocity gradient, we constructed a class of subgrid-scale models for large-eddy simulation that are consistent with important physical and mathematical properties. In particular, they preserve symmetries of the Navier-Stokes equations and exhibit the proper near-wall scaling. They furthermore show desirable dissipation behavior and are capable of describing nondissipative effects. We provided examples of such physically-consistent models and showed that existing subgrid-scale models do not all satisfy the desired properties.
New geometric design consistency model based on operating speed profiles for road safety evaluation.
Camacho-Torregrosa, Francisco J; Pérez-Zuriaga, Ana M; Campoy-Ungría, J Manuel; García-García, Alfredo
2013-12-01
To assist in the on-going effort to reduce road fatalities as much as possible, this paper presents a new methodology to evaluate road safety in both the design and redesign stages of two-lane rural highways. This methodology is based on the analysis of road geometric design consistency, a value which will be a surrogate measure of the safety level of the two-lane rural road segment. The consistency model presented in this paper is based on the consideration of continuous operating speed profiles. The models used for their construction were obtained by using an innovative GPS-data collection method that is based on continuous operating speed profiles recorded from individual drivers. This new methodology allowed the researchers to observe the actual behavior of drivers and to develop more accurate operating speed models than was previously possible with spot-speed data collection, thereby enabling a more accurate approximation to the real phenomenon and thus a better consistency measurement. Operating speed profiles were built for 33 Spanish two-lane rural road segments, and several consistency measurements based on the global and local operating speed were checked. The final consistency model takes into account not only the global dispersion of the operating speed, but also some indexes that consider both local speed decelerations and speeds over posted speeds as well. For the development of the consistency model, the crash frequency for each study site was considered, which allowed estimating the number of crashes on a road segment by means of the calculation of its geometric design consistency. Consequently, the presented consistency evaluation method is a promising innovative tool that can be used as a surrogate measure to estimate the safety of a road segment.
A Complete Transport Validated Model on a Zeolite Membrane for Carbon Dioxide Permeance and Capture
Gkanas, Evangelos I; Stubos, Athanasios K; Makridis, Sofoklis S
2013-01-01
The CO2 emissions from major industries cause serious global environment problems and their mitigation is urgently needed. The use of zeolite membranes is a very efficient way in order to capture CO2 from some flue gases. The dominant transport mechanism at low temperature andor high pressure is the diffusion through the membrane. This procedure can be divided in three steps: Adsorption of the molecules of the species in the surface of the membrane, then a driving force gives a path where the species follow inside the membrane and finally the species desorbed from the surface of the membrane. The current work is aimed at developing a simulation model for the CO2 transport through a zeolite membrane and estimate the diffusion phenomenon through a very thin membrane of 150 nm in a Wicke-Kallenbach cell. The cell is cylindrical in shape with diameter of 19 mm and consists of a retentate gas chamber, a permeate gas chamber which are separated by a cylindrical zeolite membrane. This apparatus have been modeled wit...
A bilayer-couple model of bacterial outer membrane vesicle biogenesis.
Schertzer, Jeffrey W; Whiteley, Marvin
2012-01-01
Gram-negative bacteria naturally produce outer membrane vesicles (OMVs) that arise through bulging and pinching off of the outer membrane. OMVs have several biological functions for bacteria, most notably as trafficking vehicles for toxins, antimicrobials, and signaling molecules. While their biological roles are now appreciated, the mechanism of OMV formation has not been fully elucidated. We recently demonstrated that the signaling molecule 2-heptyl-3-hydroxy-4-quinolone (PQS) is required for OMV biogenesis in P. aeruginosa. We hypothesized that PQS stimulates OMV formation through direct interaction with the outer leaflet of the outer membrane. To test this hypothesis, we employed a red blood cell (RBC) model that has been used extensively to study small-molecule-membrane interactions. Our results revealed that addition of PQS to RBCs induced membrane curvature, resulting in the formation of membrane spicules (spikes), consistent with small molecules that are inserted stably into the outer leaflet of the membrane. Radiotracer experiments demonstrated that sufficient PQS was inserted into the membrane to account for this curvature and that curvature induction was specific to PQS structure. These data suggest that a low rate of interleaflet flip-flop forces PQS to accumulate in and expand the outer leaflet relative to the inner leaflet, thus inducing membrane curvature. In support of PQS-mediated outer leaflet expansion, the PQS effect was antagonized by chlorpromazine, a molecule known to be preferentially inserted into the inner leaflet. Based on these data, we propose a bilayer-couple model to describe P. aeruginosa OMV biogenesis and suggest that this is a general mechanism for bacterial OMV formation. Despite the ubiquity and importance of outer membrane vesicle (OMV) production in Gram-negative bacteria, the molecular details of OMV biogenesis are not fully understood. Early experiments showed that 2-heptyl-3-hydroxy-4-quinolone (PQS) induces OMV formation
Simplified model for fouling of a pleated membrane filter
Sanaei, Pejman; Cummings, Linda
2014-11-01
Pleated filter cartridge are widely used to remove undesired impurities from a fluid. A filter membrane is sandwiched between porous support layers, then pleated and packed in to an annular cylindrical cartridge. Although this arrangement offers a high ratio of surface filtration area to volume, the filter performance (measured, e.g., by graph of total flux versus throughput for a given pressure drop), is not as good as a flat filter membrane. The reasons for this difference in performance are currently unclear, but likely factors include the additional resistance of the porous support layers upstream and downstream of the membrane, the pleat packing density (PPD) and possible damage to the membrane during the pleating process. To investigate this, we propose a simplified mathematical model of the filtration within a single pleat. We consider the fluid dynamics through the membrane and support layers, and propose a model by which the pores of the membrane become fouled (i) by particles smaller than the membrane pore size; and (ii) by particles larger than the pores.We present some simulations of our model, investigating how flow and fouling differ between not only flat and pleated membranes, but also for support layers of different permeability profiles. NSF DMS-1261596.
Transferable coarse-grained model for perfluorosulfonic acid polymer membranes
Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru
2017-09-01
Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.
Energy Technology Data Exchange (ETDEWEB)
Zhang, Bo; Ye, Xianggui; Edwards, Brian J., E-mail: bje@utk.edu [Materials Research and Innovation Laboratory (MRAIL), Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States)
2013-12-28
A combination of self-consistent field theory and density functional theory was used to examine the stable, 3-dimensional equilibrium morphologies formed by diblock copolymers with a tethered nanoparticle attached either between the two blocks or at the end of one of the blocks. Both neutral and interacting particles were examined, with and without favorable/unfavorable energetic potentials between the particles and the block segments. The phase diagrams of the various systems were constructed, allowing the identification of three types of ordered mesophases composed of lamellae, hexagonally packed cylinders, and spheroids. In particular, we examined the conditions under which the mesophases could be generated wherein the tethered particles were primarily located within the interface between the two blocks of the copolymer. Key factors influencing these properties were determined to be the particle position along the diblock chain, the interaction potentials of the blocks and particles, the block copolymer composition, and molecular weight of the copolymer.
The fundamental solution for a consistent complex model of the shallow shell equations
Matthew P. Coleman
1999-01-01
The calculation of the Fourier transforms of the fundamental solution in shallow shell theory ostensibly was accomplished by J. L. Sanders [J. Appl. Mech. 37 (1970), 361-366]. However, as is shown in detail in this paper, the complex model used by Sanders is, in fact, inconsistent. This paper provides a consistent version of Sanders's complex model, along with the Fourier transforms of the fundamental solution for this corrected model. The inverse Fourier transforms are then calculated for th...
Kukush, A.; Markovsky, I.; Van Huffel, S.
2002-01-01
Consistent estimators of the rank-deficient fundamental matrix yielding information on the relative orientation of two images in two-view motion analysis are derived. The estimators are derived by minimizing a corrected contrast function in a quadratic measurement error model. In addition, a consistent estimator for the measurement error variance is obtained. Simulation results show the improved accuracy of the newly proposed estimator compared to the ordinary total least-squares estimator.
Lemon, Greg; Howard, Daniel; Yang, Hongyi; Ratchev, Svetan M; Segal, Joel I; Rose, Felicity R A J; Jensen, Oliver E; Waters, Sarah L; King, John R
2011-07-01
This paper presents a mathematical model to describe the growth of tissue into a rapid-prototyped porous scaffold when it is implanted onto the chorioallantoic membrane (CAM). The scaffold was designed to study the effects of the size and shape of pores on tissue growth into conventional tissue engineering scaffolds, and consists of an array of pores each having a pre-specified shape. The experimental observations revealed that the CAM grows through each pore as an intact layer of tissue, provided the width of the pore exceeds a threshold value. Based on these results a mathematical model is described to simulate the growth of the membrane, assuming that the growth is a function of the local isotropic membrane tension. The model predictions are compared against measurements of the extent of membrane growth through the pores as a function of time for pores with different dimensions.
Directory of Open Access Journals (Sweden)
Dinh An Nguyen
2012-07-01
Full Text Available Many of the Proton Exchange Membrane Fuel Cell (PEMFC models proposed in the literature consist of mathematical equations. However, they are not adequately practical for simulating power systems. The proposed model takes into account phenomena such as activation polarization, ohmic polarization, double layer capacitance and mass transport effects present in a PEM fuel cell. Using electrical analogies and a mathematical modeling of PEMFC, the circuit model is established. To evaluate the effectiveness of the circuit model, its static and dynamic performances under load step changes are simulated and compared to the numerical results obtained by solving the mathematical model. Finally, the applicability of our model is demonstrated by simulating a practical system.
N-3 fatty acids and membrane microdomains: from model membranes to lymphocyte function.
Shaikh, Saame Raza; Teague, Heather
2012-12-01
This article summarizes the author's research on fish oil derived n-3 fatty acids, plasma membrane organization and B cell function. We first cover basic model membrane studies that investigated how docosahexaenoic acid (DHA) targeted the organization of sphingolipid-cholesterol enriched lipid microdomains. A key finding here was that DHA had a relatively poor affinity for cholesterol. This work led to a model that predicted DHA acyl chains in cells would manipulate lipid-protein microdomain organization and thereby function. We then review how the predictions of the model were tested with B cells in vitro followed by experiments using mice fed fish oil. These studies reveal a highly complex picture on how n-3 fatty acids target lipid-protein organization and B cell function. Key findings are as follows: (1) n-3 fatty acids target not just the plasma membrane but also endomembrane organization; (2) DHA, but not eicosapentaenoic acid (EPA), disrupts microdomain spatial distribution (i.e. clustering), (3) DHA alters protein lateral organization and (4) changes in membrane organization are accompanied by functional effects on both innate and adaptive B cell function. Altogether, the research over the past 10 years has led to an evolution of the original model on how DHA reorganizes membrane microdomains. The work raises the intriguing possibility of testing the model at the human level to target health and disease. Copyright © 2012 Elsevier Ltd. All rights reserved.
Temperature Driven Annealing of Perforations in Bicellar Model Membranes
Energy Technology Data Exchange (ETDEWEB)
Nieh, Mu-Ping [University of Connecticut, Storrs; Raghunathan, V.A. [Raman Research Institute, India; Pabst, Georg [Austrian Academy of Sciences, Graz, Austria; Harroun, Thad [Brock University, St. Catharines, ON, Canada; Nagashima, K [University of Toronto, Mississauga, ON, Canada; Morales, H [University of Toronto, Mississauga, ON, Canada; Katsaras, John [ORNL; Macdonald, P [University of Toronto, Mississauga, ON, Canada
2011-01-01
Bicellar model membranes composed of 1,2-dimyristoylphosphatidylcholine (DMPC) and 1,2-dihexanoylphosphatidylcholine (DHPC), with a DMPC/DHPC molar ratio of 5, and doped with the negatively charged lipid 1,2-dimyristoylphosphatidylglycerol (DMPG), at DMPG/DMPC molar ratios of 0.02 or 0.1, were examined using small angle neutron scattering (SANS), {sup 31}P NMR, and {sup 1}H pulsed field gradient (PFG) diffusion NMR with the goal of understanding temperature effects on the DHPC-dependent perforations in these self-assembled membrane mimetics. Over the temperature range studied via SANS (300-330 K), these bicellar lipid mixtures exhibited a well-ordered lamellar phase. The interlamellar spacing d increased with increasing temperature, in direct contrast to the decrease in d observed upon increasing temperature with otherwise identical lipid mixtures lacking DHPC. {sup 31}P NMR measurements on magnetically aligned bicellar mixtures of identical composition indicated a progressive migration of DHPC from regions of high curvature into planar regions with increasing temperature, and in accord with the 'mixed bicelle model' (Triba, M. N.; Warschawski, D. E.; Devaux, P. E. Biophys. J.2005, 88, 1887-1901). Parallel PFG diffusion NMR measurements of transbilayer water diffusion, where the observed diffusion is dependent on the fractional surface area of lamellar perforations, showed that transbilayer water diffusion decreased with increasing temperature. A model is proposed consistent with the SANS, {sup 31}P NMR, and PFG diffusion NMR data, wherein increasing temperature drives the progressive migration of DHPC out of high-curvature regions, consequently decreasing the fractional volume of lamellar perforations, so that water occupying these perforations redistributes into the interlamellar volume, thereby increasing the interlamellar spacing.
Temperature driven annealing of perforations in bicellar model membranes.
Nieh, Mu-Ping; Raghunathan, V A; Pabst, Georg; Harroun, Thad; Nagashima, Kazuomi; Morales, Hannah; Katsaras, John; Macdonald, Peter
2011-04-19
Bicellar model membranes composed of 1,2-dimyristoylphosphatidylcholine (DMPC) and 1,2-dihexanoylphosphatidylcholine (DHPC), with a DMPC/DHPC molar ratio of 5, and doped with the negatively charged lipid 1,2-dimyristoylphosphatidylglycerol (DMPG), at DMPG/DMPC molar ratios of 0.02 or 0.1, were examined using small angle neutron scattering (SANS), (31)P NMR, and (1)H pulsed field gradient (PFG) diffusion NMR with the goal of understanding temperature effects on the DHPC-dependent perforations in these self-assembled membrane mimetics. Over the temperature range studied via SANS (300-330 K), these bicellar lipid mixtures exhibited a well-ordered lamellar phase. The interlamellar spacing d increased with increasing temperature, in direct contrast to the decrease in d observed upon increasing temperature with otherwise identical lipid mixtures lacking DHPC. (31)P NMR measurements on magnetically aligned bicellar mixtures of identical composition indicated a progressive migration of DHPC from regions of high curvature into planar regions with increasing temperature, and in accord with the "mixed bicelle model" (Triba, M. N.; Warschawski, D. E.; Devaux, P. E. Biophys. J.2005, 88, 1887-1901). Parallel PFG diffusion NMR measurements of transbilayer water diffusion, where the observed diffusion is dependent on the fractional surface area of lamellar perforations, showed that transbilayer water diffusion decreased with increasing temperature. A model is proposed consistent with the SANS, (31)P NMR, and PFG diffusion NMR data, wherein increasing temperature drives the progressive migration of DHPC out of high-curvature regions, consequently decreasing the fractional volume of lamellar perforations, so that water occupying these perforations redistributes into the interlamellar volume, thereby increasing the interlamellar spacing.
There Is No Simple Model of the Plasma Membrane Organization
Bernardino de la Serna, Jorge; Schütz, Gerhard J.; Eggeling, Christian; Cebecauer, Marek
2016-01-01
Ever since technologies enabled the characterization of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organization such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasizing on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organization and functionality, leading to a better understanding of this essential cellular structure. PMID:27747212
There is no simple model of the plasma membrane organisation
Directory of Open Access Journals (Sweden)
Jorge Bernardino De La Serna
2016-09-01
Full Text Available Ever since technologies enabled the characterisation of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organisation such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasising on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organisation and functionality, leading to a better understanding of this essential cellular structure.
Interactions between model bacterial membranes and synthetic antimicrobials.
Yang, Lihua; Mishra, Abhijit; Som, Abhigyan; Tew, Gregory N.; Wong, Gerard C. L.
2006-03-01
Antimicrobial peptides comprise a key component of innate immunity for a wide range of multicellular organisms. It has been shown that natural antimicrobial peptides and their analogs can permeate bacterial membranes selectively. There are a number of proposed models for this action, but the detailed molecular mechanism of the induced membrane permeation remains unclear. We investigate interactions between model bacterial membranes and a prototypical family of phenylene ethynylene-based antimicrobials with controllable hydrophilic and hydrophobic volume fractions, controllable charge placement. Preliminary results from synchrotron small angle x-ray scattering (SAXS) results will be presented.
A Brownian Energy Depot Model of the Basilar Membrane Oscillation with a Braking Mechanism
Zhang, Yong; Lee, Kong-Ju-Bock; Park, Youngah
2008-01-01
High auditory sensitivity, sharp frequency selectivity, and otoacoustic emissions are signatures of active amplification of the cochlea. The human ear can also detect very large amplitude sound without being damaged as long as the exposed time is not too long. The outer hair cells are believed as the best candidate for the active force generator of the mammalian cochlea. In this paper, we propose a new model for the basilar membrane oscillation which successfully describes both the active and the protective mechanisms by employing an energy depot concept and a critical velocity of the basilar membrane. One of the main results is that thermal noise in the absence of external stimulation can be amplified leading to the spontaneous basilar membrane oscillation. The compressive response of the basilar membrane at the characteristic frequency and the dynamic response to the stimulation are consistent with the experimental results as expected. Our model also shows the nonlinear distortion of the response of the bas...
Self-consistent models of quasi-relaxed rotating stellar systems
Varri, A L
2012-01-01
Two new families of self-consistent axisymmetric truncated equilibrium models for the description of quasi-relaxed rotating stellar systems are presented. The first extends the spherical King models to the case of solid-body rotation. The second is characterized by differential rotation, designed to be rigid in the central regions and to vanish in the outer parts, where the energy truncation becomes effective. The models are constructed by solving the nonlinear Poisson equation for the self-consistent mean-field potential. For rigidly rotating configurations, the solutions are obtained by an asymptotic expansion on the rotation strength parameter. The differentially rotating models are constructed by means of an iterative approach based on a Legendre series expansion of the density and the potential. The two classes of models exhibit complementary properties. The rigidly rotating configurations are flattened toward the equatorial plane, with deviations from spherical symmetry that increase with the distance f...
Self-consistent core-pedestal transport simulations with neural network accelerated models
Meneghini, O.; Smith, S. P.; Snyder, P. B.; Staebler, G. M.; Candy, J.; Belli, E.; Lao, L.; Kostuk, M.; Luce, T.; Luda, T.; Park, J. M.; Poli, F.
2017-08-01
Fusion whole device modeling simulations require comprehensive models that are simultaneously physically accurate, fast, robust, and predictive. In this paper we describe the development of two neural-network (NN) based models as a means to perform a snon-linear multivariate regression of theory-based models for the core turbulent transport fluxes, and the pedestal structure. Specifically, we find that a NN-based approach can be used to consistently reproduce the results of the TGLF and EPED1 theory-based models over a broad range of plasma regimes, and with a computational speedup of several orders of magnitudes. These models are then integrated into a predictive workflow that allows prediction with self-consistent core-pedestal coupling of the kinetic profiles within the last closed flux surface of the plasma. The NN paradigm is capable of breaking the speed-accuracy trade-off that is expected of traditional numerical physics models, and can provide the missing link towards self-consistent coupled core-pedestal whole device modeling simulations that are physically accurate and yet take only seconds to run.
The Spectrum of the Baryon Masses in a Self-consistent SU(3) Quantum Skyrme Model
Jurciukonis, Darius; Regelskis, Vidas
2012-01-01
The semiclassical SU(3) Skyrme model is traditionally considered as describing a rigid quantum rotator with the profile function being fixed by the classical solution of the corresponding SU(2) Skyrme model. In contrast, we go beyond the classical profile function by quantizing the SU(3) Skyrme model canonically. The quantization of the model is performed in terms of the collective coordinate formalism and leads to the establishment of purely quantum corrections of the model. These new corrections are of fundamental importance. They are crucial in obtaining stable quantum solitons of the quantum SU(3) Skyrme model, thus making the model self-consistent and not dependent on the classical solution of the SU(2) case. We show that such a treatment of the model leads to a family of stable quantum solitons that describe the baryon octet and decuplet and reproduce the experimental values of their masses.
A consistency assessment of coupled cohesive zone models for mixed-mode debonding problems
Directory of Open Access Journals (Sweden)
R. Dimitri
2014-07-01
Full Text Available Due to their simplicity, cohesive zone models (CZMs are very attractive to describe mixed-mode failure and debonding processes of materials and interfaces. Although a large number of coupled CZMs have been proposed, and despite the extensive related literature, little attention has been devoted to ensuring the consistency of these models for mixed-mode conditions, primarily in a thermodynamical sense. A lack of consistency may affect the local or global response of a mechanical system. This contribution deals with the consistency check for some widely used exponential and bilinear mixed-mode CZMs. The coupling effect on stresses and energy dissipation is first investigated and the path-dependance of the mixed-mode debonding work of separation is analitically evaluated. Analytical predictions are also compared with results from numerical implementations, where the interface is described with zero-thickness contact elements. A node-to-segment strategy is here adopted, which incorporates decohesion and contact within a unified framework. A new thermodynamically consistent mixed-mode CZ model based on a reformulation of the Xu-Needleman model as modified by van den Bosch et al. is finally proposed and derived by applying the Coleman and Noll procedure in accordance with the second law of thermodynamics. The model holds monolithically for loading and unloading processes, as well as for decohesion and contact, and its performance is demonstrated through suitable examples.
A consistent modelling methodology for secondary settling tanks in wastewater treatment.
Bürger, Raimund; Diehl, Stefan; Nopens, Ingmar
2011-03-01
The aim of this contribution is partly to build consensus on a consistent modelling methodology (CMM) of complex real processes in wastewater treatment by combining classical concepts with results from applied mathematics, and partly to apply it to the clarification-thickening process in the secondary settling tank. In the CMM, the real process should be approximated by a mathematical model (process model; ordinary or partial differential equation (ODE or PDE)), which in turn is approximated by a simulation model (numerical method) implemented on a computer. These steps have often not been carried out in a correct way. The secondary settling tank was chosen as a case since this is one of the most complex processes in a wastewater treatment plant and simulation models developed decades ago have no guarantee of satisfying fundamental mathematical and physical properties. Nevertheless, such methods are still used in commercial tools to date. This particularly becomes of interest as the state-of-the-art practice is moving towards plant-wide modelling. Then all submodels interact and errors propagate through the model and severely hamper any calibration effort and, hence, the predictive purpose of the model. The CMM is described by applying it first to a simple conversion process in the biological reactor yielding an ODE solver, and then to the solid-liquid separation in the secondary settling tank, yielding a PDE solver. Time has come to incorporate established mathematical techniques into environmental engineering, and wastewater treatment modelling in particular, and to use proven reliable and consistent simulation models.
Towards an Information Model of Consistency Maintenance in Distributed Interactive Applications
Directory of Open Access Journals (Sweden)
Xin Zhang
2008-01-01
Full Text Available A novel framework to model and explore predictive contract mechanisms in distributed interactive applications (DIAs using information theory is proposed. In our model, the entity state update scheme is modelled as an information generation, encoding, and reconstruction process. Such a perspective facilitates a quantitative measurement of state fidelity loss as a result of the distribution protocol. Results from an experimental study on a first-person shooter game are used to illustrate the utility of this measurement process. We contend that our proposed model is a starting point to reframe and analyse consistency maintenance in DIAs as a problem in distributed interactive media compression.
Feng, Bin; Shi, Zelin; Zhang, Chengshuo; Xu, Baoshu; Zhang, Xiaodong
2016-05-01
The point spread function (PSF) inconsistency caused by temperature variation leads to artifacts in decoded images of a wavefront coding infrared imaging system. Therefore, this paper proposes an analytical model for the effect of temperature variation on the PSF consistency. In the proposed model, a formula for the thermal deformation of an optical phase mask is derived. This formula indicates that a cubic optical phase mask (CPM) is still cubic after thermal deformation. A proposed equivalent cubic phase mask (E-CPM) is a virtual and room-temperature lens which characterizes the optical effect of temperature variation on the CPM. Additionally, a calculating method for PSF consistency after temperature variation is presented. Numerical simulation illustrates the validity of the proposed model and some significant conclusions are drawn. Given the form parameter, the PSF consistency achieved by a Ge-material CPM is better than the PSF consistency by a ZnSe-material CPM. The effect of the optical phase mask on PSF inconsistency is much slighter than that of the auxiliary lens group. A large form parameter of the CPM will introduce large defocus-insensitive aberrations, which improves the PSF consistency but degrades the room-temperature MTF.
Precommitted Investment Strategy versus Time-Consistent Investment Strategy for a Dual Risk Model
Directory of Open Access Journals (Sweden)
Lidong Zhang
2014-01-01
Full Text Available We are concerned with optimal investment strategy for a dual risk model. We assume that the company can invest into a risk-free asset and a risky asset. Short-selling and borrowing money are allowed. Due to lack of iterated-expectation property, the Bellman Optimization Principle does not hold. Thus we investigate the precommitted strategy and time-consistent strategy, respectively. We take three steps to derive the precommitted investment strategy. Furthermore, the time-consistent investment strategy is also obtained by solving the extended Hamilton-Jacobi-Bellman equations. We compare the precommitted strategy with time-consistent strategy and find that these different strategies have different advantages: the former can make value function maximized at the original time t=0 and the latter strategy is time-consistent for the whole time horizon. Finally, numerical analysis is presented for our results.
A thermodynamically consistent phase-field model for two-phase flows with thermocapillary effects
Guo, Zhenlin
2014-01-01
In this paper, we develop a phase-field model for binary incompressible fluid with thermocapillary effects, which allows the different properties (densities, viscosities and heat conductivities) for each component and meanwhile maintains the thermodynamic consistency. The governing equations of the model including the Navier-Stokes equations, Cahn-Hilliard equations and energy balance equation are derived together within a thermodynamic framework based on the entropy generation, which guarantees the thermodynamic consistency. The sharp-interface limit analysis is carried out to show that the interfacial conditions of the classical sharp-interface models can be recovered from our phase-field model. Moreover, some numerical examples including thermocapillary migration of a bubble and thermocapillary convections in a two- layer fluid system are computed by using a continuous finite element method. The results are compared to the existing analytical solutions and theoretical predictions as validations for our mod...
Nonparametric test of consistency between cosmological models and multiband CMB measurements
Aghamousa, Amir
2015-01-01
We present a novel approach to test the consistency of the cosmological models with multiband CMB data using a nonparametric approach. In our analysis we calibrate the REACT (Risk Estimation and Adaptation after Coordinate Transformation) confidence levels associated with distances in function space (confidence distances) based on the Monte Carlo simulations in order to test the consistency of an assumed cosmological model with observation. To show the applicability of our algorithm, we confront Planck 2013 temperature data with concordance model of cosmology considering two different Planck spectra combination. In order to have an accurate quantitative statistical measure to compare between the data and the theoretical expectations, we calibrate REACT confidence distances and perform a bias control using many realizations of the data. Our results in this work using Planck 2013 temperature data put the best fit $\\Lambda$CDM model at $95\\% (\\sim 2\\sigma)$ confidence distance from the center of the nonparametri...
A simplified benchmark Stock-Flow Consistent (SFC) post-Keynesian growth model
Cláudio H. dos Santos; Zezza, Gennaro
2007-01-01
Despite being arguably one of the most active areas of research in heterodox macroeconomics, the study of the dynamic properties of stock-flow consistent (SFC) growth models of financially sophisticated economies is still in its early stages. This paper attempts to offer a contribution to this line of research by presenting a simplified Post-Keynesian SFC growth model with well-defined dynamic properties, and using it to shed light on the merits and limitations of the current heterodox SFC li...
A Consistent Direct Method for Estimating Parameters in Ordinary Differential Equations Models
Holte, Sarah E.
2016-01-01
Ordinary differential equations provide an attractive framework for modeling temporal dynamics in a variety of scientific settings. We show how consistent estimation for parameters in ODE models can be obtained by modifying a direct (non-iterative) least squares method similar to the direct methods originally developed by Himmelbau, Jones and Bischoff. Our method is called the bias-corrected least squares (BCLS) method since it is a modification of least squares methods known to be biased. Co...
Comment on Self-Consistent Model of Black Hole Formation and Evaporation
Ho, Pei-Ming
2015-01-01
In an earlier work, Kawai et al proposed a model of black-hole formation and evaporation, in which the geometry of a collapsing shell of null dust is studied, including consistently the back reaction of its Hawking radiation. In this note, we illuminate the implications of their work, focusing on the resolution of the information loss paradox and the problem of the firewall.
Consistent phase-change modeling for CO2-based heat mining operation
DEFF Research Database (Denmark)
Singh, Ashok Kumar; Veje, Christian
2017-01-01
–gas phase transition with more accuracy and consistency. Calculation of fluid properties and saturation state were based on the volume translated Peng–Robinson equation of state and results verified. The present model has been applied to a scenario to simulate a CO2-based heat mining process. In this paper...
Comment on self-consistent model of black hole formation and evaporation
Energy Technology Data Exchange (ETDEWEB)
Ho, Pei-Ming [Department of Physics and Center for Theoretical Sciences, Center for Advanced Study in Theoretical Sciences,National Taiwan University, Taipei 106, Taiwan, R.O.C. (China)
2015-08-18
In an earlier work, Kawai et al. proposed a model of black-hole formation and evaporation, in which the geometry of a collapsing shell of null dust is studied, including consistently the back reaction of its Hawking radiation. In this note, we illuminate the implications of their work, focusing on the resolution of the information loss paradox and the problem of the firewall.
Spatial coincidence modelling, automated database updating and data consistency in vector GIS.
Kufoniyi, O.
1995-01-01
This thesis presents formal approaches for automated database updating and consistency control in vector- structured spatial databases. To serve as a framework, a conceptual data model is formalized for the representation of geo-data from multiple map layers in which a map layer denotes a set of ter
Song, Y.; Wright, D.
1998-01-01
A formulation of the pressure gradient force for use in models with topography-following coordinates is proposed and diagnostically analyzed by Song. We investigate numerical consistency with respect to global energy conservation, depth-integrated momentum changes, and the represent of the bottom pressure torque.
Subjective Confidence in Perceptual Judgments: A Test of the Self-Consistency Model
Koriat, Asher
2011-01-01
Two questions about subjective confidence in perceptual judgments are examined: the bases for these judgments and the reasons for their accuracy. Confidence in perceptual judgments has been claimed to rest on qualitatively different processes than confidence in memory tasks. However, predictions from a self-consistency model (SCM), which had been…
Subjective Confidence in Perceptual Judgments: A Test of the Self-Consistency Model
Koriat, Asher
2011-01-01
Two questions about subjective confidence in perceptual judgments are examined: the bases for these judgments and the reasons for their accuracy. Confidence in perceptual judgments has been claimed to rest on qualitatively different processes than confidence in memory tasks. However, predictions from a self-consistency model (SCM), which had been…
STRONG CONSISTENCY OF M ESTIMATOR IN LINEAR MODEL FOR NEGATIVELY ASSOCIATED SAMPLES
Institute of Scientific and Technical Information of China (English)
Qunying WU
2006-01-01
This paper discusses the strong consistency of M estimator of regression parameter in linear model for negatively associated samples. As a result, the author extends Theorem 1 and Theorem 2 of Shanchao YANG (2002) to the NA errors without necessarily imposing any extra condition.
DEFF Research Database (Denmark)
Bach, Finn
2009-01-01
Notatet giver en kort introduktion til den statiske virkemåde af membraner og membrankonstruktioner......Notatet giver en kort introduktion til den statiske virkemåde af membraner og membrankonstruktioner...
Antimicrobial mechanism of flavonoids against Escherichia coli ATCC 25922 by model membrane study
Energy Technology Data Exchange (ETDEWEB)
He, Mengying; Wu, Ting; Pan, Siyi; Xu, Xiaoyun, E-mail: xiaoyunxu88@gmail.com
2014-06-01
Antimicrobial mechanism of four flavonoids (kaempferol, hesperitin, (+)-catechin hydrate, biochanin A) against Escherichia coli ATCC 25922 was investigated through cell membranes and a liposome model. The release of bacterial protein and images from transmission electron microscopy demonstrated damage to the E. coli ATCC 25922 membrane. A liposome model with dipalmitoylphosphatidylethanolamine (DPPE) (0.6 molar ratio) and dipalmitoylphosphatidylglycerol (DPPG) (0.4 molar ratio), representative of the phospholipid membrane of E. coli ATCC 25922, was used to specify the mode of action of four selected flavonoids through Raman spectroscopy and differential scanning calorimetry. It is suggested that for flavonoids, to be effective antimicrobials, interaction with the polar head-group of the model membrane followed by penetration into the hydrophobic regions must occur. The antimicrobial efficacies of the flavonoids were consistent with liposome interaction activities, kaempferol > hesperitin > (+)-catechin hydrate > biochanin A. This study provides a liposome model capable of mimicking the cell membrane of E. coli ATCC 25922. The findings are important in understanding the antibacterial mechanism on cell membranes.
Modeling and vibration control of an active membrane mirror
Ruggiero, Eric J.; Inman, Daniel J.
2009-09-01
The future of space satellite technology lies in ultra-large mirrors and radar apertures for significant improvements in imaging and communication bandwidths. The availability of optical-quality membranes drives a parallel effort for structural models that can capture the dominant dynamics of large, ultra-flexible satellite payloads. Unfortunately, the inherent flexibility of membrane mirrors wreaks havoc with the payload's on-orbit stability and maneuverability. One possible means of controlling these undesirable dynamics is by embedding active piezoelectric ceramics near the boundary of the membrane mirror. In doing so, active feedback control can be used to eliminate detrimental vibration, perform static shape control, and evaluate the health of the structure. The overall motivation of the present work is to design a control system using distributed bimorph actuators to eliminate any detrimental vibration of the membrane mirror. As a basis for this study, a piezoceramic wafer was attached in a bimorph configuration near the boundary of a tensioned rectangular membrane sample. A finite element model of the system was developed to capture the relevant system dynamics from 0 to 300 Hz. The finite element model was compared against experimental results, and fair agreement found. Using the validated finite element models, structural control using linear quadratic regulator control techniques was then used to numerically demonstrate effective vibration control. Typical results show that less than 12 V of actuation voltage is required to eliminate detrimental vibration of the membrane samples in less than 15 ms. The functional gains of the active system are also derived and presented. These spatially descriptive control terms dictate favorable regions within the membrane domain for placing sensors and can be used as a design guideline for structural control applications. The results of the present work demonstrate that thin plate theory is an appropriate modeling
Proton exchange membrane fuel cells modeling
Gao, Fengge; Miraoui, Abdellatif
2013-01-01
The fuel cell is a potential candidate for energy storage and conversion in our future energy mix. It is able to directly convert the chemical energy stored in fuel (e.g. hydrogen) into electricity, without undergoing different intermediary conversion steps. In the field of mobile and stationary applications, it is considered to be one of the future energy solutions.Among the different fuel cell types, the proton exchange membrane (PEM) fuel cell has shown great potential in mobile applications, due to its low operating temperature, solid-state electrolyte and compactness.This book pre
Modeling the Elastic Properties of Lipid Bilayer Membranes
Barry, Edward; Gibaud, Thomas; Zakhary, Mark; Dogic, Zvonimir
2011-03-01
Model membranes such as lipid bilayers have been indispensable tools for our understanding of the elastic properties of biological membranes. In this talk, I will introduce a colloidal model for membranes and demonstrate that the physical properties of these colloidal membranes are identical to lipid bilayers. The model system is unique in that the constituent molecules are homogenous and non-amphiphilic, yet their self-assembly into membranes and other hierarchical assemblages, such as a lamellar type phases and chiral ribbons, proceeds spontaneously in solution. Owing to the large size of the constituent molecules, individual molecules can be directly visualized and simultaneous observations at the continuum and molecular lengthscales are used to characterize the behavior of model membranes with unprecedented detail. Moreover, once assembled in solution, molecular interactions can be controlled in situ. In particular, the strength of chiral interactions can be varied, leading to fascinating transitions in behavior that resembles the formation of starfish vesicles. These observations point towards the important role of line tension, and have potential implications for phase separated lipid mixtures or lipid rafts.
Stability and rupture of archaebacterial cell membrane: a model study.
Li, Shuangyang; Zheng, Fengxian; Zhang, Xianren; Wang, Wenchuan
2009-01-29
It is known that the thermoacidophilic archaebacterium Sulfolobus acidocaldarius can grow in hot springs at 65-80 degrees C and live in acidic environments (pH 2-3); however, the origin of its unusual thermal stability remains unclear. In this work, using a vesicle as a model, we study the thermal stability and rupture of archaebacterial cell membrane. We perform a simulation investigation of the structure-property relationship of monolayer membrane formed by bolaform lipids and compare it with that of bilayer membrane formed by monopolar lipids. The origin of the unusually thermal stability of archaebacterial cell and the mechanism for its rupture are presented in molecular details.
Directory of Open Access Journals (Sweden)
Damiano Monelli
2010-11-01
Full Text Available We present here two self-consistent implementations of a short-term earthquake probability (STEP model that produces daily seismicity forecasts for the area of the Italian national seismic network. Both implementations combine a time-varying and a time-invariant contribution, for which we assume that the instrumental Italian earthquake catalog provides the best information. For the time-invariant contribution, the catalog is declustered using the clustering technique of the STEP model; the smoothed seismicity model is generated from the declustered catalog. The time-varying contribution is what distinguishes the two implementations: 1 for one implementation (STEP-LG, the original model parameterization and estimation is used; 2 for the other (STEP-NG, the mean abundance method is used to estimate aftershock productivity. In the STEP-NG implementation, earthquakes with magnitude up to ML= 6.2 are expected to be less productive compared to the STEP-LG implementation, whereas larger earthquakes are expected to be more productive. We have retrospectively tested the performance of these two implementations and applied likelihood tests to evaluate their consistencies with observed earthquakes. Both of these implementations were consistent with the observed earthquake data in space: STEP-NG performed better than STEP-LG in terms of forecast rates. More generally, we found that testing earthquake forecasts issued at regular intervals does not test the full power of clustering models, and future experiments should allow for more frequent forecasts starting at the times of triggering events.
Altmeyer, Guillaume; Panicaud, Benoit; Rouhaud, Emmanuelle; Wang, Mingchuan; Roos, Arjen; Kerner, Richard
2016-11-01
When constructing viscoelastic models, rate-form relations appear naturally to relate strain and stress tensors. One has to ensure that these tensors and their rates are indifferent with respect to the change of observers and to the superposition with rigid body motions. Objective transports are commonly accepted to ensure this invariance. However, the large number of transport operators developed makes the choice often difficult for the user and may lead to physically inconsistent formulation of hypoelasticity. In this paper, a methodology based on the use of the Lie derivative is proposed to model consistent hypoelasticity as an equivalent incremental formulation of hyperelasticity. Both models are shown to be reversible and completely equivalent. Extension to viscoelasticity is then proposed from this consistent model by associating consistent hypoelastic models with viscous behavior. As an illustration, Mooney-Rivlin nonlinear elasticity is coupled with Newton viscosity and a Maxwell-like material is investigated. Numerical solutions are then presented to illustrate a viscoelastic material subjected to finite deformations for a large range of strain rates.
Lu, Wei; Song, Joo Hyun; Christensen, Gary E.; Parikh, Parag J.; Bradley, Jeffrey D.; Low, Daniel A.
2006-03-01
Respiratory motion is a significant source of error in conformal radiation therapy for the thorax and upper abdomen. Four-dimensional computed tomography (4D CT) has been proposed to reduce the uncertainty caused by internal respiratory organ motion. A 4D CT dataset is retrospectively reconstructed at various stages of a respiratory cycle. An important tool for 4D treatment planning is deformable image registration. An inverse consistent image registration is used to model lung motion from one respiratory stage to another during a breathing cycle. This diffeomorphic registration jointly estimates the forward and reverse transformations providing more accurate correspondence between two images. Registration results and modeled motions in the lung are shown for three example respiratory stages. The results demonstrate that the consistent image registration satisfactorily models the large motions in the lung, providing a useful tool for 4D planning and delivering.
Rudzinski, Joseph F; Bereau, Tristan
2016-01-01
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and reference (e.g., from experiments or higher-level simulations) observables. To bound the microscopic information generated by computer simulations within reference measurements, we propose a method that reweights the microscopic transitions of the system to improve consistency with a set of coarse kinetic observables. The method employs the well-developed Markov state modeling framework to efficiently link microscopic dynamics with long-time scale constraints, thereby consistently addressing a wide range of time scales. To emphasize the robustness of the method, we consider two distinct coarse-grained models with significant kinetic inconsistencies. When applied to the simulated conformational dynamics of small peptides, the reweighting procedure systematically ...
Zhang, Zhen; Guo, Chonghui
2016-08-01
Due to the uncertainty of the decision environment and the lack of knowledge, decision-makers may use uncertain linguistic preference relations to express their preferences over alternatives and criteria. For group decision-making problems with preference relations, it is important to consider the individual consistency and the group consensus before aggregating the preference information. In this paper, consistency and consensus models for group decision-making with uncertain 2-tuple linguistic preference relations (U2TLPRs) are investigated. First of all, a formula which can construct a consistent U2TLPR from the original preference relation is presented. Based on the consistent preference relation, the individual consistency index for a U2TLPR is defined. An iterative algorithm is then developed to improve the individual consistency of a U2TLPR. To help decision-makers reach consensus in group decision-making under uncertain linguistic environment, the individual consensus and group consensus indices for group decision-making with U2TLPRs are defined. Based on the two indices, an algorithm for consensus reaching in group decision-making with U2TLPRs is also developed. Finally, two examples are provided to illustrate the effectiveness of the proposed algorithms.
The fundamental solution for a consistent complex model of the shallow shell equations
Directory of Open Access Journals (Sweden)
Matthew P. Coleman
1999-09-01
Full Text Available The calculation of the Fourier transforms of the fundamental solution in shallow shell theory ostensibly was accomplished by J. L. Sanders [J. Appl. Mech. 37 (1970, 361-366]. However, as is shown in detail in this paper, the complex model used by Sanders is, in fact, inconsistent. This paper provides a consistent version of Sanders's complex model, along with the Fourier transforms of the fundamental solution for this corrected model. The inverse Fourier transforms are then calculated for the particular cases of the shallow spherical and circular cylindrical shells, and the results of the latter are seen to be in agreement with results appearing elsewhere in the literature.
Tests and applications of self-consistent cranking in the interacting boson model
Kuyucak, S; Kuyucak, Serdar; Sugita, Michiaki
1999-01-01
The self-consistent cranking method is tested by comparing the cranking calculations in the interacting boson model with the exact results obtained from the SU(3) and O(6) dynamical symmetries and from numerical diagonalization. The method is used to study the spin dependence of shape variables in the $sd$ and $sdg$ boson models. When realistic sets of parameters are used, both models lead to similar results: axial shape is retained with increasing cranking frequency while fluctuations in the shape variable $\\gamma$ are slightly reduced.
Consistency maintenance for constraint in role-based access control model
Institute of Scientific and Technical Information of China (English)
韩伟力; 陈刚; 尹建伟; 董金祥
2002-01-01
Constraint is an important aspect of role-based access control and is sometimes argued to be the principal motivation for role-based access control (RBAC). But so far'few authors have discussed consistency maintenance for constraint in RBAC model. Based on researches of constraints among roles and types of inconsistency among constraints, this paper introduces correaponding formal rules, rulebased reasoning and corresponding methods to detect, avoid and resolve these inconsistencies. Finally,the paper introduces briefly the application of consistency maintenance in ZD-PDM, an enterprise-ori-ented product data management (PDM) system.
Consistency maintenance for constraint in role-based access control model
Institute of Scientific and Technical Information of China (English)
韩伟力; 陈刚; 尹建伟; 董金祥
2002-01-01
Constraint is an important aspect of role-based access control and is sometimes argued to be the principal motivation for role-based access control (RBAC). But so far few authors have discussed consistency maintenance for constraint in RBAC model. Based on researches of constraints among roles and types of inconsistency among constraints, this paper introduces corresponding formal rules, rule-based reasoning and corresponding methods to detect, avoid and resolve these inconsistencies. Finally, the paper introduces briefly the application of consistency maintenance in ZD-PDM, an enterprise-oriented product data management (PDM) system.
Directory of Open Access Journals (Sweden)
Hamodrakas Stavros J
2004-03-01
Full Text Available Abstract Background Integral membrane proteins constitute about 20–30% of all proteins in the fully sequenced genomes. They come in two structural classes, the α-helical and the β-barrel membrane proteins, demonstrating different physicochemical characteristics, structure and localization. While transmembrane segment prediction for the α-helical integral membrane proteins appears to be an easy task nowadays, the same is much more difficult for the β-barrel membrane proteins. We developed a method, based on a Hidden Markov Model, capable of predicting the transmembrane β-strands of the outer membrane proteins of gram-negative bacteria, and discriminating those from water-soluble proteins in large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of correct predictions rather than the likelihood of the sequences. Results The training has been performed on a non-redundant database of 14 outer membrane proteins with structures known at atomic resolution; it has been tested with a jacknife procedure, yielding a per residue accuracy of 84.2% and a correlation coefficient of 0.72, whereas for the self-consistency test the per residue accuracy was 88.1% and the correlation coefficient 0.824. The total number of correctly predicted topologies is 10 out of 14 in the self-consistency test, and 9 out of 14 in the jacknife. Furthermore, the model is capable of discriminating outer membrane from water-soluble proteins in large-scale applications, with a success rate of 88.8% and 89.2% for the correct classification of outer membrane and water-soluble proteins respectively, the highest rates obtained in the literature. That test has been performed independently on a set of known outer membrane proteins with low sequence identity with each other and also with the proteins of the training set. Conclusion Based on the above, we developed a strategy, that enabled us to screen the entire proteome of E. coli for
A New Hierarchy of Phylogenetic Models Consistent with Heterogeneous Substitution Rates.
Woodhams, Michael D; Fernández-Sánchez, Jesús; Sumner, Jeremy G
2015-07-01
When the process underlying DNA substitutions varies across evolutionary history, some standard Markov models underlying phylogenetic methods are mathematically inconsistent. The most prominent example is the general time-reversible model (GTR) together with some, but not all, of its submodels. To rectify this deficiency, nonhomogeneous Lie Markov models have been identified as the class of models that are consistent in the face of a changing process of DNA substitutions regardless of taxon sampling. Some well-known models in popular use are within this class, but are either overly simplistic (e.g., the Kimura two-parameter model) or overly complex (the general Markov model). On a diverse set of biological data sets, we test a hierarchy of Lie Markov models spanning the full range of parameter richness. Compared against the benchmark of the ever-popular GTR model, we find that as a whole the Lie Markov models perform well, with the best performing models having 8-10 parameters and the ability to recognize the distinction between purines and pyrimidines. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society of Systematic Biologists.
Self-consistent chaotic transport in a high-dimensional mean-field Hamiltonian map model
Martínez-del-Río, D; Olvera, A; Calleja, R
2016-01-01
Self-consistent chaotic transport is studied in a Hamiltonian mean-field model. The model provides a simplified description of transport in marginally stable systems including vorticity mixing in strong shear flows and electron dynamics in plasmas. Self-consistency is incorporated through a mean-field that couples all the degrees-of-freedom. The model is formulated as a large set of $N$ coupled standard-like area-preserving twist maps in which the amplitude and phase of the perturbation, rather than being constant like in the standard map, are dynamical variables. Of particular interest is the study of the impact of periodic orbits on the chaotic transport and coherent structures. Numerical simulations show that self-consistency leads to the formation of a coherent macro-particle trapped around the elliptic fixed point of the system that appears together with an asymptotic periodic behavior of the mean field. To model this asymptotic state, we introduced a non-autonomous map that allows a detailed study of th...
Resveratrol induces chain interdigitation in DPPC cell membrane model systems.
Longo, Elena; Ciuchi, Federica; Guzzi, Rita; Rizzuti, Bruno; Bartucci, Rosa
2016-12-01
Resveratrol is a natural polyphenol found in various plants with potential therapeutic activity as anti-oxidant, anti-inflammatory, cardioprotective and anti-tumoral. Lipid membranes are among cellular components that are targets of its action. In this work ESR of chain labeled lipids, calorimetry, X-ray diffraction and molecular docking are used to study the interaction of resveratrol with membrane model systems of dipalmitoylphosphatidylcholine (DPPC) as a function of resveratrol concentration (0-30 mol% of the lipid) and temperature (10-50°C). Resveratrol incorporated in DPPC bilayers induces considerable motional restriction at the lipid tail termini, removing the gradient of increasing mobility along the chain found in DPPC bilayers in the gel phase. In contrast, it leaves unperturbed the DPPC chain flexibility profile in the liquid-crystalline phase. At low concentration, resveratrol progressively reduces the pre-transition temperature and eliminates the pre-transition for content ≥5mol%. A reduced cooperativity and a downshift of the main transition temperature are observed, especially at high content. The typical diffraction pattern of DPPC multibilayers in the Lβ' phase is converted to a lamellar pattern with reduced d-spacing of untilted lipid chain in a hexagonal packing at 30 mol% of resveratrol. Molecular docking indicates that the energetically favoured anchoring site is the polar headgroup region, where resveratrol acts as a spacer. The overall results are consistent with the formation in DPPC of an interdigitated Lβi gel phase induced by 30 mol% resveratrol. Copyright © 2016 Elsevier B.V. All rights reserved.
Critical Review of Membrane Bioreactor Models
DEFF Research Database (Denmark)
Naessens, W.; Maere, T.; Ratkovich, Nicolas Rios;
2012-01-01
modelling. In this paper, the vast literature on hydrodynamic and integrated modelling in MBR is critically reviewed. Hydrodynamic models are used at different scales and focus mainly on fouling and only little on system design/optimisation. Integrated models also focus on fouling although the ones...
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
Semiparametric reproductive dispersion nonlinear model (SRDNM) is an extension of nonlinear reproductive dispersion models and semiparametric nonlinear regression models, and includes semiparametric nonlinear model and semiparametric generalized linear model as its special cases. Based on the local kernel estimate of nonparametric component, profile-kernel and backfitting estimators of parameters of interest are proposed in SRDNM, and theoretical comparison of both estimators is also investigated in this paper. Under some regularity conditions, strong consistency and asymptotic normality of two estimators are proved. It is shown that the backfitting method produces a larger asymptotic variance than that for the profile-kernel method. A simulation study and a real example are used to illustrate the proposed methodologies.
Detecting consistent patterns of directional adaptation using differential selection codon models.
Parto, Sahar; Lartillot, Nicolas
2017-06-23
Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors. However, some organisms may be subject to systematic changes in selective pressure, resulting in reproducible molecular adaptations across independent lineages subject to similar conditions. Here, we introduce a codon-based differential selection model, which aims to detect and quantify the fine-grained consistent patterns of adaptation at the protein-coding level, as a function of external conditions experienced by the organism under investigation. The model parameterizes the global mutational pressure, as well as the site- and condition-specific amino acid selective preferences. This phylogenetic model is implemented in a Bayesian MCMC framework. After validation with simulations, we applied our method to a dataset of HIV sequences from patients with known HLA genetic background. Our differential selection model detects and characterizes differentially selected coding positions specifically associated with two different HLA alleles. Our differential selection model is able to identify consistent molecular adaptations as a function of repeated changes in the environment of the organism. These models can be applied to many other problems, ranging from viral adaptation to evolution of life-history strategies in plants or animals.
Hess, Julian; Wang, Yongqi
2016-11-01
A new mixture model for granular-fluid flows, which is thermodynamically consistent with the entropy principle, is presented. The extra pore pressure described by a pressure diffusion equation and the hypoplastic material behavior obeying a transport equation are taken into account. The model is applied to granular-fluid flows, using a closing assumption in conjunction with the dynamic fluid pressure to describe the pressure-like residual unknowns, hereby overcoming previous uncertainties in the modeling process. Besides the thermodynamically consistent modeling, numerical simulations are carried out and demonstrate physically reasonable results, including simple shear flow in order to investigate the vertical distribution of the physical quantities, and a mixture flow down an inclined plane by means of the depth-integrated model. Results presented give insight in the ability of the deduced model to capture the key characteristics of granular-fluid flows. We acknowledge the support of the Deutsche Forschungsgemeinschaft (DFG) for this work within the Project Number WA 2610/3-1.
A control-oriented self-consistent model of an inductively-coupled plasma
Keville, Bernard; Turner, Miles
2009-10-01
An essential first step in the design of real time control algorithms for plasma processes is to determine dynamical relationships between actuator quantities such as gas flow rate set points and plasma states such electron density. An ideal first principles-based, control-oriented model should exhibit the simplicity and computational requirements of an empirical model and, in addition, despite sacrificing first principles detail, capture enough of the essential physics and chemistry of the process in order to provide reasonably accurate qualitative predictions. This presentation describes a control-oriented model of a cylindrical low pressure planar inductive discharge with a stove top antenna. The model consists of equivalent circuit coupled to a global model of the plasma chemistry to produce a self-consistent zero-dimensional model of the discharge. The non-local plasma conductivity and the fields in the plasma are determined from the wave equation and the two-term solution of the Boltzmann equation. Expressions for the antenna impedance and the parameters of the transformer equivalent circuit in terms of the isotropic electron distribution and the geometry of the chamber are presented.
Consistent increase in Indian monsoon rainfall and its variability across CMIP-5 models
Directory of Open Access Journals (Sweden)
A. Menon
2013-01-01
Full Text Available The possibility of an impact of global warming on the Indian monsoon is of critical importance for the large population of this region. Future projections within the Coupled Model Intercomparison Project Phase 3 (CMIP-3 showed a wide range of trends with varying magnitude and sign across models. Here the Indian summer monsoon rainfall is evaluated in 20 CMIP-5 models for the period 1850 to 2100. In the new generation of climate models a consistent increase in seasonal mean rainfall during the summer monsoon periods arises. All models simulate stronger seasonal mean rainfall in the future compared to the historic period under the strongest warming scenario RCP-8.5. Increase in seasonal mean rainfall is the largest for the RCP-8.5 scenario compared to other RCPs. The interannual variability of the Indian monsoon rainfall also shows a consistent positive trend under unabated global warming. Since both the long-term increase in monsoon rainfall as well as the increase in interannual variability in the future is robust across a wide range of models, some confidence can be attributed to these projected trends.
Non-Perturbative Self-Consistent Model in SU(N Gauge Field Theory
Directory of Open Access Journals (Sweden)
Koshelkin A.V.
2012-06-01
Full Text Available Non-perturbative quasi-classical model in a gauge theory with the Yang-Mills (YM field is developed. The self-consistent solutions of the Dirac equation in the SU(N gauge field, which is in the eikonal approximation, and the Yang-Mills (YM equations containing the external fermion current are solved. It shown that the developed model has the self-consistent solutions of the Dirac and Yang-Mills equations at N ≥ 3. In this way, the solutions take place provided that the fermion and gauge fields exist simultaneously, so that the fermion current completely compensates the current generated by the gauge field due to self-interaction of it.
Silvis, Maurits H.; Remmerswaal, Ronald A.; Verstappen, Roel
2017-01-01
We study the construction of subgrid-scale models for large-eddy simulation of incompressible turbulent flows. In particular, we aim to consolidate a systematic approach of constructing subgrid-scale models, based on the idea that it is desirable that subgrid-scale models are consistent with the mathematical and physical properties of the Navier-Stokes equations and the turbulent stresses. To that end, we first discuss in detail the symmetries of the Navier-Stokes equations, and the near-wall scaling behavior, realizability and dissipation properties of the turbulent stresses. We furthermore summarize the requirements that subgrid-scale models have to satisfy in order to preserve these important mathematical and physical properties. In this fashion, a framework of model constraints arises that we apply to analyze the behavior of a number of existing subgrid-scale models that are based on the local velocity gradient. We show that these subgrid-scale models do not satisfy all the desired properties, after which we explain that this is partly due to incompatibilities between model constraints and limitations of velocity-gradient-based subgrid-scale models. However, we also reason that the current framework shows that there is room for improvement in the properties and, hence, the behavior of existing subgrid-scale models. We furthermore show how compatible model constraints can be combined to construct new subgrid-scale models that have desirable properties built into them. We provide a few examples of such new models, of which a new model of eddy viscosity type, that is based on the vortex stretching magnitude, is successfully tested in large-eddy simulations of decaying homogeneous isotropic turbulence and turbulent plane-channel flow.
Institute of Scientific and Technical Information of China (English)
John Jack P. RIEGEL III; David DAVISON
2016-01-01
Historically, there has been little correlation between the material properties used in (1) empirical formulae, (2) analytical formulations, and (3) numerical models. The various regressions and models may each provide excellent agreement for the depth of penetration into semi-infinite targets. But the input parameters for the empirically based procedures may have little in common with either the analytical model or the numerical model. This paper builds on previous work by Riegel and Anderson (2014) to show how the Effective Flow Stress (EFS) strength model, based on empirical data, can be used as the average flow stress in the analytical Walker–Anderson Penetration model (WAPEN) (Anderson and Walker, 1991) and how the same value may be utilized as an effective von Mises yield strength in numerical hydrocode simulations to predict the depth of penetration for eroding projectiles at impact velocities in the mechanical response regime of the materials. The method has the benefit of allowing the three techniques (empirical, analytical, and numerical) to work in tandem. The empirical method can be used for many shot line calculations, but more advanced analytical or numerical models can be employed when necessary to address specific geometries such as edge effects or layering that are not treated by the simpler methods. Developing complete constitutive relationships for a material can be costly. If the only concern is depth of penetration, such a level of detail may not be required. The effective flow stress can be determined from a small set of depth of penetration experiments in many cases, especially for long penetrators such as the L/D=10 ones considered here, making it a very practical approach. In the process of performing this effort, the authors considered numerical simulations by other researchers based on the same set of experimental data that the authors used for their empirical and analytical assessment. The goals were to establish a baseline with a full
Directory of Open Access Journals (Sweden)
John (Jack P. Riegel III
2016-04-01
Full Text Available Historically, there has been little correlation between the material properties used in (1 empirical formulae, (2 analytical formulations, and (3 numerical models. The various regressions and models may each provide excellent agreement for the depth of penetration into semi-infinite targets. But the input parameters for the empirically based procedures may have little in common with either the analytical model or the numerical model. This paper builds on previous work by Riegel and Anderson (2014 to show how the Effective Flow Stress (EFS strength model, based on empirical data, can be used as the average flow stress in the analytical Walker–Anderson Penetration model (WAPEN (Anderson and Walker, 1991 and how the same value may be utilized as an effective von Mises yield strength in numerical hydrocode simulations to predict the depth of penetration for eroding projectiles at impact velocities in the mechanical response regime of the materials. The method has the benefit of allowing the three techniques (empirical, analytical, and numerical to work in tandem. The empirical method can be used for many shot line calculations, but more advanced analytical or numerical models can be employed when necessary to address specific geometries such as edge effects or layering that are not treated by the simpler methods. Developing complete constitutive relationships for a material can be costly. If the only concern is depth of penetration, such a level of detail may not be required. The effective flow stress can be determined from a small set of depth of penetration experiments in many cases, especially for long penetrators such as the L/D = 10 ones considered here, making it a very practical approach. In the process of performing this effort, the authors considered numerical simulations by other researchers based on the same set of experimental data that the authors used for their empirical and analytical assessment. The goals were to establish a
Institute of Scientific and Technical Information of China (English)
YIN; Changming; ZHAO; Lincheng; WEI; Chengdong
2006-01-01
In a generalized linear model with q × 1 responses, the bounded and fixed (or adaptive) p × q regressors Zi and the general link function, under the most general assumption on the minimum eigenvalue of ∑ni=1 ZiZ'i, the moment condition on responses as weak as possible and the other mild regular conditions, we prove that the maximum quasi-likelihood estimates for the regression parameter vector are asymptotically normal and strongly consistent.
A thermodynamically consistent model of the post-translational Kai circadian clock
Lubensky, David K.; ten Wolde, Pieter Rein
2017-01-01
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. Both domains can bind and hydrolyze ATP, but only the CII domain can be phosphorylated, at two residues, in a well-defined sequence. While this system has been studied extensively, how the clock is driven thermodynamically has remained elusive. Inspired by recent experimental observations and building on ideas from previous mathematical models, we present a new, thermodynamically consistent, statistical-mechanical model of the clock. At its heart are two main ideas: i) ATP hydrolysis in the CI domain provides the thermodynamic driving force for the clock, switching KaiC between an active conformational state in which its phosphorylation level tends to rise and an inactive one in which it tends to fall; ii) phosphorylation of the CII domain provides the timer for the hydrolysis in the CI domain. The model also naturally explains how KaiA, by acting as a nucleotide exchange factor, can stimulate phosphorylation of KaiC, and how the differential affinity of KaiA for the different KaiC phosphoforms generates the characteristic temporal order of KaiC phosphorylation. As the phosphorylation level in the CII domain rises, the release of ADP from CI slows down, making the inactive conformational state of KaiC more stable. In the inactive state, KaiC binds KaiB, which not only stabilizes this state further, but also leads to the sequestration of KaiA, and hence to KaiC dephosphorylation. Using a dedicated kinetic Monte Carlo algorithm, which makes it possible to efficiently simulate this system consisting of more than a billion reactions, we show that the model can describe a wealth of experimental data. PMID:28296888
ICFD modeling of final settlers - developing consistent and effective simulation model structures
DEFF Research Database (Denmark)
Plósz, Benedek G.; Guyonvarch, Estelle; Ramin, Elham
analysis exercises is kept to a minimum (4). Consequently, detailed information related to, for instance, design boundaries, may be ignored, and their effects may only be accounted for through calibration of model parameters used as catchalls, and by arbitrary amendments of structural uncertainty...... of (6). Further details are shown in (5). Results and discussions Factor screening. Factor screening is carried out by imposing statistically designed moderate (under-loaded) and extreme (under-, critical and overloaded) operational boundary conditions on the 2-D CFD SST model (8). Results obtained...
Self-consistent Dark Matter simplified models with an s-channel scalar mediator
Bell, Nicole F.; Busoni, Giorgio; Sanderson, Isaac W.
2017-03-01
We examine Simplified Models in which fermionic DM interacts with Standard Model (SM) fermions via the exchange of an s-channel scalar mediator. The single-mediator version of this model is not gauge invariant, and instead we must consider models with two scalar mediators which mix and interfere. The minimal gauge invariant scenario involves the mixing of a new singlet scalar with the Standard Model Higgs boson, and is tightly constrained. We construct two Higgs doublet model (2HDM) extensions of this scenario, where the singlet mixes with the 2nd Higgs doublet. Compared with the one doublet model, this provides greater freedom for the masses and mixing angle of the scalar mediators, and their coupling to SM fermions. We outline constraints on these models, and discuss Yukawa structures that allow enhanced couplings, yet keep potentially dangerous flavour violating processes under control. We examine the direct detection phenomenology of these models, accounting for interference of the scalar mediators, and interference of different quarks in the nucleus. Regions of parameter space consistent with direct detection measurements are determined.
Self-Consistent Ring Current/Electromagnetic Ion Cyclotron Waves Modeling
Khazanov, G. V.; Gamayunov, K. V.; Gallagher, D. L.
2006-01-01
The self-consistent treatment of the RC ion dynamics and EMIC waves, which are thought to exert important influences on the ion dynamical evolution, is an important missing element in our understanding of the storm-and recovery-time ring current evolution. For example, the EMlC waves cause the RC decay on a time scale of about one hour or less during the main phase of storms. The oblique EMIC waves damp due to Landau resonance with the thermal plasmaspheric electrons, and subsequent transport of the dissipating wave energy into the ionosphere below causes an ionosphere temperature enhancement. Under certain conditions, relativistic electrons, with energies 21 MeV, can be removed from the outer radiation belt by EMIC wave scattering during a magnetic storm. That is why the modeling of EMIC waves is critical and timely issue in magnetospheric physics. This study will generalize the self-consistent theoretical description of RC ions and EMIC waves that has been developed by Khazanov et al. [2002, 2003] and include the heavy ions and propagation effects of EMIC waves in the global dynamic of self-consistent RC - EMIC waves coupling. The results of our newly developed model that will be presented at the meeting, focusing mainly on the dynamic of EMIC waves and comparison of these results with the previous global RC modeling studies devoted to EMIC waves formation. We also discuss RC ion precipitations and wave induced thermal electron fluxes into the ionosphere.
Quantal self-consistent cranking model for monopole excitations in even-even light nuclei
Gulshani, P
2014-01-01
In this article, we derive a quantal self-consistent time-reversal invariant cranking model for isoscalar monopole excitation coupled to intrinsic motion in even-even light nuclei. The model uses a wavefunction that is a product of monopole and intrinsic wavefunctions and a constrained variational method to derive, from a many-particle Schrodinger equation, a pair of coupled self-consistent cranking-type Schrodinger equations for the monopole and intrinsic systems. The monopole and intrinsic wavefunctions are coupled to each other by the two cranking equations and their associated parameters and by two constraints imposed on the intrinsic system. For an isotropic Nilsson shell model and an effective residual two-body interaction, the two coupled cranking equations are solved in the Tamm Dancoff approximation. The strength of the interaction is determined from a Hartree-Fock self-consistency argument. The excitation energy of the first excited state is determined and found to agree closely with those observed ...
Predicting giant magnetoresistance using a self-consistent micromagnetic diffusion model
Abert, Claas; Bruckner, Florian; Vogler, Christoph; Praetorius, Dirk; Suess, Dieter
2015-01-01
We propose a self-consistent micromagnetic model that dynamically solves the Landau-Lifshitz-Gilbert equation coupled to the full spin-diffusion equation. The model and its finite-element implementation are validated by current driven motion of a magnetic vortex structure. Potential calculations for a magnetic multilayer structure with perpendicular current flow confirm experimental findings of a non-sinosoidal dependence of the resistivity on the tilting angle of the magnetization in the different layers. While the sinosoidal dependency is observed for certain material parameter limits, a realistic choice of these parameters leads to a notably narrower distribution.
Self-consistent tight-binding atomic-relaxation model of titanium dioxide
Energy Technology Data Exchange (ETDEWEB)
Schelling, P.K.; Yu, N.; Halley, J.W. [School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455 (United States)
1998-07-01
We report a self-consistent tight-binding atomic-relaxation model for titanium dioxide. We fit the parameters of the model to first-principles electronic structure calculations of the band structure and energy as a function of lattice parameters in bulk rutile. We report the method and results for the surface structures and energies of relaxed (110), (100), and (001) surfaces of rutile TiO{sub 2} as well as work functions for these surfaces. Good agreement with first-principles calculations and experiments, where available, is found for these surfaces. We find significant charge transfer (increased covalency) at the surfaces. {copyright} {ital 1998} {ital The American Physical Society}
Modeling Of Proton Exchange Membrane Fuel Cell Systems
DEFF Research Database (Denmark)
Nielsen, Mads Pagh
The objective of this doctoral thesis was to develop reliable steady-state and transient component models suitable to asses-, develop- and optimize proton exchange membrane (PEM) fuel cell systems. Several components in PEM fuel cell systems were characterized and modeled. The developed component...
Huang, Jin
Acid-gas removal is of great importance in many environmental or energy-related processes. Compared to current commercial technologies, membrane-based CO2 and H2S capture has the advantages of low energy consumption, low weight and space requirement, simplicity of installation/operation, and high process flexibility. However, the large-scale application of the membrane separation technology is limited by the relatively low transport properties. In this study, CO2 (H2S)-selective polymeric membranes with high permeability and high selectivity have been studied based on the facilitated transport mechanism. The membrane showed facilitated effect for both CO2 and H2S. A CO2 permeability of above 2000 Barrers, a CO2/H2 selectivity of greater than 40, and a CO2/N2 selectivity of greater than 200 at 100--150°C were observed. As a result of higher reaction rate and smaller diffusing compound, the H2S permeability and H2S/H2 selectivity were about three times higher than those properties for CO2. The novel CO2-selective membrane has been applied to capture CO 2 from flue gas and natural gas. In the CO2 capture experiments from a gas mixture with N2 and H2, a permeate CO 2 dry concentration of greater than 98% was obtained by using steam as the sweep gas. In CO2/CH4 separation, decent CO 2 transport properties were obtained with a feed pressure up to 500 psia. With the thin-film composite membrane structure, significant increase on the CO2 flux was achieved with the decrease of the selective layer thickness. With the continuous removal of CO2, CO2-selective water-gas-shift (WGS) membrane reactor is a promising approach to enhance CO conversion and increase the purity of H2 at process pressure under relatively low temperature. The simultaneous reaction and transport process in the countercurrent WGS membrane reactor was simulated by using a one-dimensional non-isothermal model. The modeling results show that a CO concentration of less than 10 ppm and a H2 recovery of greater
A Self-Consistent Model for Thermal Oxidation of Silicon at Low Oxide Thickness
Directory of Open Access Journals (Sweden)
Gerald Gerlach
2016-01-01
Full Text Available Thermal oxidation of silicon belongs to the most decisive steps in microelectronic fabrication because it allows creating electrically insulating areas which enclose electrically conductive devices and device areas, respectively. Deal and Grove developed the first model (DG-model for the thermal oxidation of silicon describing the oxide thickness versus oxidation time relationship with very good agreement for oxide thicknesses of more than 23 nm. Their approach named as general relationship is the basis of many similar investigations. However, measurement results show that the DG-model does not apply to very thin oxides in the range of a few nm. Additionally, it is inherently not self-consistent. The aim of this paper is to develop a self-consistent model that is based on the continuity equation instead of Fick’s law as the DG-model is. As literature data show, the relationship between silicon oxide thickness and oxidation time is governed—down to oxide thicknesses of just a few nm—by a power-of-time law. Given by the time-independent surface concentration of oxidants at the oxide surface, Fickian diffusion seems to be neglectable for oxidant migration. The oxidant flux has been revealed to be carried by non-Fickian flux processes depending on sites being able to lodge dopants (oxidants, the so-called DOCC-sites, as well as on the dopant jump rate.
A consistent modelling methodology for secondary settling tanks: a reliable numerical method.
Bürger, Raimund; Diehl, Stefan; Farås, Sebastian; Nopens, Ingmar; Torfs, Elena
2013-01-01
The consistent modelling methodology for secondary settling tanks (SSTs) leads to a partial differential equation (PDE) of nonlinear convection-diffusion type as a one-dimensional model for the solids concentration as a function of depth and time. This PDE includes a flux that depends discontinuously on spatial position modelling hindered settling and bulk flows, a singular source term describing the feed mechanism, a degenerating term accounting for sediment compressibility, and a dispersion term for turbulence. In addition, the solution itself is discontinuous. A consistent, reliable and robust numerical method that properly handles these difficulties is presented. Many constitutive relations for hindered settling, compression and dispersion can be used within the model, allowing the user to switch on and off effects of interest depending on the modelling goal as well as investigate the suitability of certain constitutive expressions. Simulations show the effect of the dispersion term on effluent suspended solids and total sludge mass in the SST. The focus is on correct implementation whereas calibration and validation are not pursued.
Towards a self-consistent halo model for the nonlinear large-scale structure
Schmidt, Fabian
2015-01-01
The halo model is a theoretically and empirically well-motivated framework for predicting the statistics of the nonlinear matter distribution in the Universe. However, current incarnations of the halo model suffer from two major deficiencies: $(i)$ they do not enforce the stress-energy conservation of matter; $(ii)$ they are not guaranteed to recover exact perturbation theory results on large scales. Here, we provide a formulation of the halo model ("EHM") that remedies both drawbacks in a consistent way, while attempting to maintain the predictivity of the approach. In the formulation presented here, mass and momentum conservation are guaranteed, and results of perturbation theory and the effective field theory can in principle be matched to any desired order on large scales. We find that a key ingredient in the halo model power spectrum is the halo stochasticity covariance, which has been studied to a much lesser extent than other ingredients such as mass function, bias, and profiles of halos. As written he...
Directory of Open Access Journals (Sweden)
J. G. Fyke
2013-04-01
Full Text Available A new technique for generating ice sheet preindustrial 1850 initial conditions for coupled ice-sheet/climate models is developed and demonstrated over the Greenland Ice Sheet using the Community Earth System Model (CESM. Paleoclimate end-member simulations and ice core data are used to derive continuous surface mass balance fields which are used to force a long transient ice sheet model simulation. The procedure accounts for the evolution of climate through the last glacial period and converges to a simulated preindustrial 1850 ice sheet that is geometrically and thermodynamically consistent with the 1850 preindustrial simulated CESM state, yet contains a transient memory of past climate that compares well to observations and independent model studies. This allows future coupled ice-sheet/climate projections of climate change that include ice sheets to integrate the effect of past climate conditions on the state of the Greenland Ice Sheet, while maintaining system-wide continuity between past and future climate simulations.
Amruth, B R; R., Amruth B.; Patwardhan, Ajay
2006-01-01
Cosmological inflation models with modifications to include recent cosmological observations has been an active area of research after WMAP 3 results, which have given us information about the composition of dark matter, normal matter and dark energy and the anisotropy at the 300,000 years horizon with high precision. We work on inflation models of Guth and Linde and modify them by introducing a doublet scalar field to give normal matter particles and their supersymmetric partners which result in normal and dark matter of our universe. We include the cosmological constant term as the vaccuum expectation value of the stress energy tensor, as the dark energy. We callibrate the parameters of our model using recent observations of density fluctuations. We develop a model which consistently fits with the recent observations.
SALT Spectropolarimetry and Self-Consistent SED and Polarization Modeling of Blazars
Böttcher, Markus; van Soelen, Brian; Britto, Richard; Buckley, David; Marais, Johannes; Schutte, Hester
2017-09-01
We report on recent results from a target-of-opportunity program to obtain spectropolarimetry observations with the Southern African Large Telescope (SALT) on flaring gamma-ray blazars. SALT spectropolarimetry and contemporaneous multi-wavelength spectral energy distribution (SED) data are being modelled self-consistently with a leptonic single-zone model. Such modeling provides an accurate estimate of the degree of order of the magnetic field in the emission region and the thermal contributions (from the host galaxy and the accretion disk) to the SED, thus putting strong constraints on the physical parameters of the gamma-ray emitting region. For the specific case of the $\\gamma$-ray blazar 4C+01.02, we demonstrate that the combined SED and spectropolarimetry modeling constrains the mass of the central black hole in this blazar to $M_{\\rm BH} \\sim 10^9 \\, M_{\\odot}$.
Membrane Modeling, Simulation and Optimization for Propylene/Propane Separation
Alshehri, Ali
2015-06-01
Energy efficiency is critical for sustainable industrial growth and the reduction of environmental impacts. Energy consumption by the industrial sector accounts for more than half of the total global energy usage and, therefore, greater attention is focused on enhancing this sector’s energy efficiency. It is predicted that by 2020, more than 20% of today’s energy consumption can be avoided in countries that have effectively implemented an action plan towards efficient energy utilization. Breakthroughs in material synthesis of high selective membranes have enabled the technology to be more energy efficient. Hence, high selective membranes are increasingly replacing conventional energy intensive separation processes, such as distillation and adsorption units. Moreover, the technology offers more special features (which are essential for special applications) and its small footprint makes membrane technology suitable for platform operations (e.g., nitrogen enrichment for oil and gas offshore sites). In addition, its low maintenance characteristics allow the technology to be applied to remote operations. For these reasons, amongst other, the membrane technology market is forecast to reach $16 billion by 2017. This thesis is concerned with the engineering aspects of membrane technology and covers modeling, simulation and optimization of membranes as a stand-alone process or as a unit operation within a hybrid system. Incorporating the membrane model into a process modeling software simplifies the simulation and optimization of the different membrane processes and hybrid configurations, since all other unit operations are pre-configured. Various parametric analyses demonstrated that only the membrane selectivity and transmembrane pressure ratio parameters define a membrane’s ability to accomplish a certain separation task. Moreover, it was found that both membrane selectivity and pressure ratio exhibit a minimum value that is only defined by the feed composition
Directory of Open Access Journals (Sweden)
Nobutaka Endo
2016-08-01
Full Text Available Polymer electrolyte membranes (PEMs for direct methanol fuel cell (DMFC applications were prepared from a graft-copolymer (PSF-g-PSSA consisting of a polysulfone (PSF main chain and poly(styrene sulfonic acid (PSSA side chains with various average distances between side chains (Lav and side chain lengths (Lsc. The polymers were synthesized by grafting ethyl p-styrenesulfonate (EtSS on macro-initiators of chloromethylated polysulfone with different contents of chloromethyl (CM groups, and by changing EtSS content in the copolymers by using atom transfer radical polymerization (ATRP. The DMFC performance tests using membrane electrode assemblis (MEAs with the three types of the PEMs revealed that: a PSF-g-PSSA PEM (SF-6 prepared from a graft copolymer with short average distances between side chains (Lav and medium Lsc had higher DMFC performance than PEMs with long Lav and long Lsc or with short Lav and short Lsc. SF-6 had about two times higher PDmax (68.4 mW/cm2 than Nafion® 112 at 30 wt % of methanol concentration. Furthermore, it had 58.2 mW/cm2 of PDmax at 50 wt % of methanol concentration because of it has the highest proton selectivity during DMFC operation of all the PSF-g-PSSA PEMs and Nafion® 112.
Directory of Open Access Journals (Sweden)
Marius Enachescu
2013-09-01
Full Text Available Model membrane approaches have attracted much attention in biomedical sciences to investigate and simulate biological processes. The application of model membrane systems for biosensor measurements is partly restricted by the fact that the integrity of membranes critically depends on the maintenance of an aqueous surrounding, while various biosensors require a preconditioning of dry sensors. This is for example true for the well-established surface acoustic wave (SAW biosensor SAM®5 blue. Here, a simple drying procedure of sensor-supported model membranes is introduced using the protective disaccharide trehalose. Highly reproducible model membranes were prepared by the Langmuir-Blodgett technique, transferred to SAW sensors and supplemented with a trehalose solution. Membrane rehydration after dry incorporation into the SAW device becomes immediately evident by phase changes. Reconstituted model membranes maintain their full functionality, as indicated by biotin/avidin binding experiments. Atomic force microscopy confirmed the morphological invariability of dried and rehydrated membranes. Approximating to more physiological recognition phenomena, the site-directed immobilization of the integrin VLA-4 into the reconstituted model membrane and subsequent VCAM-1 ligand binding with nanomolar affinity were illustrated. This simple drying procedure is a novel way to combine the model membrane generation by Langmuir-Blodgett technique with SAW biosensor measurements, which extends the applicability of SAM®5 blue in biomedical sciences.
Giorgi, F.; Coppola, E.; Raffaele, F.
2014-10-01
We analyze trends of six daily precipitation-based and physically interconnected hydroclimatic indices in an ensemble of historical and 21st century climate projections under forcing from increasing greenhouse gas (GHG) concentrations (Representative Concentration Pathways (RCP)8.5), along with gridded (land only) observations for the late decades of the twentieth century. The indices include metrics of intensity (SDII) and extremes (R95) of precipitation, dry (DSL), and wet spell length, the hydroclimatic intensity index (HY-INT), and a newly introduced index of precipitation area (PA). All the indices in both the 21st century and historical simulations provide a consistent picture of a predominant shift toward a hydroclimatic regime of more intense, shorter, less frequent, and less widespread precipitation events in response to GHG-induced global warming. The trends are larger and more spatially consistent over tropical than extratropical regions, pointing to the importance of tropical convection in regulating this response, and show substantial regional spatial variability. Observed trends in the indices analyzed are qualitatively and consistently in line with the simulated ones, at least at the global and full tropical scale, further supporting the robustness of the identified prevailing hydroclimatic responses. The HY-INT, PA, and R95 indices show the most consistent response to global warming, and thus offer the most promising tools for formal hydroclimatic model validation and detection/attribution studies. The physical mechanism underlying this response and some of the applications of our results are also discussed.
Fox-Rabinovitz, Michael S.; Lindzen, Richard S.
1993-01-01
Simple numerical experiments are performed in order to determine the effects of inconsistent combinations of horizontal and vertical resolution in both atmospheric models and observing systems. In both cases, we find that inconsistent spatial resolution is associated with enhanced noise generation. A rather fine horizontal resolution in a satellite-data observing system seems to be excessive when combined with the usually available relatively coarse vertical resolution. Using horizontal filters of different strengths, adjusted in such a way as to render the effective horizontal resolution more consistent with vertical resolution for the observing system, may result in improvement of the analysis accuracy. The increase of vertical resolution for a satellite data observing system with better vertically resolved data, the results are different in that little or no horizontal filtering is needed to make spatial resolution more consistent for the system. The obtained experimental estimates of consistent vertical and effective horizontal resolution are in a general agreement with consistent resolution estimates previously derived theoretically by the authors.
Relativistic Consistent Angular-Momentum Projected Shell-Model:Relativistic Mean Field
Institute of Scientific and Technical Information of China (English)
LI Yan-Song; LONG Gui-Lu
2004-01-01
We develop a relativistic nuclear structure model, relativistic consistent angular-momentum projected shellmodel (RECAPS), which combines the relativistic mean-field theory with the angular-momentum projection method.In this new model, nuclear ground-state properties are first calculated consistently using relativistic mean-field (RMF)theory. Then angular momentum projection method is used to project out states with good angular momentum from a few important configurations. By diagonalizing the hamiltonian, the energy levels and wave functions are obtained.This model is a new attempt for the understanding of nuclear structure of normal nuclei and for the prediction of nuclear properties of nuclei far from stability. In this paper, we will describe the treatment of the relativistic mean field. A computer code, RECAPS-RMF, is developed. It solves the relativistic mean field with axial-symmetric deformation in the spherical harmonic oscillator basis. Comparisons between our calculations and existing relativistic mean-field calculations are made to test the model. These include the ground-state properties of spherical nuclei 16O and 208Pb,the deformed nucleus 20Ne. Good agreement is obtained.
Rudzinski, Joseph F.; Kremer, Kurt; Bereau, Tristan
2016-02-01
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and reference (e.g., from experiments or higher-level simulations) observables. To bound the microscopic information generated by computer simulations within reference measurements, we propose a method that reweights the microscopic transitions of the system to improve consistency with a set of coarse kinetic observables. The method employs the well-developed Markov state modeling framework to efficiently link microscopic dynamics with long-time scale constraints, thereby consistently addressing a wide range of time scales. To emphasize the robustness of the method, we consider two distinct coarse-grained models with significant kinetic inconsistencies. When applied to the simulated conformational dynamics of small peptides, the reweighting procedure systematically improves the time scale separation of the slowest processes. Additionally, constraining the forward and backward rates between metastable states leads to slight improvement of their relative stabilities and, thus, refined equilibrium properties of the resulting model. Finally, we find that difficulties in simultaneously describing both the simulated data and the provided constraints can help identify specific limitations of the underlying simulation approach.
Ring current Atmosphere interactions Model with Self-Consistent Magnetic field
Energy Technology Data Exchange (ETDEWEB)
2016-09-09
The Ring current Atmosphere interactions Model with Self-Consistent magnetic field (B) is a unique code that combines a kinetic model of ring current plasma with a three dimensional force-balanced model of the terrestrial magnetic field. The kinetic portion, RAM, solves the kinetic equation to yield the bounce-averaged distribution function as a function of azimuth, radial distance, energy and pitch angle for three ion species (H+, He+, and O+) and, optionally, electrons. The domain is a circle in the Solar-Magnetic (SM) equatorial plane with a radial span of 2 to 6.5 RE. It has an energy range of approximately 100 eV to 500 KeV. The 3-D force balanced magnetic field model, SCB, balances the JxB force with the divergence of the general pressure tensor to calculate the magnetic field configuration within its domain. The domain ranges from near the Earth’s surface, where the field is assumed dipolar, to the shell created by field lines passing through the SM equatorial plane at a radial distance of 6.5 RE. The two codes work in tandem, with RAM providing anisotropic pressure to SCB and SCB returning the self-consistent magnetic field through which RAM plasma is advected.
Directory of Open Access Journals (Sweden)
G.Shanmugarathinam
2013-01-01
Full Text Available Caching is one of the important techniques in mobile computing. In caching, frequently accessed data is stored in mobile clients to avoid network traffic and improve the performance in mobile computing. In a mobile computing environment, the number of mobile users increases and requests the server for any updation, but most of the time the server is busy and the client has to wait for a long time. The cache consistency maintenance is difficult for both client and the server. This paper is proposes a technique using a queuing system consisting of one or more servers that provide services of some sort to arrive mobile hosts using agent based technology. This services mechanism of a queuing system is specified by the number of servers each server having its own queue, Agent based technology will maintain the cache consistency between the client and the server .This model saves wireless bandwidth, reduces network traffic and reduces the workload on the server. The simulation result was analyzed with previous technique and the proposed model shows significantly better performance than the earlier approach.
Silvis, Maurits H; Verstappen, Roel
2016-01-01
We study the construction of subgrid-scale models for large-eddy simulation of incompressible turbulent flows. In particular, we aim to consolidate a systematic approach of constructing subgrid-scale models, based on the idea that it is desirable that subgrid-scale models are consistent with the properties of the Navier-Stokes equations and the turbulent stresses. To that end, we first discuss in detail the symmetries of the Navier-Stokes equations, and the near-wall scaling behavior, realizability and dissipation properties of the turbulent stresses. We furthermore summarize the requirements that subgrid-scale models have to satisfy in order to preserve these important mathematical and physical properties. In this fashion, a framework of model constraints arises that we apply to analyze the behavior of a number of existing subgrid-scale models that are based on the local velocity gradient. We show that these subgrid-scale models do not satisfy all the desired properties, after which we explain that this is p...
RNA secondary structure modeling at consistent high accuracy using differential SHAPE.
Rice, Greggory M; Leonard, Christopher W; Weeks, Kevin M
2014-06-01
RNA secondary structure modeling is a challenging problem, and recent successes have raised the standards for accuracy, consistency, and tractability. Large increases in accuracy have been achieved by including data on reactivity toward chemical probes: Incorporation of 1M7 SHAPE reactivity data into an mfold-class algorithm results in median accuracies for base pair prediction that exceed 90%. However, a few RNA structures are modeled with significantly lower accuracy. Here, we show that incorporating differential reactivities from the NMIA and 1M6 reagents--which detect noncanonical and tertiary interactions--into prediction algorithms results in highly accurate secondary structure models for RNAs that were previously shown to be difficult to model. For these RNAs, 93% of accepted canonical base pairs were recovered in SHAPE-directed models. Discrepancies between accepted and modeled structures were small and appear to reflect genuine structural differences. Three-reagent SHAPE-directed modeling scales concisely to structurally complex RNAs to resolve the in-solution secondary structure analysis problem for many classes of RNA.
Continuous Modeling of Calcium Transport Through Biological Membranes
Jasielec, J. J.; Filipek, R.; Szyszkiewicz, K.; Sokalski, T.; Lewenstam, A.
2016-08-01
In this work an approach to the modeling of the biological membranes where a membrane is treated as a continuous medium is presented. The Nernst-Planck-Poisson model including Poisson equation for electric potential is used to describe transport of ions in the mitochondrial membrane—the interface which joins mitochondrial matrix with cellular cytosis. The transport of calcium ions is considered. Concentration of calcium inside the mitochondrion is not known accurately because different analytical methods give dramatically different results. We explain mathematically these differences assuming the complexing reaction inside mitochondrion and the existence of the calcium set-point (concentration of calcium in cytosis below which calcium stops entering the mitochondrion).
Davis, Charles H.; Nie, Huifen; Dokholyan, Nikolay V.
2007-05-01
Lipid aggregation into fluid bilayers is an essential process for sustaining life. Simplified models of lipid structure, which allow for long time scales or large length scales not obtainable with all-atom simulations, have recently been developed and show promise for describing lipid dynamics in biological systems. Here, we describe two simplified models, a reduced-lipid model and a bola-lipid model for thermophilic bacterial membranes, developed for use with the rapid discrete molecular dynamics simulation method. In the reduced-lipid model, we represent the lipid chain by a series of three beads interacting through pairwise discrete potentials that model hydrophobic attractions between hydrocarbon tails in implicit solvent. Our phase diagram recapitulates those produced by continuous potential models with similar coarse-grained lipid representations. We also find that phase transition temperatures for our reduced-lipid model are dependent upon the flexibility of the lipid chain, giving an insight into archaebacterial membrane stability and prompting development of a bola-lipid model specific for archaebacteria lipids. With both the reduced-lipid and bola-lipid model, we find that the reduced flexibility inherent in archaebacteria lipids yields more stable bilayers as manifested by increased phase transition temperatures. The results of these studies provide a simulation methodology for lipid molecules in biological systems and show that discrete molecular dynamics is applicable to lipid aggregation and dynamics.
Stability properties of elementary dynamic models of membrane transport.
Hernández, Julio A
2003-01-01
Living cells are characterized by their capacity to maintain a stable steady state. For instance, cells are able to conserve their volume, internal ionic composition and electrical potential difference across the plasma membrane within values compatible with the overall cell functions. The dynamics of these cellular variables is described by complex integrated models of membrane transport. Some clues for the understanding of the processes involved in global cellular homeostasis may be obtained by the study of the local stability properties of some partial cellular processes. As an example of this approach, I perform, in this study, the neighborhood stability analysis of some elementary integrated models of membrane transport. In essence, the models describe the rate of change of the intracellular concentration of a ligand subject to active and passive transport across the plasma membrane of an ideal cell. The ligand can be ionic or nonionic, and it can affect the cell volume or the plasma membrane potential. The fundamental finding of this study is that, within the physiological range, the steady states are asymptotically stable. This basic property is a necessary consequence of the general forms of the expressions employed to describe the active and passive fluxes of the transported ligand.
Gas cooling in semi-analytic models and SPH simulations: are results consistent?
Saro, A; Borgani, S; Dolag, K
2010-01-01
We present a detailed comparison between the galaxy populations within a massive cluster, as predicted by hydrodynamical SPH simulations and by a semi-analytic model (SAM) of galaxy formation. Both models include gas cooling and a simple prescription of star formation, which consists in transforming instantaneously any cold gas available into stars, while neglecting any source of energy feedback. We find that, in general, galaxy populations from SAMs and SPH have similar statistical properties, in agreement with previous studies. However, when comparing galaxies on an object-by-object basis, we find a number of interesting differences: a) the star formation histories of the brightest cluster galaxies (BCGs) from SAM and SPH models differ significantly, with the SPH BCG exhibiting a lower level of star formation activity at low redshift, and a more intense and shorter initial burst of star formation with respect to its SAM counterpart; b) while all stars associated with the BCG were formed in its progenitors i...
A Fully Nonlinear, Dynamically Consistent Numerical Model for Ship Maneuvering in a Seaway
Directory of Open Access Journals (Sweden)
Ray-Qing Lin
2011-01-01
Full Text Available This is the continuation of our research on development of a fully nonlinear, dynamically consistent, numerical ship motion model (DiSSEL. In this paper we report our results on modeling ship maneuvering in arbitrary seaway that is one of the most challenging and important problems in seakeeping. In our modeling, we developed an adaptive algorithm to maintain dynamical balances numerically as the encounter frequencies (the wave frequencies as measured on the ship varying with the ship maneuvering state. The key of this new algorithm is to evaluate the encounter frequency variation differently in the physical domain and in the frequency domain, thus effectively eliminating possible numerical dynamical imbalances. We have tested this algorithm with several well-documented maneuvering experiments, and our results agree very well with experimental data. In particular, the numerical time series of roll and pitch motions and the numerical ship tracks (i.e., surge, sway, and yaw are nearly identical to those of experiments.
Pineda, Evan J.; Bednarcyk, Brett A.; Arnold, Steven M.; Waas, Anthony M.
2013-01-01
A mesh objective crack band model was implemented within the generalized method of cells micromechanics theory. This model was linked to a macroscale finite element model to predict post-peak strain softening in composite materials. Although a mesh objective theory was implemented at the microscale, it does not preclude pathological mesh dependence at the macroscale. To ensure mesh objectivity at both scales, the energy density and the energy release rate must be preserved identically across the two scales. This requires a consistent characteristic length or localization limiter. The effects of scaling (or not scaling) the dimensions of the microscale repeating unit cell (RUC), according to the macroscale element size, in a multiscale analysis was investigated using two examples. Additionally, the ramifications of the macroscale element shape, compared to the RUC, was studied.
Consistent neutron star models with magnetic field dependent equations of state
Chatterjee, Debarati; Novak, Jerome; Oertel, Micaela
2014-01-01
We present a self-consistent model for the study of the structure of a neutron star in strong magnetic fields. Starting from a microscopic Lagrangian, this model includes the effect of the magnetic field on the equation of state, the interaction of the electromagnetic field with matter (magnetisation), and anisotropies in the energy-momentum tensor, as well as general relativistic aspects. We build numerical axisymmetric stationary models and show the applicability of the approach with one example quark matter equation of state (EoS) often employed in the recent literature for studies of strongly magnetised neutron stars. For this EoS, the effect of inclusion of magnetic field dependence or the magnetisation do not increase the maximum mass significantly in contrast to what has been claimed by previous studies.
A self consistent chemically stratified atmosphere model for the roAp star 10 Aquilae
Nesvacil, Nicole; Ryabchikova, Tanya A; Kochukhov, Oleg; Akberov, Artur; Weiss, Werner W
2012-01-01
Context: Chemically peculiar A type (Ap) stars are a subgroup of the CP2 stars which exhibit anomalous overabundances of numerous elements, e.g. Fe, Cr, Sr and rare earth elements. The pulsating subgroup of the Ap stars, the roAp stars, present ideal laboratories to observe and model pulsational signatures as well as the interplay of the pulsations with strong magnetic fields and vertical abundance gradients. Aims: Based on high resolution spectroscopic observations and observed stellar energy distributions we construct a self consistent model atmosphere, that accounts for modulations of the temperature-pressure structure caused by vertical abundance gradients, for the roAp star 10 Aquilae (HD 176232). We demonstrate that such an analysis can be used to determine precisely the fundamental atmospheric parameters required for pulsation modelling. Methods: Average abundances were derived for 56 species. For Mg, Si, Ca, Cr, Fe, Co, Sr, Pr, and Nd vertical stratification profiles were empirically derived using the...
A self-consistent model for a longitudinal discharge excited He-Sr recombination laser
Energy Technology Data Exchange (ETDEWEB)
Carman, R.J. (Centre for Lasers and Applications, Macquarie University, Sydney NSW 2109 (AU))
1990-09-01
A computer model has been developed to simulate the plasma kinetics in a high-repetition frequency, discharge excited He-Sr recombination laser. A detailed rate equation analysis, incorporating about 80 collisional and radiative processes, is used to determine the temporal and spatial (radial) behavior of the discharge parameters and the intracavity laser field during the current pulse, recombination phase, and afterglow periods. The set of coupled first-order ordinary differential equations used to describe the plasma and external electrical circuit are integrated over multiple discharge cycles to yield fully self-consistent results. The computer model has been used to simulate the behavior of the laser for a set of standard conditions corresponding to typical operating conditions. The species population densities predicted by the model are compared with radial and time-dependent Hook measurements determined experimentally for the same set of standard conditions.
A heterogeneous traffic flow model consisting of two types of vehicles with different sensitivities
Li, Zhipeng; Xu, Xun; Xu, Shangzhi; Qian, Yeqing
2017-01-01
A heterogeneous car following model is constructed for traffic flow consisting of low- and high-sensitivity vehicles. The stability criterion of new model is obtained by using the linear stability theory. We derive the neutral stability diagram for the proposed model with five distinct regions. We conclude the effect of the percentage of low-sensitivity vehicle on the traffic stability in each region. In addition, we further consider a special case that the number of the low-sensitivity vehicles is equal to that of the high-sensitivity ones. We explore the dependence of traffic stability on the average value and the standard deviation of two sensitivities characterizing two vehicle types. The direct numerical simulation results verify the conclusion of theoretical analysis.
Thermotropic phase transitions in model membranes of the outer skin layer based on ceramide 6
Gruzinov, A. Yu.; Kiselev, M. A.; Ermakova, E. V.; Zabelin, A. V.
2014-01-01
The lipid intercellular matrix stratum corneum of the outer skin layer is a multilayer membrane consisting of a complex mixture of different lipids: ceramides, fatty acids, cholesterol, and its derivatives. The basis of the multilayer membrane is the lipid bilayer, i.e., a two-dimensional liquid crystal. Currently, it is known that the main way of substance penetration through the skin is the lipid matrix. The complexity of the actual biological system does not allow reliable direct study of its properties; therefore, system modeling is often used. Phase transitions in the lipid system whose composition simulates the native lipid matrix are studied by the X-ray synchrotron radiation diffraction method.
Membrane Phospholipid Redistribution in Cytokinesis: A Theoretical Model
Institute of Scientific and Technical Information of China (English)
Mei-Wen AN; Wen-Zhou WU; Wei-Yi CHEN
2005-01-01
In cell mitosis, cytokinesis is a major deformation process, during which the site of the contractile ring is determined by the biochemical stimulus from asters of the mitotic apparatus, actin and myosin assembly is related to the motion of membrane phospholipids, and local distribution and arrangement of the microfilament cytoskeleton are different at different cytokinesis stages. Based on the Zinemanas-Nir model, a new model is proposed in this study to simulate the entire process by coupling the biochemical stimulus with the mechanical actions. There were three assumptions in this model: the movements of phospholipid proteins are driven by gradients of biochemical stimulus on the membrane surface; the local assembly of actin and myosin filament depends on the amount of phospholipid proteins at the same location;and the surface tension includes membrane tensions due to both the passive deformation of the membrane and the active contraction of actin filament, which is determined by microfilament redistribution and rearrangement. This model could explain the dynamic movement of microfilaments during cytokinesis and predict cell deformation. The calculated results from this model demonstrated that the reorientation of phospholipid proteins and the redistribution and reorientation of microfilaments may play a crucial role in cell division. This model may better represent the cytokinesis process by the introduction of biochemical stimulus.
nIFTy cosmology: the clustering consistency of galaxy formation models
Pujol, Arnau; Skibba, Ramin A.; Gaztañaga, Enrique; Benson, Andrew; Blaizot, Jeremy; Bower, Richard; Carretero, Jorge; Castander, Francisco J.; Cattaneo, Andrea; Cora, Sofia A.; Croton, Darren J.; Cui, Weiguang; Cunnama, Daniel; De Lucia, Gabriella; Devriendt, Julien E.; Elahi, Pascal J.; Font, Andreea; Fontanot, Fabio; Garcia-Bellido, Juan; Gargiulo, Ignacio D.; Gonzalez-Perez, Violeta; Helly, John; Henriques, Bruno M. B.; Hirschmann, Michaela; Knebe, Alexander; Lee, Jaehyun; Mamon, Gary A.; Monaco, Pierluigi; Onions, Julian; Padilla, Nelson D.; Pearce, Frazer R.; Power, Chris; Somerville, Rachel S.; Srisawat, Chaichalit; Thomas, Peter A.; Tollet, Edouard; Vega-Martínez, Cristian A.; Yi, Sukyoung K.
2017-07-01
We present a clustering comparison of 12 galaxy formation models [including semi-analytic models (SAMs) and halo occupation distribution (HOD) models] all run on halo catalogues and merger trees extracted from a single Λ cold dark matter N-body simulation. We compare the results of the measurements of the mean halo occupation numbers, the radial distribution of galaxies in haloes and the two-point correlation functions (2PCF). We also study the implications of the different treatments of orphan (galaxies not assigned to any dark matter subhalo) and non-orphan galaxies in these measurements. Our main result is that the galaxy formation models generally agree in their clustering predictions but they disagree significantly between HOD and SAMs for the orphan satellites. Although there is a very good agreement between the models on the 2PCF of central galaxies, the scatter between the models when orphan satellites are included can be larger than a factor of 2 for scales smaller than 1 h-1 Mpc. We also show that galaxy formation models that do not include orphan satellite galaxies have a significantly lower 2PCF on small scales, consistent with previous studies. Finally, we show that the 2PCF of orphan satellites is remarkably different between SAMs and HOD models. Orphan satellites in SAMs present a higher clustering than in HOD models because they tend to occupy more massive haloes. We conclude that orphan satellites have an important role on galaxy clustering and they are the main cause of the differences in the clustering between HOD models and SAMs.
Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle.
Sener, Melih K; Olsen, John D; Hunter, C Neil; Schulten, Klaus
2007-10-02
The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.
Connolly, Mark; He, Xing; Gonzalez, Nestor; Vespa, Paul; DiStefano, Joe; Hu, Xiao
2014-03-01
Due to the inaccessibility of the cranial vault, it is difficult to study cerebral blood flow dynamics directly. A mathematical model can be useful to study these dynamics. The model presented here is a novel combination of a one-dimensional fluid flow model representing the major vessels of the circle of Willis (CoW), with six individually parameterized auto-regulatory models of the distal vascular beds. This model has the unique ability to simulate high temporal resolution flow and velocity waveforms, amenable to pulse-waveform analysis, as well as sophisticated phenomena such as auto-regulation. Previous work with human patients has shown that vasodilation induced by CO2 inhalation causes 12 consistent pulse-waveform changes as measured by the morphological clustering and analysis of intracranial pressure algorithm. To validate this model, we simulated vasodilation and successfully reproduced 9 out of the 12 pulse-waveform changes. A subsequent sensitivity analysis found that these 12 pulse-waveform changes were most affected by the parameters associated with the shape of the smooth muscle tension response and vessel elasticity, providing insight into the physiological mechanisms responsible for observed changes in the pulse-waveform shape.
Energy Technology Data Exchange (ETDEWEB)
Guy, Aurélien, E-mail: aurelien.guy@onera.fr; Bourdon, Anne, E-mail: anne.bourdon@lpp.polytechnique.fr; Perrin, Marie-Yvonne, E-mail: marie-yvonne.perrin@ecp.fr [CNRS, UPR 288, Laboratoire d' Énergétique Moléculaire et Macroscopique, Combustion (EM2C), Grande Voie des Vignes, 92295 Châtenay-Malabry (France); Ecole Centrale Paris, Grande Voie des Vignes, 92295 Châtenay-Malabry (France)
2015-04-15
In this work, a state-to-state vibrational and electronic collisional model is developed to investigate nonequilibrium phenomena behind a shock wave in an ionized nitrogen flow. In the ionization dynamics behind the shock wave, the electron energy budget is of key importance and it is found that the main depletion term corresponds to the electronic excitation of N atoms, and conversely the major creation terms are the electron-vibration term at the beginning, then replaced by the electron ions elastic exchange term. Based on these results, a macroscopic multi-internal-temperature model for the vibration of N{sub 2} and the electronic levels of N atoms is derived with several groups of vibrational levels of N{sub 2} and electronic levels of N with their own internal temperatures to model the shape of the vibrational distribution of N{sub 2} and of the electronic excitation of N, respectively. In this model, energy and chemistry source terms are calculated self-consistently from the rate coefficients of the state-to-state database. For the shock wave condition studied, a good agreement is observed on the ionization dynamics as well as on the atomic bound-bound radiation between the state-to-state model and the macroscopic multi-internal temperature model with only one group of vibrational levels of N{sub 2} and two groups of electronic levels of N.
Validity test and its consistency in the construction of patient loyalty model
Yanuar, Ferra
2016-04-01
The main objective of this present study is to demonstrate the estimation of validity values and its consistency based on structural equation model. The method of estimation was then implemented to an empirical data in case of the construction the patient loyalty model. In the hypothesis model, service quality, patient satisfaction and patient loyalty were determined simultaneously, each factor were measured by any indicator variables. The respondents involved in this study were the patients who ever got healthcare at Puskesmas in Padang, West Sumatera. All 394 respondents who had complete information were included in the analysis. This study found that each construct; service quality, patient satisfaction and patient loyalty were valid. It means that all hypothesized indicator variables were significant to measure their corresponding latent variable. Service quality is the most measured by tangible, patient satisfaction is the most mesured by satisfied on service and patient loyalty is the most measured by good service quality. Meanwhile in structural equation, this study found that patient loyalty was affected by patient satisfaction positively and directly. Service quality affected patient loyalty indirectly with patient satisfaction as mediator variable between both latent variables. Both structural equations were also valid. This study also proved that validity values which obtained here were also consistence based on simulation study using bootstrap approach.
Buchanan, John J; Dean, Noah
2014-02-01
The experiment undertaken was designed to elucidate the impact of model skill level on observational learning processes. The task was bimanual circle tracing with a 90° relative phase lead of one hand over the other hand. Observer groups watched videos of either an instruction model, a discovery model, or a skilled model. The instruction and skilled model always performed the task with the same movement strategy, the right-arm traced clockwise and the left-arm counterclockwise around circle templates with the right-arm leading. The discovery model used several movement strategies (tracing-direction/hand-lead) during practice. Observation of the instruction and skilled model provided a significant benefit compared to the discovery model when performing the 90° relative phase pattern in a post-observation test. The observers of the discovery model had significant room for improvement and benefited from post-observation practice of the 90° pattern. The benefit of a model is found in the consistency with which that model uses the same movement strategy, and not within the skill level of the model. It is the consistency in strategy modeled that allows observers to develop an abstract perceptual representation of the task that can be implemented into a coordinated action. Theoretically, the results show that movement strategy information (relative motion direction, hand lead) and relative phase information can be detected through visual perception processes and be successfully mapped to outgoing motor commands within an observational learning context.
[Membrane model of the cupula of the vestibular semicircular canals].
Kondrachuk, A V; Shipov, A A; Sirenko, S P
1987-01-01
A mathematical model of the time-course variations of the cupula of the semicircular canals of the vestibular apparatus is presented. The model is found to be in good agreement with experimental data which suggests that the cupular matter has viscosity-elasticity properties. Their role in the functioning of the vestibular apparatus is discussed in qualitative terms. The applicability of the membrane model to the description of the time-course variations of the cupula is considered.
A Globally Consistent Methodology for an Exposure Model for Natural Catastrophe Risk Assessment
Gunasekera, Rashmin; Ishizawa, Oscar; Pandey, Bishwa; Saito, Keiko
2013-04-01
There is a high demand for the development of a globally consistent and robust exposure data model employing a top down approach, to be used in national level catastrophic risk profiling for the public sector liability. To this effect, there are currently several initiatives such as UN-ISDR Global Assessment Report (GAR) and Global Exposure Database for Global Earthquake Model (GED4GEM). However, the consistency and granularity differs from region to region, a problem that is overcome in this proposed approach using national datasets for example in Latin America and the Caribbean Region (LCR). The methodology proposed in this paper aim to produce a global open exposure dataset based upon population, country specific building type distribution and other global/economic indicators such as World Bank indices that are suitable for natural catastrophe risk modelling purposes. The output would be a GIS raster grid at approximately 1 km spatial resolution which would highlight urbaness (building typology distribution, occupancy and use) for each cell at sub national level and compatible with other global initiatives and datasets. It would make use of datasets on population, census, demographic, building data and land use/land cover which are largely available in the public domain. The resultant exposure dataset could be used in conjunction with hazard and vulnerability components to create views of risk for multiple hazards that include earthquake, flood and windstorms. The model we hope would also assist in steps towards future initiatives for open, interchangeable and compatible databases for catastrophe risk modelling. The findings, interpretations, and conclusions expressed in this paper are entirely those of the authors. They do not necessarily represent the views of the International Bank for Reconstruction and Development/World Bank and its affiliated organizations, or those of the Executive Directors of the World Bank or the governments they represent.
Self-consistent Spectral Functions in the $O(N)$ Model from the FRG
Strodthoff, Nils
2016-01-01
We present the first self-consistent direct calculation of a spectral function in the framework of the Functional Renormalization Group. The study is carried out in the relativistic $O(N)$ model, where the full momentum dependence of the propagators in the complex plane as well as momentum-dependent vertices are considered. The analysis is supplemented by a comparative study of the Euclidean momentum dependence and of the complex momentum dependence on the level of spectral functions. This work lays the groundwork for the computation of full spectral functions in more complex systems.
Self-consistent description of $\\Lambda$ hypernuclei in the quark-meson coupling model
Tsushima, K; Thomas, A W
1997-01-01
The quark-meson coupling model, which has been successfully used to describe the properties of both finite nuclei and infinite nuclear matter, is applied to a study of $\\Lambda$ hypernuclei. With the assumption that the (self-consistent) exchanged scalar, and vector, mesons couple only to the u and d quarks, a very weak spin-orbit force in the $\\Lambda$-nucleus interaction is achieved automatically. This can be interpreted as a direct consequence of the quark structure of the $\\Lambda$ hyperon. Possible implications and extensions of the present investigation are also discussed.
Premixed Combustion Simulations with a Self-Consistent Plasma Model for Initiation
Energy Technology Data Exchange (ETDEWEB)
Sitaraman, Hariswaran; Grout, Ray
2016-01-08
Combustion simulations of H2-O2 ignition are presented here, with a self-consistent plasma fluid model for ignition initiation. The plasma fluid equations for a nanosecond pulsed discharge are solved and coupled with the governing equations of combustion. The discharge operates with the propagation of cathode directed streamer, with radical species produced at streamer heads. These radical species play an important role in the ignition process. The streamer propagation speeds and radical production rates were found to be sensitive to gas temperature and fuel-oxidizer equivalence ratio. The oxygen radical production rates strongly depend on equivalence ratio and subsequently results in faster ignition of leaner mixtures.
Supporting Consistency in Linked Specialized Engineering Models Through Bindings and Updating
Institute of Scientific and Technical Information of China (English)
Albertus H. Olivier; Gert C. van Rooyen; Berthold Firmenich; Karl E. Beucke
2008-01-01
Currently, some commercial software applications support users to work in an integrated environ-ment. However, this is limited to the suite of models provided by the software vendor and consequently it forces all the parties to use the same software. In contrast, the research described in this paper investigates ways of using standard software applications, which may be specialized for different professional domains.These are linked for effective transfer of information and a binding mechanism is provided to support consis-tency. The proposed solution was implemented using a CAD application and an independent finite element application in order to verify the theoretical aspects of this work.
A “Minsky crisis” in a Stock-Flow Consistent model
Mouakil, Tarik
2014-01-01
This study uses the Stock-Flow Consistent modelling approach to assess the relevance of Minsky’s demonstration of his financial instability hypothesis. We show that this demonstration, based on the assumption of a pro-cyclical leverage ratio, is incompatible with the Kaleckian analysis of profits endorsed by Minsky. Therefore we suggest replacing the assumption of a pro-cyclical leverage ratio with one of a pro-cyclical short-term borrowing, which also appears in Minsky’s work. Cet article...
Keller, D. E.; Fischer, A. M.; Frei, C.; Liniger, M. A.; Appenzeller, C.; Knutti, R.
2014-07-01
Many climate impact assessments over topographically complex terrain require high-resolution precipitation time-series that have a spatio-temporal correlation structure consistent with observations. This consistency is essential for spatially distributed modelling of processes with non-linear responses to precipitation input (e.g. soil water and river runoff modelling). In this regard, weather generators (WGs) designed and calibrated for multiple sites are an appealing technique to stochastically simulate time-series that approximate the observed temporal and spatial dependencies. In this study, we present a stochastic multi-site precipitation generator and validate it over the hydrological catchment Thur in the Swiss Alps. The model consists of several Richardson-type WGs that are run with correlated random number streams reflecting the observed correlation structure among all possible station pairs. A first-order two-state Markov process simulates intermittence of daily precipitation, while precipitation amounts are simulated from a mixture model of two exponential distributions. The model is calibrated separately for each month over the time-period 1961-2011. The WG is skilful at individual sites in representing the annual cycle of the precipitation statistics, such as mean wet day frequency and intensity as well as monthly precipitation sums. It reproduces realistically the multi-day statistics such as the frequencies of dry and wet spell lengths and precipitation sums over consecutive wet days. Substantial added value is demonstrated in simulating daily areal precipitation sums in comparison to multiple WGs that lack the spatial dependency in the stochastic process: the multi-site WG is capable to capture about 95% of the observed variability in daily area sums, while the summed time-series from multiple single-site WGs only explains about 13%. Limitation of the WG have been detected in reproducing observed variability from year to year, a component that has
Modeling and Simulation for Fuel Cell Polymer Electrolyte Membrane
Directory of Open Access Journals (Sweden)
Takahiro Hayashi
2013-01-01
Full Text Available We have established methods to evaluate key properties that are needed to commercialize polyelectrolyte membranes for fuel cell electric vehicles such as water diffusion, gas permeability, and mechanical strength. These methods are based on coarse-graining models. For calculating water diffusion and gas permeability through the membranes, the dissipative particle dynamics–Monte Carlo approach was applied, while mechanical strength of the hydrated membrane was simulated by coarse-grained molecular dynamics. As a result of our systematic search and analysis, we can now grasp the direction necessary to improve water diffusion, gas permeability, and mechanical strength. For water diffusion, a map that reveals the relationship between many kinds of molecular structures and diffusion constants was obtained, in which the direction to enhance the diffusivity by improving membrane structure can be clearly seen. In order to achieve high mechanical strength, the molecular structure should be such that the hydrated membrane contains narrow water channels, but these might decrease the proton conductivity. Therefore, an optimal design of the polymer structure is needed, and the developed models reviewed here make it possible to optimize these molecular structures.
Rácz, A; Bajusz, D; Héberger, K
2015-01-01
Recent implementations of QSAR modelling software provide the user with numerous models and a wealth of information. In this work, we provide some guidance on how one should interpret the results of QSAR modelling, compare and assess the resulting models, and select the best and most consistent ones. Two QSAR datasets are applied as case studies for the comparison of model performance parameters and model selection methods. We demonstrate the capabilities of sum of ranking differences (SRD) in model selection and ranking, and identify the best performance indicators and models. While the exchange of the original training and (external) test sets does not affect the ranking of performance parameters, it provides improved models in certain cases (despite the lower number of molecules in the training set). Performance parameters for external validation are substantially separated from the other merits in SRD analyses, highlighting their value in data fusion.
Tides, Rotation Or Anisotropy? Self-consistent Nonspherical Models For Globular Clusters
Varri, Anna L.; Bertin, G.
2011-01-01
Spherical models of quasi-relaxed stellar systems provide a successful zeroth-order description of globular clusters. Yet, the great progress made in recent years in the acquisition of detailed information of the structure of these stellar systems calls for a renewed effort on the side of modeling. In particular, more general analytical models would allow to address the long-standing issue of the physical origin of the deviations from spherical symmetry of the globular clusters, that now can be properly measured. In fact, it remains to be established which is the cause of the observed flattening, among external tides, internal rotation, and pressure anisotropy. In this paper we focus on the first two physical ingredients. We start by briefly describing a recently studied family of triaxial models that incorporate in a self-consistent way the tidal effects of the host galaxy, as a collisionless analogue of the Roche problem (Varri & Bertin ApJ 2009). We then present two new families of axisymmetric models in which the deviations from spherical symmetry are induced by the presence of internal rotation. The first one is an extension of the well-known family of King models to the case of axisymmetric equilibria flattened by solid-body rotation. The second family is characterized by differential rotation, designed to be rigid in the center and to vanish in the outer parts, where the imposed truncation in phase space becomes effective. For possible application to globular clusters, models of interest should be those, in both families, characterized by low values of the rotation strength parameter and quasi-spherical shape. For general interest in stellar dynamics, we show that, for high values of that parameter, the differentially rotating models may exhibit unexpected morphologies, even with a toroidal core.
Sezgin, Erdinc; Levental, Ilya; Grzybek, Michal; Schwarzmann, Günter; Mueller, Veronika; Honigmann, Alf; Belov, Vladimir N; Eggeling, Christian; Coskun, Unal; Simons, Kai; Schwille, Petra
2012-07-01
Several simplified membrane models featuring coexisting liquid disordered (Ld) and ordered (Lo) lipid phases have been developed to mimic the heterogeneous organization of cellular membranes, and thus, aid our understanding of the nature and functional role of ordered lipid-protein nanodomains, termed "rafts". In spite of their greatly reduced complexity, quantitative characterization of local lipid environments using model membranes is not trivial, and the parallels that can be drawn to cellular membranes are not always evident. Similarly, various fluorescently labeled lipid analogs have been used to study membrane organization and function in vitro, although the biological activity of these probes in relation to their native counterparts often remains uncharacterized. This is particularly true for raft-preferring lipids ("raft lipids", e.g. sphingolipids and sterols), whose domain preference is a strict function of their molecular architecture, and is thus susceptible to disruption by fluorescence labeling. Here, we analyze the phase partitioning of a multitude of fluorescent raft lipid analogs in synthetic Giant Unilamellar Vesicles (GUVs) and cell-derived Giant Plasma Membrane Vesicles (GPMVs). We observe complex partitioning behavior dependent on label size, polarity, charge and position, lipid headgroup, and membrane composition. Several of the raft lipid analogs partitioned into the ordered phase in GPMVs, in contrast to fully synthetic GUVs, in which most raft lipid analogs mis-partitioned to the disordered phase. This behavior correlates with the greatly enhanced order difference between coexisting phases in the synthetic system. In addition, not only partitioning, but also ligand binding of the lipids is perturbed upon labeling: while cholera toxin B binds unlabeled GM1 in the Lo phase, it binds fluorescently labeled GMI exclusively in the Ld phase. Fluorescence correlation spectroscopy (FCS) by stimulated emission depletion (STED) nanoscopy on intact
A new self-consistent hybrid chemistry model for Mars and cometary environments
Wedlund, Cyril Simon; Kallio, Esa; Jarvinen, Riku; Dyadechkin, Sergey; Alho, Markku
2014-05-01
Over the last 15 years, a 3-D hybrid-PIC planetary plasma interaction modelling platform, named HYB, has been developed, which was applied to several planetary environment such as those of Mars, Venus, Mercury, and more recently, the Moon. We present here another evolution of HYB including a fully consistent ionospheric-chemistry package designed to reproduce the main ions in the lower boundary of the model. This evolution, also permitted by the increase in computing power and the switch to spherical coordinates for higher spatial resolution (Dyadechkin et al., 2013), is motivated by the imminent arrival of the Rosetta spacecraft in the vicinity of comet 67P/Churyumov-Gerasimenko. In this presentation we show the application of the new HYB-ionosphere model to 1D and 2D hybrid simulations at Mars above 100 km altitude and demonstrate that with a limited number of chemical reactions, good agreement with 1D kinetic models may be found. This is a first validation step before applying the model to the 67P/CG comet environment, which, like Mars, is expected be rich in carbon oxide compounds.
[THE MODEL OF NEUROVASCULAR UNIT IN VITRO CONSISTING OF THREE CELLS TYPES].
Khilazheva, E D; Boytsova, E B; Pozhilenkova, E A; Solonchuk, Yu R; Salmina, A B
2015-01-01
There are many ways to model blood brain barrier and neurovascular unit in vitro. All existing models have their disadvantages, advantages and some peculiarities of preparation and usage. We obtained the three-cells neurovascular unit model in vitro using progenitor cells isolated from the rat embryos brain (Wistar, 14-16 d). After withdrawal of the progenitor cells the neurospheres were cultured with subsequent differentiation into astrocytes and neurons. Endothelial cells were isolated from embryonic brain too. During the differentiation of progenitor cells the astrocytes monolayer formation occurs after 7-9 d, neurons monolayer--after 10-14 d, endothelial cells monolayer--after 7 d. Our protocol for simultaneous isolation and cultivation of neurons, astrocytes and endothelial cells reduces the time needed to obtain neurovascular unit model in vitro, consisting of three cells types and reduce the number of animals used. It is also important to note the cerebral origin of all cell types, which is also an advantage of our model in vitro.
Application of a Multigrid Method to a Mass-Consistent Diagnostic Wind Model.
Wang, Yansen; Williamson, Chatt; Garvey, Dennis; Chang, Sam; Cogan, James
2005-07-01
A multigrid numerical method has been applied to a three-dimensional, high-resolution diagnostic model for flow over complex terrain using a mass-consistent approach. The theoretical background for the model is based on a variational analysis using mass conservation as a constraint. The model was designed for diagnostic wind simulation at the microscale in complex terrain and in urban areas. The numerical implementation takes advantage of a multigrid method that greatly improves the computation speed. Three preliminary test cases for the model's numerical efficiency and its accuracy are given. The model results are compared with an analytical solution for flow over a hemisphere. Flow over a bell-shaped hill is computed to demonstrate that the numerical method is applicable in the case of parameterized lee vortices. A simulation of the mean wind field in an urban domain has also been carried out and compared with observational data. The comparison indicated that the multigrid method takes only 3%-5% of the time that is required by the traditional Gauss-Seidel method.
Ultrafast spectroscopy of model biological membranes
Ghosh, Avishek
2009-01-01
In this PhD thesis, I have described the novel time-resolved sum-frequency generation (TR-SFG) spectroscopic technique that I developed during the course of my PhD research and used it study the ultrafast vibrational, structural and orientational dynamics of water molecules at model biological membr
Self-Consistent Model for Pulsed Direct-Current N2 Glow Discharge
Institute of Scientific and Technical Information of China (English)
Liu Chengsen; Wang Dezhen
2005-01-01
A self-consistent analysis of a pulsed direct-current (DC) N2 glow discharge is presented. The model is based on a numerical solution of the continuity equations for electron and ions coupled with Poisson's equation. The spatial-temporal variations of ionic and electronic densities and electric field are obtained. The electric field structure exhibits all the characteristic regions of a typical glow discharge (the cathode fall, the negative glow, and the positive column).Current-voltage characteristics of the discharge can be obtained from the model. The calculated current-voltage results using a constant secondary electron emission coefficient for the gas pressure 133.32 Pa are in reasonable agreement with experiment.
Consistency in Regularizations of the Gauged NJL Model at One Loop Level
Battistel, O A
1999-01-01
In this work we revisit questions recently raised in the literature associated to relevant but divergent amplitudes in the gauged NJL model. The questions raised involve ambiguities and symmetry violations which concern the model's predictive power at one loop level. Our study shows by means of an alternative prescription to handle divergent amplitudes, that it is possible to obtain unambiguous and symmetry preserving amplitudes. The procedure adopted makes use solely of {\\it general} properties of an eventual regulator, thus avoiding an explicit form. We find, after a thorough analysis of the problem that there are well established conditions to be fulfiled by any consistent regularization prescription in order to avoid the problems of concern at one loop level.
Macro-particle FEL model with self-consistent spontaneous radiation
Litvinenko, Vladimir N
2015-01-01
Spontaneous radiation plays an important role in SASE FELs and storage ring FELs operating in giant pulse mode. It defines the correlation function of the FEL radiation as well as its many spectral features. Simulations of these systems using randomly distributed macro-particles with charge much higher that of a single electron create the problem of anomalously strong spontaneous radiation, limiting the capabilities of many FEL codes. In this paper we present a self-consistent macro-particle model which provided statistically exact simulation of multi-mode, multi-harmonic and multi-frequency short-wavelength 3-D FELs including the high power and saturation effects. The use of macro-particle clones allows both spontaneous and induced radiation to be treated in the same fashion. Simulations using this model do not require a seed and provide complete temporal and spatial structure of the FEL optical field.
Scale-consistent two-way coupling of land-surface and atmospheric models
Schomburg, A.; Venema, V.; Ament, F.; Simmer, C.
2009-04-01
Processes at the land surface and in the atmosphere act on different spatial scales. While in the atmosphere small-scale heterogeneity is smoothed out quickly by turbulent mixing, this is not the case at the land surface where small-scale variability of orography, land cover, soil texture, soil moisture etc. varies only slowly in time. For the modelling of the fluxes between the land-surface and the atmosphere it is consequently more scale consistent to model the surface processes at a higher spatial resolution than the atmospheric processes. The mosaic approach is one way to deal with this problem. Using this technique the Soil Vegetation Atmosphere Transfer (SVAT) scheme is solved on a higher resolution than the atmosphere, which is possible since a SVAT module generally demands considerably less computation time than the atmospheric part. The upscaling of the turbulent fluxes of sensible and latent heat at the interface to the atmosphere is realized by averaging, due to the nonlinearities involved this is a more sensible approach than averaging the soil properties and computing the fluxes in a second step. The atmospheric quantities are usually assumed to be homogeneous for all soil-subpixels pertaining to one coarse atmospheric grid box. In this work, the aim is to develop a downscaling approach in which the atmospheric quantities at the lowest model layer are disaggregated before they enter the SVAT module at the higher mosaic resolution. The overall aim is a better simulation of the heat fluxes which play an important role for the energy and moisture budgets at the surface. The disaggregation rules for the atmospheric variables will depend on high-resolution surface properties and the current atmospheric conditions. To reduce biases due to nonlinearities we will add small-scale variability according to such rules as well as noise for the variability we can not explain. The model used in this work is the COSMO-model, the weather forecast model (and regional
Esteves, M; Ferreira, M J; Kozica, A; Fernandes, A C; Gonçalves da Silva, A; Saramago, B
2015-08-18
To understand the role of bile acids (BAs) in cell function, many authors have investigated their effect on biomembrane models which are less complex systems, but there are still many open questions. The present study aims to contribute for the deepening of the knowledge of the interaction between BAs and model membranes, in particular, focusing on the effect of BA mixtures. The cytotoxic deoxycholic acid (DCA), the cytoprotective ursodeoxycholic acid (UDCA), and the equimolar mixture (DCA + UDCA) were investigated. Monolayers and liposomes were taken as model membranes with two lipid compositions: an equimolar mixture of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), sphingomyelin (SM), and cholesterol (Chol)) traditionally associated with the formation of lipid rafts and an equimolar POPC/SM binary mixture. The obtained results showed that DCA causes the fluidization of monolayers and bilayers, leading to the eventual rupture of POPC/SM liposomes at high concentration. UDCA may provide a stabilization of POPC/SM membranes but has a negligible effect on the Chol-containing liposomes. In the case of equimolar mixture DCA/UDCA, the interactions depend not only on the lipid composition but also on the design of the experiment. The BA mixture has a greater impact on the monolayers than do pure BAs, suggesting a cooperative DCA-UDCA interaction that enhances the penetration of UDCA in both POPC/SM and POPC/SM/Chol monolayers. For the bilayers, the presence of UDCA in the mixture decreases the disturbing effect of DCA.
Microwave air plasmas in capillaries at low pressure I. Self-consistent modeling
Coche, P.; Guerra, V.; Alves, L. L.
2016-06-01
This work presents the self-consistent modeling of micro-plasmas generated in dry air using microwaves (2.45 GHz excitation frequency), within capillaries (model couples the system of rate balance equations for the most relevant neutral and charged species of the plasma to the homogeneous electron Boltzmann equation. The maintenance electric field is self-consistently calculated adopting a transport theory for low to intermediate pressures, taking into account the presence of O- ions in addition to several positive ions, the dominant species being O{}2+ , NO+ and O+ . The low-pressure small-radius conditions considered yield very-intense reduced electric fields (˜600-1500 Td), coherent with species losses controlled by transport and wall recombination, and kinetic mechanisms strongly dependent on electron-impact collisions. The charged-particle transport losses are strongly influenced by the presence of the negative ion, despite its low-density (˜10% of the electron density). For electron densities in the range (1-≤ft. 4\\right)× {{10}12} cm-3, the system exhibits high dissociation degrees for O2 (˜20-70%, depending on the working conditions, in contrast with the ˜0.1% dissociation obtained for N2), a high concentration of O2(a) (˜1014 cm-3) and NO(X) (5× {{10}14} cm-3) and low ozone production (<{{10}-3}% ).
Institute of Scientific and Technical Information of China (English)
2008-01-01
In this paper,we explore some weakly consistent properties of quasi-maximum likelihood estimates(QMLE) concerning the quasi-likelihood equation in=1 Xi(yi-μ(Xiβ)) = 0 for univariate generalized linear model E(y |X) = μ(X’β).Given uncorrelated residuals {ei = Yi-μ(Xiβ0),1 i n} and other conditions,we prove that βn-β0 = Op(λn-1/2) holds,where βn is a root of the above equation,β0 is the true value of parameter β and λn denotes the smallest eigenvalue of the matrix Sn = ni=1 XiXi.We also show that the convergence rate above is sharp,provided independent non-asymptotically degenerate residual sequence and other conditions.Moreover,paralleling to the elegant result of Drygas(1976) for classical linear regression models,we point out that the necessary condition guaranteeing the weak consistency of QMLE is Sn-1→ 0,as the sample size n →∞.
Institute of Scientific and Technical Information of China (English)
ZHANG SanGuo; LIAO Yuan
2008-01-01
In this paper, we explore some weakly consistent properties of quasi-maximum likelihood estimates(QMLE)concerning the quasi-likelihood equation ∑ni=1 Xi(yi-μ(X1iβ)) =0 for univariate generalized linear model E(y|X) =μ(X1β). Given uncorrelated residuals{ei=Yi-μ(X1iβ0), 1≤i≤n}and other conditions, we prove that (β)n-β0=Op(λ--1/2n)holds, where (β)n is a root of the above equation,β0 is the true value of parameter β and λ-n denotes the smallest eigenvalue of the matrix Sn=Σni=1 XiX1i. We also show that the convergence rate above is sharp, provided independent nonasymptotically degenerate residual sequence and other conditions. Moreover, paralleling to the elegant result of Drygas(1976)for classical linear regression models,we point out that the necessary condition guaranteeing the weak consistency of QMLE is S-1n→0, as the sample size n→∞.
SELF-CONSISTENT FIELD MODEL OF BRUSHES FORMED BY ROOT-TETHERED DENDRONS
Directory of Open Access Journals (Sweden)
E. B. Zhulina
2015-05-01
Full Text Available We present an analytical self-consistent field (scf theory that describes planar brushes formed by regularly branched root-tethered dendrons of the second and third generations. The developed approach gives the possibility for calculation of the scf molecular potential acting at monomers of the tethered chains. In the linear elasticity regime for stretched polymers, the molecular potential has a parabolic shape with the parameter k depending on architectural parameters of tethered macromolecules: polymerization degrees of spacers, branching functionalities, and number of generations. For dendrons of the second generation, we formulate a general equation for parameter k and analyze how variations in the architectural parameters of these dendrons affect the molecular potential. For dendrons of the third generation, an analytical expression for parameter k is available only for symmetric macromolecules with equal lengths of all spacers and equal branching functionalities in all generations. We analyze how the thickness of dendron brush in a good solvent is affected by variations in the chain architecture. Results of the developed scf theory are compared with predictions of boxlike scaling model. We demonstrate that in the limit of high branching functionalities, the results of both approaches become consistent if the value of exponent bin boxlike model is put to unity.In conclusion, we briefly discuss the systems to which the developed scf theory is applicable. These are: planar and concave spherical and cylindrical brushes under various solvent conditions (including solvent-free melted brushes and brush-like layers of ionic (polyelectrolyte dendrons.
Khajepor, Sorush; Chen, Baixin
2016-01-01
A method is developed to analytically and consistently implement cubic equations of state into the recently proposed multipseudopotential interaction (MPI) scheme in the class of two-phase lattice Boltzmann (LB) models [S. Khajepor, J. Wen, and B. Chen, Phys. Rev. E 91, 023301 (2015)]10.1103/PhysRevE.91.023301. An MPI forcing term is applied to reduce the constraints on the mathematical shape of the thermodynamically consistent pseudopotentials; this allows the parameters of the MPI forces to be determined analytically without the need of curve fitting or trial and error methods. Attraction and repulsion parts of equations of state (EOSs), representing underlying molecular interactions, are modeled by individual pseudopotentials. Four EOSs, van der Waals, Carnahan-Starling, Peng-Robinson, and Soave-Redlich-Kwong, are investigated and the results show that the developed MPI-LB system can satisfactorily recover the thermodynamic states of interest. The phase interface is predicted analytically and controlled via EOS parameters independently and its effect on the vapor-liquid equilibrium system is studied. The scheme is highly stable to very high density ratios and the accuracy of the results can be enhanced by increasing the interface resolution. The MPI drop is evaluated with regard to surface tension, spurious velocities, isotropy, dynamic behavior, and the stability dependence on the relaxation time.
Towards self-consistent modelling of the Sgr A* accretion flow: linking theory and observation
Roberts, Shawn R.; Jiang, Yan-Fei; Wang, Q. Daniel; Ostriker, Jeremiah P.
2017-04-01
The interplay between supermassive black holes (SMBHs) and their environments is believed to command an essential role in galaxy evolution. The majority of these SMBHs are in the radiative inefficient accretion phase where this interplay remains elusive, but suggestively important, due to few observational constraints. To remedy this, we directly fit 2D hydrodynamic simulations to Chandra observations of Sgr A* with Markov chain Monte Carlo sampling, self-consistently modelling the 2D inflow-outflow solution for the first time. We find the temperature and density at flow onset are consistent with the origin of the gas in the stellar winds of massive stars in the vicinity of Sgr A*. We place the first observational constraints on the angular momentum of the gas and estimate the centrifugal radius, rc ≈ 0.056 rb ≈ 8 × 10-3 pc, where rb is the Bondi radius. Less than 1 per cent of the inflowing gas accretes on to the SMBH, the remainder being ejected in a polar outflow. We decouple the quiescent point-like emission from the spatially extended flow. We find this point-like emission, accounting for ˜4 per cent of the quiescent flux, is spectrally too steep to be explained by unresolved flares, nor bremsstrahlung, but is likely a combination of a relatively steep synchrotron power law and the high-energy tail of inverse-Compton emission. With this self-consistent model of the accretion flow structure, we make predictions for the flow dynamics and discuss how future X-ray spectroscopic observations can further our understanding of the Sgr A* accretion flow.
Thermodynamically Consistent Algorithms for the Solution of Phase-Field Models
Vignal, Philippe
2016-02-11
Phase-field models are emerging as a promising strategy to simulate interfacial phenomena. Rather than tracking interfaces explicitly as done in sharp interface descriptions, these models use a diffuse order parameter to monitor interfaces implicitly. This implicit description, as well as solid physical and mathematical footings, allow phase-field models to overcome problems found by predecessors. Nonetheless, the method has significant drawbacks. The phase-field framework relies on the solution of high-order, nonlinear partial differential equations. Solving these equations entails a considerable computational cost, so finding efficient strategies to handle them is important. Also, standard discretization strategies can many times lead to incorrect solutions. This happens because, for numerical solutions to phase-field equations to be valid, physical conditions such as mass conservation and free energy monotonicity need to be guaranteed. In this work, we focus on the development of thermodynamically consistent algorithms for time integration of phase-field models. The first part of this thesis focuses on an energy-stable numerical strategy developed for the phase-field crystal equation. This model was put forward to model microstructure evolution. The algorithm developed conserves, guarantees energy stability and is second order accurate in time. The second part of the thesis presents two numerical schemes that generalize literature regarding energy-stable methods for conserved and non-conserved phase-field models. The time discretization strategies can conserve mass if needed, are energy-stable, and second order accurate in time. We also develop an adaptive time-stepping strategy, which can be applied to any second-order accurate scheme. This time-adaptive strategy relies on a backward approximation to give an accurate error estimator. The spatial discretization, in both parts, relies on a mixed finite element formulation and isogeometric analysis. The codes are
Immunology of membranous nephropathy: from animal models to humans.
Sinico, R A; Mezzina, N; Trezzi, B; Ghiggeri, G M; Radice, A
2016-02-01
Membranous nephropathy (MN), the leading cause of nephrotic syndrome in adults, is characterized by the deposition of subepithelial immune deposits that consist mainly of immunoglobulin (Ig)G and complement. Most of the cases are primary or idiopathic (iMN), while only approximately 25% of the cases are secondary to some known disease such as systemic lupus erythematosus, hepatitis B, drugs and malignancies. Most of our knowledge on the pathogenesis of iMN has relied upon old experimental models (i.e. Heymann nephritis) that have shown that immune deposits are formed in situ by the reaction of autoantibodies against the respective podocyte antigen. Recent findings indicate that podocyte proteins also act as an autoantigen in human iMN. The M-type phospholipase A2 receptor (PLA2R) has been identified as the main target antigen, as it can be found in approximately 70% of iMN patients but only rarely in other glomerulonephritides. Podocytes damage in the experimental model of Heymann nephritis is complement-mediated. In humans, the presence of complement within the subepithelial deposits is well established, but IgG4, which does not activate complement by classical or alternative pathways, represents the predominant subclass of IgG anti-PLA2R. Some evidence suggests that IgG4 anti-PLA2R autoantibodies can bind mannan-binding lectin (MBL) and activate the lectin complement pathway. A genetic background for iMN has been demonstrated by genome-wide association studies that have shown highly significant associations of the PLA2R1 and the human leucocyte antigen (HLA)-DQA1 loci with iMN. In addition to their diagnostic value, anti-PLA2R antibodies may be useful to monitor disease activity and predict response to treatment.
A parameter study of self-consistent disk models around Herbig AeBe stars
Meijer, J; De Koter, A; Dullemond, C P; Van Boekel, R; Waters, L B F M
2008-01-01
We present a parameter study of self-consistent models of protoplanetary disks around Herbig AeBe stars. We use the code developed by Dullemond and Dominik, which solves the 2D radiative transfer problem including an iteration for the vertical hydrostatic structure of the disk. This grid of models will be used for several studies on disk emission and mineralogy in followup papers. In this paper we take a first look on the new models, compare them with previous modeling attempts and focus on the effects of various parameters on the overall structure of the SED that leads to the classification of Herbig AeBe stars into two groups, with a flaring (group I) or self-shadowed (group II) SED. We find that the parameter of overriding importance to the SED is the total mass in grains smaller than 25um, confirming the earlier results by Dullemond and Dominik. All other parameters studied have only minor influences, and will alter the SED type only in borderline cases. We find that there is no natural dichotomy between ...
A Time-Dependent Λ and G Cosmological Model Consistent with Cosmological Constraints
Directory of Open Access Journals (Sweden)
L. Kantha
2016-01-01
Full Text Available The prevailing constant Λ-G cosmological model agrees with observational evidence including the observed red shift, Big Bang Nucleosynthesis (BBN, and the current rate of acceleration. It assumes that matter contributes 27% to the current density of the universe, with the rest (73% coming from dark energy represented by the Einstein cosmological parameter Λ in the governing Friedmann-Robertson-Walker equations, derived from Einstein’s equations of general relativity. However, the principal problem is the extremely small value of the cosmological parameter (~10−52 m2. Moreover, the dark energy density represented by Λ is presumed to have remained unchanged as the universe expanded by 26 orders of magnitude. Attempts to overcome this deficiency often invoke a variable Λ-G model. Cosmic constraints from action principles require that either both G and Λ remain time-invariant or both vary in time. Here, we propose a variable Λ-G cosmological model consistent with the latest red shift data, the current acceleration rate, and BBN, provided the split between matter and dark energy is 18% and 82%. Λ decreases (Λ~τ-2, where τ is the normalized cosmic time and G increases (G~τn with cosmic time. The model results depend only on the chosen value of Λ at present and in the far future and not directly on G.
Self-consistent modeling of terahertz waveguide and cavity with frequency-dependent conductivity
Huang, Y. J.; Chu, K. R.; Thumm, M.
2015-01-01
The surface resistance of metals, and hence the Ohmic dissipation per unit area, scales with the square root of the frequency of an incident electromagnetic wave. As is well recognized, this can lead to excessive wall losses at terahertz (THz) frequencies. On the other hand, high-frequency oscillatory motion of conduction electrons tends to mitigate the collisional damping. As a result, the classical theory predicts that metals behave more like a transparent medium at frequencies above the ultraviolet. Such a behavior difference is inherent in the AC conductivity, a frequency-dependent complex quantity commonly used to treat electromagnetics of metals at optical frequencies. The THz region falls in the gap between microwave and optical frequencies. However, metals are still commonly modeled by the DC conductivity in currently active vacuum electronics research aimed at the development of high-power THz sources (notably the gyrotron), although a small reduction of the DC conductivity due to surface roughness is sometimes included. In this study, we present a self-consistent modeling of the gyrotron interaction structures (a metallic waveguide or cavity) with the AC conductivity. The resulting waveguide attenuation constants and cavity quality factors are compared with those of the DC-conductivity model. The reduction in Ohmic losses under the AC-conductivity model is shown to be increasingly significant as the frequency reaches deeper into the THz region. Such effects are of considerable importance to THz gyrotrons for which the minimization of Ohmic losses constitutes a major design consideration.
Rate of strong consistency of quasi maximum likelihood estimate in generalized linear models
Institute of Scientific and Technical Information of China (English)
无
2004-01-01
［1］McCullagh, P., Nelder, J. A., Generalized Linear Models, New York: Chapman and Hall, 1989.［2］Wedderbum, R. W. M., Quasi-likelihood functions, generalized linear models and Gauss-Newton method,Biometrika, 1974, 61:439-447.［3］Fahrmeir, L., Maximum likelihood estimation in misspecified generalized linear models, Statistics, 1990, 21:487-502.［4］Fahrmeir, L., Kaufmann, H., Consistency and asymptotic normality of the maximum likelihood estimator in generalized linear models, Ann. Statist., 1985, 13: 342-368.［5］Melder, J. A., Pregibon, D., An extended quasi-likelihood function, Biometrika, 1987, 74: 221-232.［6］Bennet, G., Probability inequalities for the sum of independent random variables, JASA, 1962, 57: 33-45.［7］Stout, W. F., Almost Sure Convergence, New York:Academic Press, 1974.［8］Petrov, V, V., Sums of Independent Random Variables, Berlin, New York: Springer-Verlag, 1975.
Consistent post-reaction vibrational energy redistribution in DSMC simulations using TCE model
Borges Sebastião, Israel; Alexeenko, Alina
2016-10-01
The direct simulation Monte Carlo (DSMC) method has been widely applied to study shockwaves, hypersonic reentry flows, and other nonequilibrium flow phenomena. Although there is currently active research on high-fidelity models based on ab initio data, the total collision energy (TCE) and Larsen-Borgnakke (LB) models remain the most often used chemistry and relaxation models in DSMC simulations, respectively. The conventional implementation of the discrete LB model, however, may not satisfy detailed balance when recombination and exchange reactions play an important role in the flow energy balance. This issue can become even more critical in reacting mixtures involving polyatomic molecules, such as in combustion. In this work, this important shortcoming is addressed and an empirical approach to consistently specify the post-reaction vibrational states close to thermochemical equilibrium conditions is proposed within the TCE framework. Following Bird's quantum-kinetic (QK) methodology for populating post-reaction states, the new TCE-based approach involves two main steps. The state-specific TCE reaction probabilities for a forward reaction are first pre-computed from equilibrium 0-D simulations. These probabilities are then employed to populate the post-reaction vibrational states of the corresponding reverse reaction. The new approach is illustrated by application to exchange and recombination reactions relevant to H2-O2 combustion processes.
Motte, Fabrice; Bugler-Lamb, Samuel L.; Falcoz, Quentin
2015-07-01
The attraction of solar energy is greatly enhanced by the possibility of it being used during times of reduced or non-existent solar flux, such as weather induced intermittences or the darkness of the night. Therefore optimizing thermal storage for use in solar energy plants is crucial for the success of this sustainable energy source. Here we present a study of a structured bed filler dedicated to Thermocline type thermal storage, believed to outweigh the financial and thermal benefits of other systems currently in use such as packed bed Thermocline tanks. Several criterions such as Thermocline thickness and Thermocline centering are defined with the purpose of facilitating the assessment of the efficiency of the tank to complement the standard concepts of power output. A numerical model is developed that reduces to two dimensions the modeling of such a tank. The structure within the tank is designed to be built using simple bricks harboring rectangular channels through which the solar heat transfer and storage fluid will flow. The model is scrutinized and tested for physical robustness, and the results are presented in this paper. The consistency of the model is achieved within particular ranges for each physical variable.
Energy Technology Data Exchange (ETDEWEB)
Liberton, Michelle; Saha, Rajib; Jacobs, Jon M.; Nguyen, Amelia Y.; Gritsenko, Marina A.; Smith, Richard D.; Koppenaal, David W.; Pakrasi, Himadri B.
2016-04-07
Cyanobacteria are photosynthetic microbes with highly differentiated membrane systems. These organisms contain an outer membrane, plasma membrane, and an internal system of thylakoid membranes where the photosynthetic and respiratory machinery are found. This existence of compartmentalization and differentiation of membrane systems poses a number of challenges for cyanobacterial cells in terms of organization and distribution of proteins to the correct membrane system. Proteomics studies have long sought to identify the components of the different membrane systems, and to date about 450 different proteins have been attributed to either the plasma membrane or thylakoid membrane. Given the complexity of these membranes, many more proteins remain to be identified in these membrane systems, and a comprehensive catalog of plasma membrane and thylakoid membrane proteins is needed. Here we describe the identification of 635 proteins in Synechocystis sp. PCC 6803 by quantitative iTRAQ isobaric labeling; of these, 459 proteins were localized to the plasma membrane and 176 were localized to the thylakoid membrane. Surprisingly, we found over 2.5 times the number of unique proteins identified in the plasma membrane compared to the thylakoid membrane. This suggests that the protein composition of the thylakoid membrane is more homogeneous than the plasma membrane, consistent with the role of the plasma membrane in diverse cellular processes including protein trafficking and nutrient import, compared to a more specialized role for the thylakoid membrane in cellular energetics. Overall, the protein composition of the Synechocystis 6803 plasma membrane and thylakoid membrane is quite similar to the E.coli plasma membrane and Arabidopsis thylakoid membrane, respectively. Synechocystis 6803 can therefore be described as a gram-negative bacterium that has an additional internal membrane system that fulfils the energetic requirements of the cell.
Liberton, Michelle; Saha, Rajib; Jacobs, Jon M; Nguyen, Amelia Y; Gritsenko, Marina A; Smith, Richard D; Koppenaal, David W; Pakrasi, Himadri B
2016-06-01
Cyanobacteria are photosynthetic microbes with highly differentiated membrane systems. These organisms contain an outer membrane, plasma membrane, and an internal system of thylakoid membranes where the photosynthetic and respiratory machinery are found. This existence of compartmentalization and differentiation of membrane systems poses a number of challenges for cyanobacterial cells in terms of organization and distribution of proteins to the correct membrane system. Proteomics studies have long sought to identify the components of the different membrane systems in cyanobacteria, and to date about 450 different proteins have been attributed to either the plasma membrane or thylakoid membrane. Given the complexity of these membranes, many more proteins remain to be identified, and a comprehensive catalogue of plasma membrane and thylakoid membrane proteins is needed. Here we describe the identification of 635 differentially localized proteins in Synechocystis sp. PCC 6803 by quantitative iTRAQ isobaric labeling; of these, 459 proteins were localized to the plasma membrane and 176 were localized to the thylakoid membrane. Surprisingly, we found over 2.5 times the number of unique proteins identified in the plasma membrane compared with the thylakoid membrane. This suggests that the protein composition of the thylakoid membrane is more homogeneous than the plasma membrane, consistent with the role of the plasma membrane in diverse cellular processes including protein trafficking and nutrient import, compared with a more specialized role for the thylakoid membrane in cellular energetics. Thus, our data clearly define the two membrane systems with distinct functions. Overall, the protein compositions of the Synechocystis 6803 plasma membrane and thylakoid membrane are quite similar to that of the plasma membrane of Escherichia coli and thylakoid membrane of Arabidopsis chloroplasts, respectively. Synechocystis 6803 can therefore be described as a Gram
Energy Technology Data Exchange (ETDEWEB)
Liberton, Michelle; Saha, Rajib; Jacobs, Jon M.; Nguyen, Amelia Y.; Gritsenko, Marina A.; Smith, Richard D.; Koppenaal, David W.; Pakrasi, Himadri B.
2016-04-07
Cyanobacteria are photosynthetic microbes with highlydifferentiated membrane systems. These organisms contain an outer membrane, plasma membrane, and an internal system of thylakoid membranes where the photosynthetic and respiratory machinery are found. This existence of compartmentalization and differentiation of membrane systems poses a number of challenges for cyanobacterial cells in terms of organization and distribution of proteins to the correct membrane system. Proteomics studies have long sought to identify the components of the different membrane systems in cyanobacteria, and to date about 450 different proteins have been attributed to either the plasma membrane or thylakoid membrane. Given the complexity of these membranes, many more proteins remain to be identified, and a comprehensive catalogue of plasma membrane and thylakoid membrane proteins is needed. Here we describe the identification of 635 differentially localized proteins in Synechocystis sp. PCC 6803 by quantitative iTRAQ isobaric labeling; of these, 459 proteins were localized to the plasma membrane and 176 were localized to the thylakoid membrane. Surprisingly, we found over 2.5 times the number of unique proteins identified in the plasma membrane compared with the thylakoid membrane. This suggests that the protein composition of the thylakoid membrane is more homogeneous than the plasma membrane, consistent with the role of the plasma membrane in diverse cellular processes including protein trafficking and nutrient import, compared with a more specialized role for the thylakoid membrane in cellular energetics. Thus, our data clearly define the two membrane systems with distinct functions. Overall, the protein compositions of the Synechocystis 6803 plasma membrane and thylakoid membrane are quite similar to that of the plasma membrane of Escherichia coli and thylakoid membrane of Arabidopsis chloroplasts, respectively. Synechocystis 6803 can therefore be described as a Gram
New hybrid model of proton exchange membrane fuel cell
Institute of Scientific and Technical Information of China (English)
WANG Rui-min; CAO Guang-yi; ZHU Xin-jian
2007-01-01
Model and simulation are good tools for design optimization of fuel cell systems. This paper proposes a new hybrid model of proton exchange membrane fuel cell (PEMFC). The hybrid model includes physical component and black-box component. The physical component represents the well-known part of PEMFC, while artificial neural network (ANN) component estimates the poorly known part of PEMFC. The ANN model can compensate the performance of the physical model. This hybrid model is implemented on Matlab/Simulink software. The hybrid model shows better accuracy than that of the physical model and ANN model. Simulation results suggest that the hybrid model can be used as a suitable and accurate model for PEMFC.
Kinetic modelling of coupled transport across biological membranes.
Korla, Kalyani; Mitra, Chanchal K
2014-04-01
In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.
Modeling Extreme Solar Energetic Particle Acceleration with Self-Consistent Wave Generation
Arthur, A. D.; le Roux, J. A.
2015-12-01
Observations of extreme solar energetic particle (SEP) events associated with coronal mass ejection driven shocks have detected particle energies up to a few GeV at 1 AU within the first ~10 minutes to 1 hour of shock acceleration. Whether or not acceleration by a single shock is sufficient in these events or if some combination of multiple shocks or solar flares is required is currently not well understood. Furthermore, the observed onset times of the extreme SEP events place the shock in the corona when the particles escape upstream. We have updated our focused transport theory model that has successfully been applied to the termination shock and traveling interplanetary shocks in the past to investigate extreme SEP acceleration in the solar corona. This model solves the time-dependent Focused Transport Equation including particle preheating due to the cross shock electric field and the divergence, adiabatic compression, and acceleration of the solar wind flow. Diffusive shock acceleration of SEPs is included via the first-order Fermi mechanism for parallel shocks. To investigate the effects of the solar corona on the acceleration of SEPs, we have included an empirical model for the plasma number density, temperature, and velocity. The shock acceleration process becomes highly time-dependent due to the rapid variation of these coronal properties with heliocentric distance. Additionally, particle interaction with MHD wave turbulence is modeled in terms of gyroresonant interactions with parallel propagating Alfven waves. However, previous modeling efforts suggest that the background amplitude of the solar wind turbulence is not sufficient to accelerate SEPs to extreme energies over the short time scales observed. To account for this, we have included the transport and self-consistent amplification of MHD waves by the SEPs through wave-particle gyroresonance. We will present the results of this extended model for a single fast quasi-parallel CME driven shock in the
Bibliographic Relationships in MARC and Consistent with FRBR Model According to RDA Rules
Directory of Open Access Journals (Sweden)
Mahsa Fardehoseiny
2013-03-01
Full Text Available This study was conducted to investigate the bibliographic relationships in the MARC and it’s consistency with the FRBR model. With establishing the necessary relations between bibliographic records, users will retrieve their necessary information faster and more easily. It is important to make a good communication in existing bibliographic records to help users to find what they need. This study’s purpose was to define the relationships between bibliographic records in the National Library's OPAC database and the study’s method was descriptive content analysis approach. In this study, the online catalog (OPAC National Library of Iran has been used to collect information. All records with the mentioned criteria listed in the final report of the IFLA bibliographic relations about the first group entities in FRBR model and RDA rules has been implemented and analyzed. According to this study, if software has been developed in which the data transferring was based on the conceptual model and the MARC’s data that already exists in the National Library's bibliographic database, these relationships will not be transferable. Withal, in this study the relationships on consistent FRBR and MARC concluded with an intelligent mind and the machine is unable to detect them. The results of this study showed that the relations which conveyed from MARC to FRBR, was about 47/70 percent of the MARC fields, in other hand by FRBR to MARC with the use of all intelligent efforts, and diagnosis of MARC relationships, only 31/38 percent of the relations can be covered through the MARC. But based on real data and usable fields in Boostan-e-Saadi with MARC pattern, records on the National Library of Iran showed that the results reduced to 16/95 percent..
Formulation of a self-consistent model for quantum well pin solar cells
Ramey, S.; Khoie, R.
1997-04-01
A self-consistent numerical simulation model for a pin single-cell solar cell is formulated. The solar cell device consists of a p-AlGaAs region, an intrinsic i-AlGaAs/GaAs region with several quantum wells, and a n-AlGaAs region. Our simulator solves a field-dependent Schrödinger equation self-consistently with Poisson and Drift-Diffusion equations. The emphasis is given to the study of the capture of electrons by the quantum wells, the escape of electrons from the quantum wells, and the absorption and recombination within the quantum wells. We believe this would be the first such comprehensive model ever reported. The field-dependent Schrödinger equation is solved using the transfer matrix method. The eigenfunctions and eigenenergies obtained are used to calculate the escape rate of electrons from the quantum wells, and the non-radiative recombination rates of electrons at the boundaries of the quantum wells. These rates together with the capture rates of electrons by the quantum wells are then used in a self-consistent numerical Poisson-Drift-Diffusion solver. The resulting field profiles are then used in the field-dependent Schrödinger solver, and the iteration process is repeated until convergence is reached. In a p-AlGaAs i-AlGaAs/GaAs n-AlGaAs cell with aluminum mole fraction of 0.3, with one 100 Å-wide 284 meV-deep quantum well, the eigenenergies with zero field are 36meV, 136meV, and 267meV, for the first, second and third subbands, respectively. With an electric field of 50 kV/cm, the eigenenergies are shifted to 58meV, 160meV, and 282meV, respectively. With these eigenenergies, the thermionic escape time of electrons from the GaAs Γ-valley, varies from 220 pS to 90 pS for electric fields ranging from 10 to 50 kV/cm. These preliminary results are in good agreement with those reported by other researchers.
Understanding Peptide Dendrimer Interactions with Model Cell Membrane Mimics
DEFF Research Database (Denmark)
Lind, Tania Kjellerup
membranes or highly conserved motifs, effectively making resistance due to mutations less likely to develop and spread. For this we studied the conditions to form supported lipid bilayers with basic systems and further established a protocol for producing biomimetic bacterial model membranes via the vesicle...... fusion method, which presents improved means for studying drug-membrane interactions in the future. The interaction mechanism of a family of dendrimers was examined and in particular one dendrimer (BALY) was extensively studied by the combined use of quartz crystal microbalance, atomic force microscopy...... and neutron reection. The application of several complementary surface-sensitive techniques allowed for systematically addressing the interface-related processes and gain insights into different aspects of the interaction. BALY was found to interact via a uidity-dependent mechanism. It inserted into the outer...
Effects of the local anesthetic benzocaine on the human erythrocyte membrane and molecular models.
Suwalsky, Mario; Schneider, Carlos; Villena, Fernando; Norris, Beryl; Cárdenas, Hernán; Cuevas, Francisco; Sotomayor, Carlos P
2004-04-01
The interaction of the local anesthetic benzocaine with the human erythrocyte membrane and molecular models is described. The latter consisted of isolated unsealed human erythrocyte membranes (IUM), large unilamellar vesicles (LUV) of dimyristoylphospatidylcholine (DMPC), and phospholipid multilayers of DMPC and dimyristoylphospatidyletanolamine (DMPE), representatives of phospholipid classes located in the outer and inner monolayers of the human erythrocyte membrane, respectively. Optical and scanning electron microscopy of human erythrocytes revealed that benzocaine induced the formation of echinocytes. Experiments performed on IUM and DMPC LUV by fluorescence spectroscopy showed that benzocaine interacted with the phospholipid bilayer polar groups and hydrophobic acyl chains. X-ray diffraction analysis of DMPC confirmed these results and showed that benzocaine had no effects on DMPE. The effect on sodium transport was also studied using the isolated toad skin. Electrophysiological measurements indicated a significant decrease in the potential difference (PD) and in the short-circuit current (Isc) after the application of benzocaine, reflecting inhibition of active ion transport.
Percolative model of proton conductivity of Nafion {sup registered} membranes
Energy Technology Data Exchange (ETDEWEB)
Costamagna, Paola; Grosso, Simone; Di Felice, Renzo [DICheP, Department of Chemical and Process Engineering ' G.B. Bonino' , University of Genoa, Via Opera Pia 15, 16145 Genoa (Italy)
2008-04-01
A model is proposed for the simulation of Nafion {sup registered} proton conductivity, where it is assumed that proton conduction occurs only in the water present in the membrane pores. Water is considered to be present in the pores due to two different phenomena: adsorption and capillary condensation. In the latter case, the pore is flooded and proton conduction occurs throughout the whole pore section. The conditions under which capillary condensation occurs are simulated in the model through the Kelvin-Cohan equation for condensation. The Kelvin-Cohan equation is a function of RH, temperature and the pore radius; the larger the pore, the higher the RH for which capillary condensation takes place. If the conditions for capillary condensation are not satisfied, then water is present in the pore due to adsorption under the form of a water layer which covers the pore walls and provides a path for proton conduction. In this case, the modified Brunauer-Emmet-Teller (BET) equation has been used in the model to simulate the thickness of the water layer. In both cases of capillary condensation and adsorption, the conductance g of a pore has then been calculated through the formula g = {kappa}S/l, where {kappa} is the proton conductivity of water, S the cross-section of the pore volume which is occupied by water, and l is the pore length. Pores of different size are present in the membrane (data of pore size distribution have been extracted from the literature); connectivity of the water layers present in the different pores is necessary in order to achieve a continuous path of proton conduction through the membrane, which is a percolation problem. To this end, the structure of the membrane pores has been simulated in the model through the effective medium approximation (EMA). The simulation results of proton conductivity of the membrane show good agreement with literature experimental data, even when varying the RH operating conditions. (author)
Zimmermann, Eva; Seifert, Udo
2015-02-01
Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F(1)-ATPase and the kinesin motor.
McGlynn, Thomas; Fabbiano, Giuseppina; Accomazzi, Alberto; Smale, Alan; White, Richard L.; Donaldson, Thomas; Aloisi, Alessandra; Dower, Theresa; Mazzerella, Joseph M.; Ebert, Rick; Pevunova, Olga; Imel, David; Berriman, Graham B.; Teplitz, Harry I.; Groom, Steve L.; Desai, Vandana R.; Landry, Walter
2016-07-01
Since the turn of the millennium a constant concern of astronomical archives have begun providing data to the public through standardized protocols unifying data from disparate physical sources and wavebands across the electromagnetic spectrum into an astronomical virtual observatory (VO). In October 2014, NASA began support for the NASA Astronomical Virtual Observatories (NAVO) program to coordinate the efforts of NASA astronomy archives in providing data to users through implementation of protocols agreed within the International Virtual Observatory Alliance (IVOA). A major goal of the NAVO collaboration has been to step back from a piecemeal implementation of IVOA standards and define what the appropriate presence for the US and NASA astronomy archives in the VO should be. This includes evaluating what optional capabilities in the standards need to be supported, the specific versions of standards that should be used, and returning feedback to the IVOA, to support modifications as needed. We discuss a standard archive model developed by the NAVO for data archive presence in the virtual observatory built upon a consistent framework of standards defined by the IVOA. Our standard model provides for discovery of resources through the VO registries, access to observation and object data, downloads of image and spectral data and general access to archival datasets. It defines specific protocol versions, minimum capabilities, and all dependencies. The model will evolve as the capabilities of the virtual observatory and needs of the community change.
Consistency of non-flat $\\Lambda$CDM model with the new result from BOSS
Kumar, Suresh
2015-01-01
Using 137,562 quasars in the redshift range $2.1\\leq z\\leq3.5$ from the Data Release 11 (DR11) of the Baryon Oscillation Spectroscopic Survey (BOSS) of Sloan Digital Sky Survey (SDSS)-III, the BOSS-SDSS collaboration estimated the expansion rate $H(z=2.34)=222\\pm7$ km/s/Mpc of Universe, and reported that this value is in tension with the predictions of flat $\\Lambda$CDM model at around 2.5$\\sigma$ level. In this letter, we briefly describe some attempts made in the literature to relieve the tension, and show that the tension can naturally be alleviated in non-flat $\\Lambda$CDM model with positive curvature. However, this idea confronts with the inflation paradigm which predicts almost a spatially flat Universe. Nevertheless, the theoretical consistency of the non-flat $\\Lambda$CDM model with the new result from BOSS deserves attention of the community.
Baraffe, I; Méra, D; Chabrier, G; Beaulieu, J P
1998-01-01
We have computed stellar evolutionary models for stars in a mass range characteristic of Cepheid variables ($3
Hernández-Pajares, Manuel; Roma-Dollase, David; Krankowski, Andrzej; García-Rigo, Alberto; Orús-Pérez, Raül
2017-05-01
A summary of the main concepts on global ionospheric map(s) [hereinafter GIM(s)] of vertical total electron content (VTEC), with special emphasis on their assessment, is presented in this paper. It is based on the experience accumulated during almost two decades of collaborative work in the context of the international global navigation satellite systems (GNSS) service (IGS) ionosphere working group. A representative comparison of the two main assessments of ionospheric electron content models (VTEC-altimeter and difference of Slant TEC, based on independent global positioning system data GPS, dSTEC-GPS) is performed. It is based on 26 GPS receivers worldwide distributed and mostly placed on islands, from the last quarter of 2010 to the end of 2016. The consistency between dSTEC-GPS and VTEC-altimeter assessments for one of the most accurate IGS GIMs (the tomographic-kriging GIM `UQRG' computed by UPC) is shown. Typical error RMS values of 2 TECU for VTEC-altimeter and 0.5 TECU for dSTEC-GPS assessments are found. And, as expected by following a simple random model, there is a significant correlation between both RMS and specially relative errors, mainly evident when large enough number of observations per pass is considered. The authors expect that this manuscript will be useful for new analysis contributor centres and in general for the scientific and technical community interested in simple and truly external ways of validating electron content models of the ionosphere.
Towards Self-Consistent Modelling of the Sgr A* Accretion Flow: Linking Theory and Observation
Roberts, Shawn R; Jiang, Yan-Fei; Ostriker, Jeremiah P
2016-01-01
The interplay between supermassive black holes (SMBHs) and their environments is believed to command an essential role in galaxy evolution. The majority of these SMBHs are in the radiative inefficient accretion phase where this interplay remains elusive, but suggestively important, due to few observational constraints. To remedy this, we directly fit 2-D hydrodynamic simulations to Chandra observations of Sgr A* with Markov Chain Monte Carlo sampling, self-consistently modelling the 2-D inflow-outflow solution for the first time. We find the temperature and density at flow onset are consistent with the origin of the gas in the stellar winds of massive stars in the vicinity of Sgr A*. We place the first observational constraints on the angular momentum of the gas and estimate the centrifugal radius, r$_c$ $\\approx$ 0.056 r$_b$ $\\approx8\\times10^{-3}$ pc, where r$_b$ is the Bondi radius. Less than 1\\% of the inflowing gas accretes onto the SMBH, the remainder being ejected in a polar outflow. For the first time...
A self-consistent linear-mode model of stellar convection
Macauslan, J.
1985-01-01
A normal-mode expansion of the linearized fluid equations in terms of small subset of spherical harmonics can provide a foundation for a physically motivated, self-consistent description of a solar-type convection zone. In the absence of dissipation, a second-order differential equation governs the radial dependence of the modes, so that interpretation of the effects on convection quantities of the normal-form 'potential well' is straightforward. The philosophy is quite different from the more recent work of Narasimha and Antia (1982): all envelopes presented here differ substantially from MLT envelopes, and therefore, from theirs, which are constructed to be consistent with MLT. The amplitude of all modes is set by a Kelvin-Helmholtz-('shear'-) instability argument unrelated to solar observations, with the result that the convection description may be considered to arise from 'first-hueristic-principles'. The thermodynamics modelled vaguely resemble the sun's, and more vigorously convective envelopes show some phenomena qualitatively like solar observations (e.g., atmospheric velocity spectra).
The self-consistent field model for Fermi systems with account of three-body interactions
Directory of Open Access Journals (Sweden)
Yu.M. Poluektov
2015-12-01
Full Text Available On the basis of a microscopic model of self-consistent field, the thermodynamics of the many-particle Fermi system at finite temperatures with account of three-body interactions is built and the quasiparticle equations of motion are obtained. It is shown that the delta-like three-body interaction gives no contribution into the self-consistent field, and the description of three-body forces requires their nonlocality to be taken into account. The spatially uniform system is considered in detail, and on the basis of the developed microscopic approach general formulas are derived for the fermion's effective mass and the system's equation of state with account of contribution from three-body forces. The effective mass and pressure are numerically calculated for the potential of "semi-transparent sphere" type at zero temperature. Expansions of the effective mass and pressure in powers of density are obtained. It is shown that, with account of only pair forces, the interaction of repulsive character reduces the quasiparticle effective mass relative to the mass of a free particle, and the attractive interaction raises the effective mass. The question of thermodynamic stability of the Fermi system is considered and the three-body repulsive interaction is shown to extend the region of stability of the system with the interparticle pair attraction. The quasiparticle energy spectrum is calculated with account of three-body forces.
Self-consistent 2-phase AGN torus models: SED library for observers
Siebenmorgen, Ralf; Efstathiou, Andreas
2015-01-01
We assume that dust near active galactic nuclei (AGN) is distributed in a torus-like geometry, which may be described by a clumpy medium or a homogeneous disk or as a combination of the two (i.e. a 2-phase medium). The dust particles considered are fluffy and have higher submillimeter emissivities than grains in the diffuse ISM. The dust-photon interaction is treated in a fully self-consistent three dimensional radiative transfer code. We provide an AGN library of spectral energy distributions (SEDs). Its purpose is to quickly obtain estimates of the basic parameters of the AGN, such as the intrinsic luminosity of the central source, the viewing angle, the inner radius, the volume filling factor and optical depth of the clouds, and the optical depth of the disk midplane, and to predict the flux at yet unobserved wavelengths. The procedure is simple and consists of finding an element in the library that matches the observations. We discuss the general properties of the models and in particular the 10mic. silic...
Height-Diameter Models for Mixed-Species Forests Consisting of Spruce, Fir, and Beech
Directory of Open Access Journals (Sweden)
Petráš Rudolf
2014-06-01
Full Text Available Height-diameter models define the general relationship between the tree height and diameter at each growth stage of the forest stand. This paper presents generalized height-diameter models for mixed-species forest stands consisting of Norway spruce (Picea abies Karst., Silver fir (Abies alba L., and European beech (Fagus sylvatica L. from Slovakia. The models were derived using two growth functions from the exponential family: the two-parameter Michailoff and three-parameter Korf functions. Generalized height-diameter functions must normally be constrained to pass through the mean stand diameter and height, and then the final growth model has only one or two parameters to be estimated. These “free” parameters are then expressed over the quadratic mean diameter, height and stand age and the final mathematical form of the model is obtained. The study material included 50 long-term experimental plots located in the Western Carpathians. The plots were established 40-50 years ago and have been repeatedly measured at 5 to 10-year intervals. The dataset includes 7,950 height measurements of spruce, 21,661 of fir and 5,794 of beech. As many as 9 regression models were derived for each species. Although the “goodness of fit” of all models showed that they were generally well suited for the data, the best results were obtained for silver fir. The coefficient of determination ranged from 0.946 to 0.948, RMSE (m was in the interval 1.94-1.97 and the bias (m was -0.031 to 0.063. Although slightly imprecise parameter estimation was established for spruce, the estimations of the regression parameters obtained for beech were quite less precise. The coefficient of determination for beech was 0.854-0.860, RMSE (m 2.67-2.72, and the bias (m ranged from -0.144 to -0.056. The majority of models using Korf’s formula produced slightly better estimations than Michailoff’s, and it proved immaterial which estimated parameter was fixed and which parameters
Effects of phenylpropanolamine (PPA) on in vitro human erythrocyte membranes and molecular models
Energy Technology Data Exchange (ETDEWEB)
Suwalsky, Mario, E-mail: msuwalsk@udec.cl [Faculty of Chemical Sciences, University of Concepcion, Concepcion (Chile); Zambrano, Pablo; Mennickent, Sigrid [Faculty of Pharmacy, University of Concepcion, Concepcion (Chile); Villena, Fernando [Faculty of Biological Sciences, University of Concepcion, Concepcion (Chile); Sotomayor, Carlos P.; Aguilar, Luis F. [Instituto de Quimica, Pontificia Universidad Catolica de Valparaiso, Valparaiso (Chile); Bolognin, Silvia [CNR-Institute for Biomedical Technologies, University of Padova, Padova (Italy)
2011-03-18
Research highlights: {yields} PPA is a common ingredient in cough-cold medication and appetite suppressants. {yields} Reports on its effects on human erythrocytes are very scarce. {yields} We found that PPA induced in vitro morphological changes to human erythrocytes. {yields} PPA interacted with isolated unsealed human erythrocyte membranes. {yields} PPA interacted with class of lipid present in the erythrocyte membrane outer monolayer. -- Abstract: Norephedrine, also called phenylpropanolamine (PPA), is a synthetic form of the ephedrine alkaloid. After reports of the occurrence of intracranial hemorrhage and other adverse effects, including several deaths, PPA is no longer sold in USA and Canada. Despite the extensive information about PPA toxicity, reports on its effects on cell membranes are scarce. With the aim to better understand the molecular mechanisms of the interaction of PPA with cell membranes, ranges of concentrations were incubated with intact human erythrocytes, isolated unsealed human erythrocyte membranes (IUM), and molecular models of cell membranes. The latter consisted in bilayers built-up of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylethanolamine (DMPE), phospholipid classes present in the outer and inner monolayers of most plasmatic cell membranes, respectively. The capacity of PPA to perturb the bilayer structures of DMPC and DMPE was assessed by X-ray diffraction, DMPC large unilamellar vesicles (LUV) and IUM were studied by fluorescence spectroscopy, and intact human erythrocytes were observed by scanning electron microscopy (SEM). This study presents evidence that PPA affects human red cell membranes as follows: (a) in SEM studies on human erythrocytes it was observed that 0.5 mM PPA induced shape changes; (b) in IUM PPA induced a sharp decrease in the fluorescence anisotropy in the lipid bilayer acyl chains in a concentration range lower than 100 {mu}M; (c) X-ray diffraction studies showed that PPA in the 0.1-0.5 m
Motion of the Philippine Sea plate consistent with the NUVEL-1A model
Zang, Shao Xian; Chen, Qi Yong; Ning, Jie Yuan; Shen, Zheng Kang; Liu, Yong Gang
2002-09-01
We determine Euler vectors for 12 plates, including the Philippine Sea plate (PH), relative to the fixed Pacific plate (PA) by inverting the earthquake slip vectors along the boundaries of the Philippine Sea plate, GPS observed velocities, and 1122 data from the NUVEL-1 and the NUVEL-1A global plate motion model, respectively. This analysis thus also yields Euler vectors for the Philippine Sea plate relative to adjacent plates. Our results are consistent with observed data and can satisfy the geological and geophysical constraints along the Caroline (CR)-PH and PA-CR boundaries. The results also give insight into internal deformation of the Philippine Sea plate. The area enclosed by the Ryukyu Trench-Nankai Trough, Izu-Bonin Trench and GPS stations S102, S063 and Okino Torishima moves uniformly as a rigid plate, but the areas near the Philippine Trench, Mariana Trough and Yap-Palau Trench have obvious deformation.
Plasma Processes : A self-consistent kinetic modeling of a 1-D, bounded, plasma in equilibrium
Indian Academy of Sciences (India)
Monojoy Goswami; H Ramachandran
2000-11-01
A self-consistent kinetic treatment is presented here, where the Boltzmann equation is solved for a particle conserving Krook collision operator. The resulting equations have been implemented numerically. The treatment solves for the entire quasineutral column, making no assumptions about mfp/, where mfp is the ion-neutral collision mean free path and the size of the device. Coulomb collisions are neglected in favour of collisions with neutrals, and the particle source is modeled as a uniform Maxwellian. Electrons are treated as an inertialess but collisional ﬂuid. The ion distribution function for the trapped and the transiting orbits is obtained. Interesting ﬁndings include the anomalous heating of ions as they approach the presheath, the development of strongly non-Maxwellian features near the last mfp, and strong modiﬁcations of the sheath criterion.
Pranger, C. C.; Le Pourhiet, L.; May, D.; van Dinther, Y.; Gerya, T.
2016-12-01
Subduction zones evolve over millions of years. The state of stress, the distribution of materials, and the strength and structure of the interface between the two plates is intricately tied to a host of time-dependent physical processes, such as damage, friction, (nonlinear) viscous relaxation, and fluid migration. In addition, the subduction interface has a complex three-dimensional geometry that evolves with time and can adjust in response to a changing stress environment or in response to impinging topographical features, and can even branch off as a splay fault. All in all, the behaviour of (large) earthquakes at the millisecond to minute timescale is heavily dependent on the pattern of stress accumulation during the 100 year inter-seismic period, the events occurring on or near the interface in the past thousands of years, as well as the extended geological history of the region. We address the aforementioned modeling requirements by developing a self-consistent 3D staggered grid finite difference continuum description of motion, thermal advection-diffusion, and poro-visco-elastic two-phase flow. Faults are modelled as plastic shear bands that can develop and evolve in response to a changing stress environment without having a prescribed geometry. They obey a Mohr-Coulomb or Drucker-Prager yield criterion and a rate-and-state friction law. For a sound treatment of plasticity, we borrow elements from mechanical engineering, and extend these with high-quality nonlinear iteration schemes and adaptive time-stepping to resolve the rupture process at all time scales. We will present these techniques together with proof-of-concept examples of self-consistently developing seismic cycles in 2D and 3D, including phases of stress accumulation, fault nucleation, dynamic rupture, and healing.
Energy Technology Data Exchange (ETDEWEB)
BRANNON,REBECCA M.
2000-11-01
A theory is developed for the response of moderately porous solids (no more than {approximately}20% void space) to high-strain-rate deformations. The model is consistent because each feature is incorporated in a manner that is mathematically compatible with the other features. Unlike simple p-{alpha} models, the onset of pore collapse depends on the amount of shear present. The user-specifiable yield function depends on pressure, effective shear stress, and porosity. The elastic part of the strain rate is linearly related to the stress rate, with nonlinear corrections from changes in the elastic moduli due to pore collapse. Plastically incompressible flow of the matrix material allows pore collapse and an associated macroscopic plastic volume change. The plastic strain rate due to pore collapse/growth is taken normal to the yield surface. If phase transformation and/or pore nucleation are simultaneously occurring, the inelastic strain rate will be non-normal to the yield surface. To permit hardening, the yield stress of matrix material is treated as an internal state variable. Changes in porosity and matrix yield stress naturally cause the yield surface to evolve. The stress, porosity, and all other state variables vary in a consistent manner so that the stress remains on the yield surface throughout any quasistatic interval of plastic deformation. Dynamic loading allows the stress to exceed the yield surface via an overstress ordinary differential equation that is solved in closed form for better numerical accuracy. The part of the stress rate that causes no plastic work (i.e-, the part that has a zero inner product with the stress deviator and the identity tensor) is given by the projection of the elastic stressrate orthogonal to the span of the stress deviator and the identity tensor.The model, which has been numerically implemented in MIG format, has been exercised under a wide array of extremal loading and unloading paths. As will be discussed in a companion
Modeling Of Proton Exchange Membrane Fuel Cell Systems
DEFF Research Database (Denmark)
Nielsen, Mads Pagh
The objective of this doctoral thesis was to develop reliable steady-state and transient component models suitable to asses-, develop- and optimize proton exchange membrane (PEM) fuel cell systems. Several components in PEM fuel cell systems were characterized and modeled. The developed component...... cell systems. Consequences of indirectly fueling PEM stacks with hydrocarbons using reforming technology were investigated using a PEM stack model including CO poisoning kinetics and a transient Simulink steam reforming system model. Aspects regarding the optimization of PEM fuel cell systems...
Computational model for amoeboid motion: Coupling membrane and cytosol dynamics.
Moure, Adrian; Gomez, Hector
2016-10-01
A distinguishing feature of amoeboid motion is that the migrating cell undergoes large deformations, caused by the emergence and retraction of actin-rich protrusions, called pseudopods. Here, we propose a cell motility model that represents pseudopod dynamics, as well as its interaction with membrane signaling molecules. The model accounts for internal and external forces, such as protrusion, contraction, adhesion, surface tension, or those arising from cell-obstacle contacts. By coupling the membrane and cytosol interactions we are able to reproduce a realistic picture of amoeboid motion. The model results are in quantitative agreement with experiments and show how cells may take advantage of the geometry of their microenvironment to migrate more efficiently.
A Self-consistent and Spatially Dependent Model of the Multiband Emission of Pulsar Wind Nebulae
Lu, Fang-Wu; Gao, Quan-Gui; Zhang, Li
2017-01-01
A self-consistent and spatially dependent model is presented to investigate the multiband emission of pulsar wind nebulae (PWNe). In this model, a spherically symmetric system is assumed and the dynamical evolution of the PWN is included. The processes of convection, diffusion, adiabatic loss, radiative loss, and photon–photon pair production are taken into account in the electron’s evolution equation, and the processes of synchrotron radiation, inverse Compton scattering, synchrotron self-absorption, and pair production are included for the photon’s evolution equation. Both coupled equations are simultaneously solved. The model is applied to explain observed results of the PWN in MSH 15–52. Our results show that the spectral energy distributions (SEDs) of both electrons and photons are all a function of distance. The observed photon SED of MSH 15–52 can be well reproduced in this model. With the parameters obtained by fitting the observed SED, the spatial variations of photon index and surface brightness observed in the X-ray band can also be well reproduced. Moreover, it can be derived that the present-day diffusion coefficient of MSH 15–52 at the termination shock is {κ }0=6.6× {10}24 {{cm}}2 {{{s}}}-1, the spatial average has a value of \\bar{κ }=1.4× {10}25 {{cm}}2 {{{s}}}-1, and the present-day magnetic field at the termination shock has a value of {B}0=26.6 μ {{G}} and the spatial averaged magnetic field is \\bar{B}=14.9 μ {{G}}. The spatial changes of the spectral index and surface brightness at different bands are predicted.
Subgrid-scale physical parameterization in atmospheric modeling: How can we make it consistent?
Yano, Jun-Ichi
2016-07-01
Approaches to subgrid-scale physical parameterization in atmospheric modeling are reviewed by taking turbulent combustion flow research as a point of reference. Three major general approaches are considered for its consistent development: moment, distribution density function (DDF), and mode decomposition. The moment expansion is a standard method for describing the subgrid-scale turbulent flows both in geophysics and engineering. The DDF (commonly called PDF) approach is intuitively appealing as it deals with a distribution of variables in subgrid scale in a more direct manner. Mode decomposition was originally applied by Aubry et al (1988 J. Fluid Mech. 192 115-73) in the context of wall boundary-layer turbulence. It is specifically designed to represent coherencies in compact manner by a low-dimensional dynamical system. Their original proposal adopts the proper orthogonal decomposition (empirical orthogonal functions) as their mode-decomposition basis. However, the methodology can easily be generalized into any decomposition basis. Among those, wavelet is a particularly attractive alternative. The mass-flux formulation that is currently adopted in the majority of atmospheric models for parameterizing convection can also be considered a special case of mode decomposition, adopting segmentally constant modes for the expansion basis. This perspective further identifies a very basic but also general geometrical constraint imposed on the massflux formulation: the segmentally-constant approximation. Mode decomposition can, furthermore, be understood by analogy with a Galerkin method in numerically modeling. This analogy suggests that the subgrid parameterization may be re-interpreted as a type of mesh-refinement in numerical modeling. A link between the subgrid parameterization and downscaling problems is also pointed out.
Self-consistent modeling of CFETR baseline scenarios for steady-state operation
Chen, Jiale; Jian, Xiang; Chan, Vincent S.; Li, Zeyu; Deng, Zhao; Li, Guoqiang; Guo, Wenfeng; Shi, Nan; Chen, Xi; CFETR Physics Team
2017-07-01
Integrated modeling for core plasma is performed to increase confidence in the proposed baseline scenario in the 0D analysis for the China Fusion Engineering Test Reactor (CFETR). The steady-state scenarios are obtained through the consistent iterative calculation of equilibrium, transport, auxiliary heating and current drives (H&CD). Three combinations of H&CD schemes (NB + EC, NB + EC + LH, and EC + LH) are used to sustain the scenarios with q min > 2 and fusion power of ˜70-150 MW. The predicted power is within the target range for CFETR Phase I, although the confinement based on physics models is lower than that assumed in 0D analysis. Ideal MHD stability analysis shows that the scenarios are stable against n = 1-10 ideal modes, where n is the toroidal mode number. Optimization of RF current drive for the RF-only scenario is also presented. The simulation workflow for core plasma in this work provides a solid basis for a more extensive research and development effort for the physics design of CFETR.
Toward A Self Consistent MHD Model of Chromospheres and Winds From Late Type Evolved Stars
Airapetian, V. S.; Leake, J. E.; Carpenter, Kenneth G.
2015-01-01
We present the first magnetohydrodynamic model of the stellar chromospheric heating and acceleration of the outer atmospheres of cool evolved stars, using α Tau as a case study. We used a 1.5D MHD code with a generalized Ohm's law that accounts for the effects of partial ionization in the stellar atmosphere to study Alfvén wave dissipation and wave reflection. We have demonstrated that due to inclusion of the effects of ion-neutral collisions in magnetized weakly ionized chromospheric plasma on resistivity and the appropriate grid resolution, the numerical resistivity becomes 1-2 orders of magnitude smaller than the physical resistivity. The motions introduced by non-linear transverse Alfvé waves can explain non-thermally broadened and non-Gaussian profiles of optically thin UV lines forming in the stellar chromosphere of α Tau and other late-type giant and supergiant stars. The calculated heating rates in the stellar chromosphere due to resistive (Joule) dissipation of electric currents, induced by upward propagating non-linear Alfvé waves, are consistent with observational constraints on the net radiative losses in UV lines and the continuum from α Tau. At the top of the chromosphere, Alfvé waves experience significant reflection, producing downward propagating transverse waves that interact with upward propagating waves and produce velocity shear in the chromosphere. Our simulations also suggest that momentum deposition by non-linear Alfvé waves becomes significant in the outer chromosphere at 1 stellar radius from the photosphere. The calculated terminal velocity and the mass loss rate are consistent with the observationally derived wind properties in α Tau.
Hazard-consistent ground motions generated with a stochastic fault-rupture model
Energy Technology Data Exchange (ETDEWEB)
Nishida, Akemi, E-mail: nishida.akemi@jaea.go.jp [Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871 (Japan); Igarashi, Sayaka, E-mail: igrsyk00@pub.taisei.co.jp [Technology Center, Taisei Corporation, 344-1 Nase-cho, Totsuka-ku, Yokohama 245-0051 (Japan); Sakamoto, Shigehiro, E-mail: shigehiro.sakamoto@sakura.taisei.co.jp [Technology Center, Taisei Corporation, 344-1 Nase-cho, Totsuka-ku, Yokohama 245-0051 (Japan); Uchiyama, Yasuo, E-mail: yasuo.uchiyama@sakura.taisei.co.jp [Technology Center, Taisei Corporation, 344-1 Nase-cho, Totsuka-ku, Yokohama 245-0051 (Japan); Yamamoto, Yu, E-mail: ymmyu-00@pub.taisei.co.jp [Technology Center, Taisei Corporation, 344-1 Nase-cho, Totsuka-ku, Yokohama 245-0051 (Japan); Muramatsu, Ken, E-mail: kmuramat@tcu.ac.jp [Department of Nuclear Safety Engineering, Tokyo City University, 1-28-1 Tamazutsumi, Setagaya-ku, Tokyo 158-8557 (Japan); Takada, Tsuyoshi, E-mail: takada@load.arch.t.u-tokyo.ac.jp [Department of Architecture, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)
2015-12-15
Conventional seismic probabilistic risk assessments (PRAs) of nuclear power plants consist of probabilistic seismic hazard and fragility curves. Even when earthquake ground-motion time histories are required, they are generated to fit specified response spectra, such as uniform hazard spectra at a specified exceedance probability. These ground motions, however, are not directly linked with seismic-source characteristics. In this context, the authors propose a method based on Monte Carlo simulations to generate a set of input ground-motion time histories to develop an advanced PRA scheme that can explain exceedance probability and the sequence of safety-functional loss in a nuclear power plant. These generated ground motions are consistent with seismic hazard at a reference site, and their seismic-source characteristics can be identified in detail. Ground-motion generation is conducted for a reference site, Oarai in Japan, the location of a hypothetical nuclear power plant. A total of 200 ground motions are generated, ranging from 700 to 1100 cm/s{sup 2} peak acceleration, which corresponds to a 10{sup −4} to 10{sup −5} annual exceedance frequency. In the ground-motion generation, seismic sources are selected according to their hazard contribution at the site, and Monte Carlo simulations with stochastic parameters for the seismic-source characteristics are then conducted until ground motions with the target peak acceleration are obtained. These ground motions are selected so that they are consistent with the hazard. Approximately 110,000 simulations were required to generate 200 ground motions with these peak accelerations. Deviations of peak ground motion acceleration generated for 1000–1100 cm/s{sup 2} range from 1.5 to 3.0, where the deviation is evaluated with peak ground motion accelerations generated from the same seismic source. Deviations of 1.0 to 3.0 for stress drops, one of the stochastic parameters of seismic-source characteristics, are required to
Towards three-dimensional continuum models of self-consistent along-strike megathrust segmentation
Pranger, Casper; van Dinther, Ylona; May, Dave; Le Pourhiet, Laetitia; Gerya, Taras
2016-04-01
into one algorithm. We are working towards presenting the first benchmarked 3D dynamic rupture models as an important step towards seismic cycle modelling of megathrust segmentation in a three-dimensional subduction setting with slow tectonic loading, self consistent fault development, and spontaneous seismicity.
Saro, A.; De Lucia, G.; Borgani, S.; Dolag, K.
2010-08-01
We present a detailed comparison between the galaxy populations within a massive cluster, as predicted by hydrodynamical smoothed particle hydrodynamics (SPH) simulations and by a semi-analytic model (SAM) of galaxy formation. Both models include gas cooling and a simple prescription of star formation, which consists in transforming instantaneously any cold gas available into stars, while neglecting any source of energy feedback. This simplified comparison is thus not meant to be compared with observational data, but is aimed at understanding the level of agreement, at the stripped-down level considered, between two techniques that are widely used to model galaxy formation in a cosmological framework and which present complementary advantages and disadvantages. We find that, in general, galaxy populations from SAMs and SPH have similar statistical properties, in agreement with previous studies. However, when comparing galaxies on an object-by-object basis, we find a number of interesting differences: (i) the star formation histories of the brightest cluster galaxies (BCGs) from SAM and SPH models differ significantly, with the SPH BCG exhibiting a lower level of star formation activity at low redshift, and a more intense and shorter initial burst of star formation with respect to its SAM counterpart; (ii) while all stars associated with the BCG were formed in its progenitors in the SAM used here, this holds true only for half of the final BCG stellar mass in the SPH simulation, the remaining half being contributed by tidal stripping of stars from the diffuse stellar component associated with galaxies accreted on the cluster halo; (iii) SPH satellites can lose up to 90 per cent of their stellar mass at the time of accretion, due to tidal stripping, a process not included in the SAM used in this paper; (iv) in the SPH simulation, significant cooling occurs on the most massive satellite galaxies and this lasts for up to 1 Gyr after accretion. This physical process is
Campelo, Felix; Arnarez, Clement; Marrink, Siewert J; Kozlov, Michael M
2014-06-01
Helfrich model of membrane bending elasticity has been most influential in establishment and development of Soft-Matter Physics of lipid bilayers and biological membranes. Recently, Helfrich theory has been extensively used in Cell Biology to understand the phenomena of shaping, fusion and fission of cellular membranes. The general background of Helfrich theory on the one hand, and the ways of specifying the model parameters on the other, are important for quantitative treatment of particular biologically relevant membrane phenomena. Here we present the origin of Helfrich model within the context of the general Gibbs theory of capillary interfaces, and review the strategies of computing the membrane elastic moduli based on considering a lipid monolayer as a three-dimensional thick layer characterized by trans-monolayer profiles of elastic parameters. We present the results of original computations of these profiles by a state-of-the-art numerical approach.
A model for a liquid membrane separation stage
Energy Technology Data Exchange (ETDEWEB)
NONE
1997-02-01
The coupled mixer-settlers having a common settling zone suggested for use to extract fission products from a conversion reactor blanket are analogues of membrane apparatuses and at a first glance in terms of hydrodynamics do not differ from conventional mixer-settlers. However, the common settling zone complicates both the design solutions and their modelling. For example, different emulsion types can result in mixers and it is not known how this fact will affect phenomena such as separation rates, disperse phase entrainment under conditions close to flooding. For initial studies of the feasibility of the process in principle and the primary optimization of the structure of the transfer scheme one needs to have a model and a program to calculate the statics of a multistage membrane facility of this type.
Interaction of tea tree oil with model and cellular membranes.
Giordani, Cristiano; Molinari, Agnese; Toccacieli, Laura; Calcabrini, Annarica; Stringaro, Annarita; Chistolini, Pietro; Arancia, Giuseppe; Diociaiuti, Marco
2006-07-27
Tea tree oil (TTO) is the essential oil steam-distilled from Melaleuca alternifolia, a species of northern New South Wales, Australia. It exhibits a broad-spectrum antimicrobial activity and an antifungal activity. Only recently has TTO been shown to inhibit the in vitro growth of multidrug resistant (MDR) human melanoma cells. It has been suggested that the effect of TTO on tumor cells could be mediated by its interaction with the plasma membrane, most likely by inducing a reorganization of lipid architecture. In this paper we report biophysical and structural results obtained using simplified planar model membranes (Langmuir films) mimicking lipid "rafts". We also used flow cytometry analysis (FCA) and freeze-fracturing transmission electron microscopy to investigate the effects of TTO on actual MDR melanoma cell membranes. Thermodynamic (compression isotherms and adsorption kinetics) and structural (Brewster angle microscopy) investigation of the lipid monolayers clearly indicates that TTO interacts preferentially with the less ordered DPPC "sea" and that it does not alter the more ordered lipid "rafts". Structural observations, performed by freeze fracturing, confirm that TTO interacts with the MDR melanoma cell plasma membrane. Moreover, experiments performed by FCA demonstrate that TTO does not interfere with the function of the MDR drug transporter P-gp. We therefore propose that the effect exerted on MDR melanoma cells is mediated by the interaction with the fluid DPPC phase, rather than with the more organized "rafts" and that this interaction preferentially influences the ATP-independent antiapoptotic activity of P-gp likely localized outside "rafts".
Simulation modeling of supported lipid membranes - a review.
Hirtz, Michael; Kumar, Naresh; Chi, Lifeng
2014-03-01
Lipid membranes are of great importance for many biological systems and biotechnological applications. One method to gain a profound understanding of the dynamics in lipid membranes and their interaction with other system components is by modeling these systems by computer simulations. Many different approaches have been undertaken in this endeavor that have led to molecular level insights into the underlying mechanisms of several experimental observations and biological processes with an extremely high temporal resolution. As compared to the free-standing lipid bilayers, there are fewer simulation studies addressing the systems of supported lipid membranes. Nevertheless, these have significantly enhanced our understanding of the behavior of lipid layers employed in applications spanning from biosensors to drug delivery and for biological processes such as the breathing cycle of lung surfactants. In this review, we give an account of the state of the art of methods and applications of the simulations of supported lipid bilayers, interfacial membranes at the air/water interface and on solid surfaces.
Ex vivo model for pre-clinical evaluation of dialyzers containing new membranes.
Mahiout, A; Meinhold, H; Jörres, A; Krieg, R; Kessel, M; Tretzel, J; Baurmeister, U
1985-01-01
The ex vivo model which reflects hemodialysis modulating factors during the first twenty minutes of blood membrane interaction, is applicable as a pre-clinical test for new membranes. The biocompatibility of a new cellulosic membrane (MC) proved to be superior to regenerated cellulose and comparable to synthetic membranes such as PAN regarding complement activation.
Self-consistent modeling of radio-frequency plasma generation in stellarators
Moiseenko, V. E.; Stadnik, Yu. S.; Lysoivan, A. I.; Korovin, V. B.
2013-11-01
A self-consistent model of radio-frequency (RF) plasma generation in stellarators in the ion cyclotron frequency range is described. The model includes equations for the particle and energy balance and boundary conditions for Maxwell's equations. The equation of charged particle balance takes into account the influx of particles due to ionization and their loss via diffusion and convection. The equation of electron energy balance takes into account the RF heating power source, as well as energy losses due to the excitation and electron-impact ionization of gas atoms, energy exchange via Coulomb collisions, and plasma heat conduction. The deposited RF power is calculated by solving the boundary problem for Maxwell's equations. When describing the dissipation of the energy of the RF field, collisional absorption and Landau damping are taken into account. At each time step, Maxwell's equations are solved for the current profiles of the plasma density and plasma temperature. The calculations are performed for a cylindrical plasma. The plasma is assumed to be axisymmetric and homogeneous along the plasma column. The system of balance equations is solved using the Crank-Nicholson scheme. Maxwell's equations are solved in a one-dimensional approximation by using the Fourier transformation along the azimuthal and longitudinal coordinates. Results of simulations of RF plasma generation in the Uragan-2M stellarator by using a frame antenna operating at frequencies lower than the ion cyclotron frequency are presented. The calculations show that the slow wave generated by the antenna is efficiently absorbed at the periphery of the plasma column, due to which only a small fraction of the input power reaches the confinement region. As a result, the temperature on the axis of the plasma column remains low, whereas at the periphery it is substantially higher. This leads to strong absorption of the RF field at the periphery via the Landau mechanism.
Toward self-consistent tectono-magmatic numerical model of rift-to-ridge transition
Gerya, Taras; Bercovici, David; Liao, Jie
2017-04-01
Natural data from modern and ancient lithospheric extension systems suggest three-dimensional (3D) character of deformation and complex relationship between magmatism and tectonics during the entire rift-to-ridge transition. Therefore, self-consistent high-resolution 3D magmatic-thermomechanical numerical approaches stand as a minimum complexity requirement for modeling and understanding of this transition. Here we present results from our new high-resolution 3D finite-difference marker-in-cell rift-to-ridge models, which account for magmatic accretion of the crust and use non-linear strain-weakened visco-plastic rheology of rocks that couples brittle/plastic failure and ductile damage caused by grain size reduction. Numerical experiments suggest that nucleation of rifting and ridge-transform patterns are decoupled in both space and time. At intermediate stages, two patterns can coexist and interact, which triggers development of detachment faults, failed rift arms, hyper-extended margins and oblique proto-transforms. En echelon rift patterns typically develop in the brittle upper-middle crust whereas proto-ridge and proto-transform structures nucleate in the lithospheric mantle. These deep proto-structures propagate upward, inter-connect and rotate toward a mature orthogonal ridge-transform patterns on the timescale of millions years during incipient thermal-magmatic accretion of the new oceanic-like lithosphere. Ductile damage of the extending lithospheric mantle caused by grain size reduction assisted by Zenner pinning plays critical role in rift-to-ridge transition by stabilizing detachment faults and transform structures. Numerical results compare well with observations from incipient spreading regions and passive continental margins.
A self-consistent first-principle based approach to model carrier mobility in organic materials
Energy Technology Data Exchange (ETDEWEB)
Meded, Velimir; Friederich, Pascal; Symalla, Franz; Neumann, Tobias; Danilov, Denis; Wenzel, Wolfgang [Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)
2015-12-31
Transport through thin organic amorphous films, utilized in OLEDs and OPVs, has been a challenge to model by using ab-initio methods. Charge carrier mobility depends strongly on the disorder strength and reorganization energy, both of which are significantly affected by the details in environment of each molecule. Here we present a multi-scale approach to describe carrier mobility in which the materials morphology is generated using DEPOSIT, a Monte Carlo based atomistic simulation approach, or, alternatively by molecular dynamics calculations performed with GROMACS. From this morphology we extract the material specific hopping rates, as well as the on-site energies using a fully self-consistent embedding approach to compute the electronic structure parameters, which are then used in an analytic expression for the carrier mobility. We apply this strategy to compute the carrier mobility for a set of widely studied molecules and obtain good agreement between experiment and theory varying over several orders of magnitude in the mobility without any freely adjustable parameters. The work focuses on the quantum mechanical step of the multi-scale workflow, explains the concept along with the recently published workflow optimization, which combines density functional with semi-empirical tight binding approaches. This is followed by discussion on the analytic formula and its agreement with established percolation fits as well as kinetic Monte Carlo numerical approaches. Finally, we skatch an unified multi-disciplinary approach that integrates materials science simulation and high performance computing, developed within EU project MMM@HPC.
Self-consistent Keldysh approach to quenches in the weakly interacting Bose-Hubbard model
Lo Gullo, N.; Dell'Anna, L.
2016-11-01
We present a nonequilibrium Green's-functional approach to study the dynamics following a quench in weakly interacting Bose-Hubbard model (BHM). The technique is based on the self-consistent solution of a set of equations which represents a particular case of the most general set of Hedin's equations for the interacting single-particle Green's function. We use the ladder approximation as a skeleton diagram for the two-particle scattering amplitude useful, through the self-energy in the Dyson equation, for finding the interacting single-particle Green's function. This scheme is then implemented numerically by a parallelized code. We exploit this approach to study the correlation propagation after a quench in the interaction parameter, for one and two dimensions. In particular, we show how our approach is able to recover the crossover from the ballistic to the diffusive regime by increasing the boson-boson interaction. Finally we also discuss the role of a thermal initial state on the dynamics both for one- and two-dimensional BHMs, finding that, surprisingly, at high temperature a ballistic evolution is restored.
Self-consistent model of a solid for the description of lattice and magnetic properties
Balcerzak, T.; Szałowski, K.; Jaščur, M.
2017-03-01
In the paper a self-consistent theoretical description of the lattice and magnetic properties of a model system with magnetoelastic interaction is presented. The dependence of magnetic exchange integrals on the distance between interacting spins is assumed, which couples the magnetic and the lattice subsystem. The framework is based on summation of the Gibbs free energies for the lattice subsystem and magnetic subsystem. On the basis of minimization principle for the Gibbs energy, a set of equations of state for the system is derived. These equations of state combine the parameters describing the elastic properties (relative volume deformation) and the magnetic properties (magnetization changes). The formalism is extensively illustrated with the numerical calculations performed for a system of ferromagnetically coupled spins S=1/2 localized at the sites of simple cubic lattice. In particular, the significant influence of the magnetic subsystem on the elastic properties is demonstrated. It manifests itself in significant modification of such quantities as the relative volume deformation, thermal expansion coefficient or isothermal compressibility, in particular, in the vicinity of the magnetic phase transition. On the other hand, the influence of lattice subsystem on the magnetic one is also evident. It takes, for example, the form of dependence of the critical (Curie) temperature and magnetization itself on the external pressure, which is thoroughly investigated.
How consistent is cloudiness over Canada from satellite observations and modeling data?
Trishchenko, A. P.; Khlopenkov, K.; Latifovic, R.
2004-05-01
Being one of the major modulators of radiation budget and hydrological cycle, clouds are still significant challenge for modeling and satellite retrievals. For example, our analysis shows that for Western Canada the systematic difference in total cloud amounts between NCAR/NCEP Reanalysis-2 and ISCCP reaches 20-30 per cent. Especially difficult are satellite retrievals for Northern climate regions over snow-covered surface and during night-time. To understand better these differences and their influence on earth radiation budget in Northern latitudes, we are attempting to undertake the re-analysis of satellite AVHRR data over Canada using improved data processing and cloud detection algorithms. Details of cloud detection algorithm for day-time and night-time conditions over snow-free and snow-covered surfaces are discussed. Selected results of satellite retrievals for typical summer and winter conditions over Canada are compared to previous analyses, such as ISCCP and Pathfinder projects. Consistency between our cloud retrievals using AVHRR data and those available from MODIS will be also considered.
An internally consistent inverse model to calculate ridge-axis hydrothermal fluxes
Coogan, L. A.; Dosso, S.
2010-12-01
Fluid and chemical fluxes from high-temperature, on-axis, hydrothermal systems at mid-ocean ridges have been estimated in a number of ways. These generally use simple mass balances based on either vent fluid compositions or the compositions of altered sheeted dikes. Here we combine these approaches in an internally consistent model. Seawater is assumed to enter the crust and react with the sheeted dike complex at high temperatures. Major element fluxes for both the rock and fluid are calculated from balanced stoichiometric reactions. These reactions include end-member components of the minerals plagioclase, pyroxene, amphibole, chlorite and epidote along with pure anhydrite, quartz, pyrite, pyrrhotite, titanite, magnetite, ilmenite and ulvospinel and the fluid species H2O, Mg2+, Ca2+, Fe2+, Na+, Si4+, H2S, H+ and H2. Trace element abundances (Li, B, K, Rb, Cs, Sr, Ba, U, Tl, Mn, Cu, Zn, Co, Ni, Pb and Os) and isotopic ratios (Li, B, O, Sr, Tl, Os) are calculated from simple mass balance of a fluid-rock reaction. A fraction of the Cu, Zn, Pb, Co, Ni, Os and Mn in the fluid after fluid-rock reaction is allowed to precipitate during discharge before the fluid reaches the seafloor. S-isotopes are tied to mineralogical reactions involving S-bearing phases. The free parameters in the model are the amounts of each mineralogical reaction that occurs, the amounts of the metals precipitated during discharge, and the water-to-rock ratio. These model parameters, and their uncertainties, are constrained by: (i) mineral abundances and mineral major element compositions in altered dikes from ODP Hole 504B and the Pito and Hess Deep tectonic windows (EPR crust); (ii) changes in dike bulk-rock trace element and isotopic compositions from these locations relative to fresh MORB glass compositions; and (iii) published vent fluid compositions from basalt-hosted high-temperature ridge axis hydrothermal systems. Using a numerical inversion algorithm, the probability density of different
Functional connectivity modeling of consistent cortico-striatal degeneration in Huntington's disease
Directory of Open Access Journals (Sweden)
Imis Dogan
2015-01-01
Full Text Available Huntington's disease (HD is a progressive neurodegenerative disorder characterized by a complex neuropsychiatric phenotype. In a recent meta-analysis we identified core regions of consistent neurodegeneration in premanifest HD in the striatum and middle occipital gyrus (MOG. For early manifest HD convergent evidence of atrophy was most prominent in the striatum, motor cortex (M1 and inferior frontal junction (IFJ. The aim of the present study was to functionally characterize this topography of brain atrophy and to investigate differential connectivity patterns formed by consistent cortico-striatal atrophy regions in HD. Using areas of striatal and cortical atrophy at different disease stages as seeds, we performed task-free resting-state and task-based meta-analytic connectivity modeling (MACM. MACM utilizes the large data source of the BrainMap database and identifies significant areas of above-chance co-activation with the seed-region via the activation-likelihood-estimation approach. In order to delineate functional networks formed by cortical as well as striatal atrophy regions we computed the conjunction between the co-activation profiles of striatal and cortical seeds in the premanifest and manifest stages of HD, respectively. Functional characterization of the seeds was obtained using the behavioral meta-data of BrainMap. Cortico-striatal atrophy seeds of the premanifest stage of HD showed common co-activation with a rather cognitive network including the striatum, anterior insula, lateral prefrontal, premotor, supplementary motor and parietal regions. A similar but more pronounced co-activation pattern, additionally including the medial prefrontal cortex and thalamic nuclei was found with striatal and IFJ seeds at the manifest HD stage. The striatum and M1 were functionally connected mainly to premotor and sensorimotor areas, posterior insula, putamen and thalamus. Behavioral characterization of the seeds confirmed that experiments
Modeling and optimization of membrane lifetime in dead-end ultra filtration
Zondervan, Edwin; Roffel, Brian
2008-01-01
In this paper, a membrane lifetime model is developed and experimentally validated. The lifetime model is based on the Weibull probability density function. The lifetime model can be used to determine an unambiguous characteristic membrane lifetime. Experimental results showed that membrane lifetime
DEFF Research Database (Denmark)
Sogachev, Andrey; Kelly, Mark C.; Leclerc, Monique Y.
2012-01-01
A self-consistent two-equation closure treating buoyancy and plant drag effects has been developed, through consideration of the behaviour of the supplementary equation for the length-scale-determining variable in homogeneous turbulent flow. Being consistent with the canonical flow regimes of gri...
A Consistent Fuzzy Preference Relations Based ANP Model for R&D Project Selection
Directory of Open Access Journals (Sweden)
Chia-Hua Cheng
2017-08-01
Full Text Available In today’s rapidly changing economy, technology companies have to make decisions on research and development (R&D projects investment on a routine bases with such decisions having a direct impact on that company’s profitability, sustainability and future growth. Companies seeking profitable opportunities for investment and project selection must consider many factors such as resource limitations and differences in assessment, with consideration of both qualitative and quantitative criteria. Often, differences in perception by the various stakeholders hinder the attainment of a consensus of opinion and coordination efforts. Thus, in this study, a hybrid model is developed for the consideration of the complex criteria taking into account the different opinions of the various stakeholders who often come from different departments within the company and have different opinions about which direction to take. The decision-making trial and evaluation laboratory (DEMATEL approach is used to convert the cause and effect relations representing the criteria into a visual network structure. A consistent fuzzy preference relations based analytic network process (CFPR-ANP method is developed to calculate the preference-weights of the criteria based on the derived network structure. The CFPR-ANP is an improvement over the original analytic network process (ANP method in that it reduces the problem of inconsistency as well as the number of pairwise comparisons. The combined complex proportional assessment (COPRAS-G method is applied with fuzzy grey relations to resolve conflicts arising from differences in information and opinions provided by the different stakeholders about the selection of the most suitable R&D projects. This novel combination approach is then used to assist an international brand-name company to prioritize projects and make project decisions that will maximize returns and ensure sustainability for the company.
Penetration of alkali atoms throughout a graphene membrane: theoretical modeling.
Boukhvalov, D W; Virojanadara, C
2012-03-07
Theoretical studies of penetration of various alkali atoms (Li, Na, Rb, Cs) throughout a graphene membrane grown on a silicon carbide substrate are reported and compared with recent experimental results. Results of first principles modeling demonstrate a rather low (about 0.8 eV) energy barrier for the formation of temporary defects in the carbon layer required for the penetration of Li at a high concentration of adatoms, a higher (about 2 eV) barrier for Na, and barriers above 4 eV for Rb and Cs. Experiments prove migration of lithium adatoms from the graphene surface to the buffer layer and SiC substrate at room temperature, sodium at 100 °C and impenetrability of the graphene membrane for Rb and Cs. Differences between epitaxial and free-standing graphene for the penetration of alkali ions are also discussed.
Self-consistent Maxwell-Bloch model of quantum-dot photonic-crystal-cavity lasers
Cartar, William; Mørk, Jesper; Hughes, Stephen
2017-08-01
We present a powerful computational approach to simulate the threshold behavior of photonic-crystal quantum-dot (QD) lasers. Using a finite-difference time-domain (FDTD) technique, Maxwell-Bloch equations representing a system of thousands of statistically independent and randomly positioned two-level emitters are solved numerically. Phenomenological pure dephasing and incoherent pumping is added to the optical Bloch equations to allow for a dynamical lasing regime, but the cavity-mediated radiative dynamics and gain coupling of each QD dipole (artificial atom) is contained self-consistently within the model. These Maxwell-Bloch equations are implemented by using Lumerical's flexible material plug-in tool, which allows a user to define additional equations of motion for the nonlinear polarization. We implement the gain ensemble within triangular-lattice photonic-crystal cavities of various length N (where N refers to the number of missing holes), and investigate the cavity mode characteristics and the threshold regime as a function of cavity length. We develop effective two-dimensional model simulations which are derived after studying the full three-dimensional passive material structures by matching the cavity quality factors and resonance properties. We also demonstrate how to obtain the correct point-dipole radiative decay rate from Fermi's golden rule, which is captured naturally by the FDTD method. Our numerical simulations predict that the pump threshold plateaus around cavity lengths greater than N =9 , which we identify as a consequence of the complex spatial dynamics and gain coupling from the inhomogeneous QD ensemble. This behavior is not expected from simple rate-equation analysis commonly adopted in the literature, but is in qualitative agreement with recent experiments. Single-mode to multimode lasing is also observed, depending on the spectral peak frequency of the QD ensemble. Using a statistical modal analysis of the average decay rates, we also
Biophysical studies of cholesterol in unsaturated phospholipid model membranes
Williams, Justin Adam
Cellular membranes contain a staggering diversity of lipids. The lipids are heterogeneously distributed to create regions, or domains, whose physical properties differ from the bulk membrane and play an essential role in modulating the function of resident proteins. Many basic questions pertaining to the formation of these lateral assemblies remain. This research employs model membranes of well-defined composition to focus on the potential role of polyunsaturated fatty acids (PUFAs) and their interaction with cholesterol (chol) in restructuring the membrane environment. Omega-3 (n-3) PUFAs are the main bioactive components of fish oil, whose consumption alleviates a variety of health problems by a molecular mechanism that is unclear. We hypothesize that the incorporation of PUFAs into membrane lipids and the effect they have on molecular organization may be, in part, responsible. Chol is a major constituent in the plasma membrane of mammals. It determines the arrangement and collective properties of neighboring lipids, driving the formation of domains via differential affinity for different lipids. The molecular organization of 1-[2H31]palmitoyl-2-eicosapentaenoylphosphatidylcholine (PEPC-d31) and 1-[2H31]palmitoyl-2-docosahexaenoylphosphatidylcholine (PDPC-d31) in membranes with sphingomyelin (SM) and chol (1:1:1 mol) was compared by solid-state 2H NMR spectroscopy. Eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids are the two major n-3 PUFAs found in fish oil, while PEPC-d31 and PDPC-d31 are phospholipids containing the respective PUFAs at the sn-2 position and a perdeuterated palmitic acid at the sn-1 position. Analysis of spectra recorded as a function of temperature indicates that in both cases, formation of PUFA-rich (less ordered) and SM-rich (more ordered) domains occurred. A surprisingly substantial proportion of PUFA was found to infiltrate the more ordered domain. There was almost twice as much DHA (65%) as EPA (30%). The implication is that n-3
Meso-scale Modeling of Block Copolymers Self-Assembly in Casting Solutions for Membrane Manufacture
Moreno Chaparro, Nicolas
2016-05-01
Isoporous membranes manufactured from diblock copolymer are successfully produced at laboratory scale under controlled conditions. Because of the complex phenomena involved, membrane preparation requires trial and error methodologies to find the optimal conditions, leading to a considerable demand of resources. Experimental insights demonstrate that the self-assembly of the block copolymers in solution has an effect on the final membrane structure. Nevertheless, the complete understanding of these multi-scale phenomena is elusive. Herein we use the coarse-grained method Dissipative Particle Dynamics to study the self-assembly of block copolymers that are used for the preparation of the membranes. To simulate representative time and length scales, we introduce a framework for model reduction of polymer chain representations for dissipative particle dynamics, which preserves the properties governing the phase equilibria. We reduce the number of degrees of freedom by accounting for the correlation between beads in fine-grained models via power laws and the consistent scaling of the simulation parameters. The coarse-graining models are consistent with the experimental evidence, showing a morphological transition of the aggregates as the polymer concentration and solvent affinity change. We show that hexagonal packing of the micelles can occur in solution within different windows of polymer concentration depending on the solvent affinity. However, the shape and size dispersion of the micelles determine the characteristic arrangement. We describe the order of crew-cut micelles using a rigid-sphere approximation and propose different phase parameters that characterize the emergence of monodisperse-spherical micelles in solution. Additionally, we investigate the effect of blending asymmetric diblock copolymers (AB/AC) over the properties of the membranes. We observe that the co-assembly mechanism localizes the AC molecules at the interface of A and B domains, and induces
Wan, Li; Xu, Shixin; Liao, Maijia; Liu, Chun; Sheng, Ping
2014-01-01
In this work, we treat the Poisson-Nernst-Planck (PNP) equations as the basis for a consistent framework of the electrokinetic effects. The static limit of the PNP equations is shown to be the charge-conserving Poisson-Boltzmann (CCPB) equation, with guaranteed charge neutrality within the computational domain. We propose a surface potential trap model that attributes an energy cost to the interfacial charge dissociation. In conjunction with the CCPB, the surface potential trap can cause a surface-specific adsorbed charge layer σ. By defining a chemical potential μ that arises from the charge neutrality constraint, a reformulated CCPB can be reduced to the form of the Poisson-Boltzmann equation, whose prediction of the Debye screening layer profile is in excellent agreement with that of the Poisson-Boltzmann equation when the channel width is much larger than the Debye length. However, important differences emerge when the channel width is small, so the Debye screening layers from the opposite sides of the channel overlap with each other. In particular, the theory automatically yields a variation of σ that is generally known as the "charge regulation" behavior, attendant with predictions of force variation as a function of nanoscale separation between two charged surfaces that are in good agreement with the experiments, with no adjustable or additional parameters. We give a generalized definition of the ζ potential that reflects the strength of the electrokinetic effect; its variations with the concentration of surface-specific and surface-nonspecific salt ions are shown to be in good agreement with the experiments. To delineate the behavior of the electro-osmotic (EO) effect, the coupled PNP and Navier-Stokes equations are solved numerically under an applied electric field tangential to the fluid-solid interface. The EO effect is shown to exhibit an intrinsic time dependence that is noninertial in its origin. Under a step-function applied electric field, a
Extension of CAVS coarse-grained model to phospholipid membranes: The importance of electrostatics.
Shen, Hujun; Deng, Mingsen; Zhang, Yachao
2017-05-15
It is evident from experiment that electrostatic potential (or dipole potential) is positive inside PC or PE lipid bilayers in the absence of ions. MARTINI coarse-grained (CG) model, which has been widely used in simulating physical properties of lipid bilayers, fails to reproduce the positive value for the dipole potential in the membrane interior. Although the total dipole potential can be correctly described by the BMW/MARTINI model, the contribution from the ester dipoles, playing a nontrivial role in the electrostatic potential across lipid membranes, is neglected by this hybrid approach. In the ELBA CG model, the role of the ester dipoles is considered, but it is overweighed because various atomistic models have consistently shown that water is actually the leading contributor of dipole potential. Here, we present a CG approach by combining the BMW-like water model (namely CAVS model) with the ELBA-like lipid model proposed in this work. Our CG model was designed not only to correctly reproduce the positive values for the dipole potential inside PC and PE lipid bilayers but also to properly balance the individual contributions from the ester dipoles and water, surmounting the limitations of current CG models in the calculations of dipole potential. © 2017 Wiley Periodicals, Inc.
Mutual structural effect of bilirubin and model membranes by vibrational circular dichroism.
Novotná, Pavlína; Goncharova, Iryna; Urbanová, Marie
2014-03-01
In this study, vibrational circular dichroism (VCD) spectroscopy was employed for the first time to study the bilirubin (BR) interaction with model membranes and models for membrane proteins. An enantioselective interaction of BR with zwitterionic 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and sphingomyelin (SPM) liposomes was observed by VCD and electronic circular dichroism (ECD) complemented by absorption and fluorescence spectroscopy. The M-form of BR was preferentially recognized in the BR/DMPC system at concentration above 1×10(-4)M, for lower concentrations the P-form of BR was recognized by the DMPC liposomes. The VCD spectra also showed that the SPM liposomes, which represent the main component of nerve cell membrane, were significantly more disturbed by the presence of BR than the DMPC liposomes-a stable association with a strong VCD signal was observed providing the explanations for the supposed BR neurotoxicity. The effect of time and pH on the BR/DMPC or SPM liposome systems was shown to be essential while the effect of temperature in the range of 15-70°C was negligible demonstrating the surprisingly high temperature stability of BR when interacting with the studied membranes. The influence of a membrane protein was tested on a model consisting of poly-l-arginine (PLAG) bound in the α-helical form to the surface of 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) liposomes and sodium dodecyl sulfate micelles. VCD and also ECD spectra showed that a variety of BR diastereoisomers interacted with PLAG in such systems. In a system of PLAG with micelles composed of sodium dodecyl sulfate, the M-form of bound BR was observed. Copyright © 2013 Elsevier B.V. All rights reserved.
Oscillations and multiple steady states in active membrane transport models.
Vieira, F M; Bisch, P M
1994-01-01
The dynamic behavior of some non-linear extensions of the six-state alternating access model for active membrane transport is investigated. We use stoichio-metric network analysis to study the stability of steady states. The bifurcation analysis has been done through standard numerical methods. For the usual six-state model we have proved that there is only one steady state, which is globally asymptotically stable. When we added an autocatalytic step we found self-oscillations. For the competition between a monomer cycle and a dimer cycle, with steps of dimer formation, we have also found self-oscillations. We have also studied models involving the formation of a complex with other molecules. The addition of two steps for formation of a complex of the monomer with another molecule does not alter either the number or the stability of steady states of the basic six-state model. The model which combines the formation of a complex with an autocatalytic step shows both self-oscillations and multiple steady states. The results lead us to conclude that oscillations could be produced by active membrane transport systems if the transport cycle contains a sufficiently large number of steps (six in the present case) and is coupled to at least one autocatalytic reaction,. Oscillations are also predicted when the monomer cycle is coupled to a dimer cycle. In fact, the autocatalytic reaction can be seen as a simplification of the model involving competition between monomer and dimer cycles, which seems to be a more realistic description of biological systems. A self-regulation mechanism of the pumps, related to the multiple stationary states, is expected only for a combined effect of autocatalysis and formation of complexes with other molecules. Within the six-state model this model also leads to oscillation.
Martinez, Guillermo F.; Gupta, Hoshin V.
2011-12-01
Methods to select parsimonious and hydrologically consistent model structures are useful for evaluating dominance of hydrologic processes and representativeness of data. While information criteria (appropriately constrained to obey underlying statistical assumptions) can provide a basis for evaluating appropriate model complexity, it is not sufficient to rely upon the principle of maximum likelihood (ML) alone. We suggest that one must also call upon a "principle of hydrologic consistency," meaning that selected ML structures and parameter estimates must be constrained (as well as possible) to reproduce desired hydrological characteristics of the processes under investigation. This argument is demonstrated in the context of evaluating the suitability of candidate model structures for lumped water balance modeling across the continental United States, using data from 307 snow-free catchments. The models are constrained to satisfy several tests of hydrologic consistency, a flow space transformation is used to ensure better consistency with underlying statistical assumptions, and information criteria are used to evaluate model complexity relative to the data. The results clearly demonstrate that the principle of consistency provides a sensible basis for guiding selection of model structures and indicate strong spatial persistence of certain model structures across the continental United States. Further work to untangle reasons for model structure predominance can help to relate conceptual model structures to physical characteristics of the catchments, facilitating the task of prediction in ungaged basins.
DEFF Research Database (Denmark)
Bendix, Pól Martin
2015-01-01
Current topics include membrane-protein interactions with regard to membrane deformation or curvature sensing by BAR domains. Also, we study the dynamics of membrane tubes of both cells and simple model membrane tubes. Finally, we study membrane phase behavior which has important implications...... for the lateral organization of membranes as wells as for physical properties like bending, permeability and elasticity...
Modelling wastewater treatment in a submerged anaerobic membrane bioreactor.
Spagni, Alessandro; Ferraris, Marco; Casu, Stefania
2015-01-01
Mathematical modelling has been widely applied to membrane bioreactor (MBRs) processes. However, to date, very few studies have reported on the application of the anaerobic digestion model N.1 (ADM1) to anaerobic membrane processes. The aim of this study was to evaluate the applicability of the ADM1 to a submerged anaerobic MBR (SAMBR) treating simulated industrial wastewater composed of cheese whey and sucrose. This study demonstrated that the biological processes involved in SAMBRs can be modelled by using the ADM1. Moreover, the results showed that very few modifications of the parameters describing the ADM1 were required to reasonably fit the experimental data. In particular, adaptation to the specific conditions of the coefficients describing the wastewater characterisation and the reduction of the hydrolysis rate of particulate carbohydrate (khyd,ch) from 0.25 d(-1) (as suggested by the ADM1 for high-rate mesophilic reactors) to 0.13 d(-1) were required to fit the experimental data.
Energy Technology Data Exchange (ETDEWEB)
Ming, Y; Ramaswamy, V; Donner, L J; Phillips, V T; Klein, S A; Ginoux, P A; Horowitz, L H
2005-05-02
This paper describes a self-consistent prognostic cloud scheme that is able to predict cloud liquid water, amount and droplet number (N{sub d}) from the same updraft velocity field, and is suitable for modeling aerosol-cloud interactions in general circulation models (GCMs). In the scheme, the evolution of droplets fully interacts with the model meteorology. An explicit treatment of cloud condensation nuclei (CCN) activation allows the scheme to take into account the contributions to N{sub d} of multiple types of aerosol (i.e., sulfate, organic and sea-salt aerosols) and kinetic limitations of the activation process. An implementation of the prognostic scheme in the Geophysical Fluid Dynamics Laboratory (GFDL) AM2 GCM yields a vertical distribution of N{sub d} characteristic of maxima in the lower troposphere differing from that obtained through diagnosing N{sub d} empirically from sulfate mass concentrations. As a result, the agreement of model-predicted present-day cloud parameters with satellite measurements is improved compared to using diagnosed N{sub d}. The simulations with pre-industrial and present-day aerosols show that the combined first and second indirect effects of anthropogenic sulfate and organic aerosols give rise to a global annual mean flux change of -1.8 W m{sup -2} consisting of -2.0 W m{sup -2} in shortwave and 0.2 W m{sup -2} in longwave, as model response alters cloud field, and subsequently longwave radiation. Liquid water path (LWP) and total cloud amount increase by 19% and 0.6%, respectively. Largely owing to high sulfate concentrations from fossil fuel burning, the Northern Hemisphere mid-latitude land and oceans experience strong cooling. So does the tropical land which is dominated by biomass burning organic aerosol. The Northern/Southern Hemisphere and land/ocean ratios are 3.1 and 1.4, respectively. The calculated annual zonal mean flux changes are determined to be statistically significant, exceeding the model's natural
Requirements for UML and OWL Integration Tool for User Data Consistency Modeling and Testing
DEFF Research Database (Denmark)
Nytun, J. P.; Jensen, Christian Søndergaard; Oleshchuk, V. A.
2003-01-01
. In this paper we analyze requirements for a tool that support integration of UML models and ontologies written in languages like the W3C Web Ontology Language (OWL). The tool can be used in the following way: after loading two legacy models into the tool, the tool user connects them by inserting modeling...
Using open sidewalls for modelling self-consistent lithosphere subduction dynamics
Chertova, M.V.; Geenen, T.; van den Berg, A.; Spakman, W.
2012-01-01
Subduction modelling in regional model domains, in 2-D or 3-D, is commonly performed using closed (impermeable) vertical boundaries. Here we investigate the merits of using open boundaries for 2-D modelling of lithosphere subduction. Our experiments are focused on using open and closed (free
Model for probing membrane-cortex adhesion by micropipette aspiration and fluctuation spectroscopy
Alert, Ricard; Brugués, Jan; Sens, Pierre
2016-01-01
We propose a model for membrane-cortex adhesion which couples membrane deformations, hydrodynamics and kinetics of membrane-cortex ligands. In its simplest form, the model gives explicit predictions for the critical pressure for membrane detachment and for the value of adhesion energy. We show that these quantities exhibit a significant dependence on the active acto-myosin stresses. The model provides a simple framework to access quantitative information on cortical activity by means of micropipette experiments. We also extend the model to incorporate fluctuations and show that detailed information on the stability of membrane-cortex coupling can be obtained by a combination of micropipette aspiration and fluctuation spectroscopy measurements.
Smart, John C.; Ethington, Corinna A.; Umbach, Paul D.
2009-01-01
This study examines the extent to which faculty members in the disparate academic environments of Holland's theory devote different amounts of time in their classes to alternative pedagogical approaches and whether such differences are comparable for those in "consistent" and "inconsistent" environments. The findings show wide variations in the…
Self-consistent tight-binding model of B and N doping in graphene
DEFF Research Database (Denmark)
Pedersen, Thomas Garm; Pedersen, Jesper Goor
2013-01-01
Boron and nitrogen substitutional impurities in graphene are analyzed using a self-consistent tight-binding approach. An analytical result for the impurity Green's function is derived taking broken electron-hole symmetry into account and validated by comparison to numerical diagonalization...
Smart, John C.; Ethington, Corinna A.; Umbach, Paul D.
2009-01-01
This study examines the extent to which faculty members in the disparate academic environments of Holland's theory devote different amounts of time in their classes to alternative pedagogical approaches and whether such differences are comparable for those in "consistent" and "inconsistent" environments. The findings show wide variations in the…
Directory of Open Access Journals (Sweden)
Roy E Barnewall
2012-06-01
Full Text Available Repeated low-level exposures to Bacillus anthracis could occur before or after the remediation of an environmental release. This is especially true for persistent agents such as Bacillus anthracis spores, the causative agent of anthrax. Studies were conducted to examine aerosol methods needed for consistent daily low aerosol concentrations to deliver a low-dose (less than 106 colony forming units (CFU of B. anthracis spores and included a pilot feasibility characterization study, acute exposure study, and a multiple fifteen day exposure study. This manuscript focuses on the state-of-the-science aerosol methodologies used to generate and aerosolize consistent daily low aerosol concentrations and resultant low inhalation doses. The pilot feasibility characterization study determined that the aerosol system was consistent and capable of producing very low aerosol concentrations. In the acute, single day exposure experiment, targeted inhaled doses of 1 x 102, 1 x 103, 1 x 104, and 1 x 105 CFU were used. In the multiple daily exposure experiment, rabbits were exposed multiple days to targeted inhaled doses of 1 x 102, 1 x 103, and 1 x 104 CFU. In all studies, targeted inhaled doses remained fairly consistent from rabbit to rabbit and day to day. The aerosol system produced aerosolized spores within the optimal mass median aerodynamic diameter particle size range to reach deep lung alveoli. Consistency of the inhaled dose was aided by monitoring and recording respiratory parameters during the exposure with real-time plethysmography. Overall, the presented results show that the animal aerosol system was stable and highly reproducible between different studies and multiple exposure days.
Time-dependent cell membrane damage under mechanical tension: Experiments and modeling
Lu, Bo; Chang, Jay Han-Chieh; Tai, Yu-Chong
2011-01-01
This paper reports a study of cancer cell membrane damage during filtration caused by cell membrane tension. The membrane tension was induced when cells were captured on a microfabricated parylene-C filter during the constant-pressure-driven filtration. This work includes both experiments and modeling to explore the underlying biomechanics of the cell membrane damage. The developed model not only agrees with our time-dependent cell damage data, but also fits well with previous results on red ...
Poorasgari, Eskandar; Farsi, Ali; Christensen, Morten Lykkegaard
2016-01-01
Membrane retention of the humic-like substances present in a soluble microbial products (SMP) suspension was studied by using a dead-end filtration system. The SMP suspension was extracted from the sludge of an enhanced biological phosphorus removal-membrane bioreactor. Our results showed that both adsorption and steric retention of the humic-like substances governed their transport through the membrane during the filtration. The adsorption, which followed pseudo-first order kinetics, did not cause substantial decline of permeate flux. The steric retention, on the other hand, formed a gel layer, which in turn led to a major decrease in the flux. The reduction of permeate flux was well predicted by cake filtration theory. Based on the adsorption and the steric retention, a new model was developed for predicting the overall membrane retention of the humic-like substances. The general trend of the modelled overall retention was in partial agreement with the experimental results.
Mathematical modelling of methane steam reforming in a membrane reactor: an isothermal model
Energy Technology Data Exchange (ETDEWEB)
Assaf, E.M. [Sao Paulo Univ., Sao Carlos, SP (Brazil). Dept. de Fisico-Quimica; Jesus, C.D.F.; Assaf, J.M. [Sao Carlos Univ., SP (Brazil). Dept. de Engenharia Quimica
1998-06-01
A mathematical modelling of one-dimensional, stationary and isothermic membrane reactor for methane steam reforming was developed to compare the maximum yield for methane conversion in this reactor with that in a conventional fixed-bed reactor. Fick`s first law was used to describe the mechanism of hydrogen permeation. The variables studied include: reaction temperature, hydrogen feed flow rate and membrane thickness. The results show that the membrane reactor presents a higher methane conversion yield than the conventional fixed-bed reactor. (author) 16 refs., 5 figs., 1 tab.; e-mail: eassaf at iqsc.sc.usp.br; mansur at power.ufscar.br
MATHEMATICAL MODELLING OF METHANE STEAM REFORMING IN A MEMBRANE REACTOR: AN ISOTHERMIC MODEL
Directory of Open Access Journals (Sweden)
E.M. ASSAF
1998-06-01
Full Text Available A mathematical modelling of one-dimensional, stationary and isothermic membrane reactor for methane steam reforming was developed to compare the maximum yield for methane conversion in this reactor with that in a conventional fixed-bed reactor. Fick's first law was used to describe the mechanism of hydrogen permeation. The variables studied include: reaction temperature, hydrogen feed flow rate and membrane thickness. The results show that the membrane reactor presents a higher methane conversion yield than the conventional fixed-bed reactor.
A Delay Model of Multiple-Valued Logic Circuits Consisting of Min, Max, and Literal Operations
Takagi, Noboru
Delay models for binary logic circuits have been proposed and clarified their mathematical properties. Kleene's ternary logic is one of the simplest delay models to express transient behavior of binary logic circuits. Goto first applied Kleene's ternary logic to hazard detection of binary logic circuits in 1948. Besides Kleene's ternary logic, there are many delay models of binary logic circuits, Lewis's 5-valued logic etc. On the other hand, multiple-valued logic circuits recently play an important role for realizing digital circuits. This is because, for example, they can reduce the size of a chip dramatically. Though multiple-valued logic circuits become more important, there are few discussions on delay models of multiple-valued logic circuits. Then, in this paper, we introduce a delay model of multiple-valued logic circuits, which are constructed by Min, Max, and Literal operations. We then show some of the mathematical properties of our delay model.
Physically-consistent wall boundary conditions for the k-ω turbulence model
DEFF Research Database (Denmark)
Fuhrman, David R.; Dixen, Martin; Jacobsen, Niels Gjøl
2010-01-01
A model solving Reynolds-averaged Navier–Stokes equations, coupled with k-v turbulence closure, is used to simulate steady channel flow on both hydraulically smooth and rough beds. Novel experimental data are used as model validation, with k measured directly from all three components of the fluc......A model solving Reynolds-averaged Navier–Stokes equations, coupled with k-v turbulence closure, is used to simulate steady channel flow on both hydraulically smooth and rough beds. Novel experimental data are used as model validation, with k measured directly from all three components...
Antoniu, Gabriel; Cudennec, Loïc; Monnet, Sébastien
2006-01-01
This paper addresses the problem of efficient visualization of shared data within code coupling grid applications. These applications are structured as a set of distributed, autonomous, weakly-coupled codes. We focus on the case where the codes are able to interact using the abstraction of a shared data space. We propose an efficient visualization scheme by adapting the mechanisms used to maintain the data consistency. We introduce a new operation called relaxed read, as an extension to the e...
Recombinant Dengue virus protein NS2B alters membrane permeability in different membrane models
León-Juárez, Moisés; Martínez-Castillo, Macario; Shrivastava, Gaurav; García-Cordero, Julio; Villegas-Sepulveda, Nicolás; Mondragón-Castelán, Mónica; Mondragón-Flores, Ricardo; Cedillo-Barrón, Leticia
2016-01-01
Background One of the main phenomena occurring in cellular membranes during virus infection is a change in membrane permeability. It has been observed that numerous viral proteins can oligomerize and form structures known as viroporins that alter the permeability of membranes. Previous findings have identified such proteins in cells infected with Japanese encephalitis virus (JEV), a member of the same family that Dengue virus (DENV) belongs to (Flaviviridae). In the present work, we investiga...
Mathematical Model of Natural Gas Desulfurization Based on Membrane Absorption
Institute of Scientific and Technical Information of China (English)
Wang Shuli; Ma Jun; Wang Ganyu; Zhou Heng
2014-01-01
Models of mass transfer kinetics combined with mass transfer differential equation and mass transfer resistance equation were established on the basis of double-iflm theory. Mass transfer process of H2S absorption by means of polypro-pylene hydrophobic microporous hollow ifber membrane contactor was simulated using MDEA (N-methyldiethanolamine) as the absorption liquid and corresponding experiments of natural gas desulfurization were performed. The simulation re-sults indicated that the removal rate of hydrogen sulifde showed positive dependence on the absorption liquid concentration and gas pressure. However, the desulfurization rate showed negative dependence on gas lfow. The simulated values were in good agreement with the experimental results. The in-tube concentration of hydrogen sulifde at the same point increased with increase in the gas velocity. Axial concentration of hydrogen sulifde decreased rapidly at the beginning, and the de-crease saw a slowdown during the latter half period. Hydrogen sulifde concentration dropped quickly in the radial direction, and the reduction in the radial direction was weakened with the increase of axial length due to the gradual reduction of hy-drogen sulifde concentration along the tube. The desulfurization rate under given operating conditions can be predicted by this model, and the theoretical basis for membrane module design can also be provided.
Woitke, P.; Min, M.; Pinte, C.; Thi, W. -F; Kamp, I.; Rab, C.; Anthonioz, F.; Antonellini, S.; Baldovin-Saavedra, C.; Carmona, A.; Dominik, C.; Dionatos, O.; Greaves, J.; Güdel, M.; Ilee, J. D.; Liebhart, A.; Ménard, F.; Rigon, L.; Waters, L. B. F. M.; Aresu, G.; Meijerink, R.; Spaans, M.
2016-01-01
We propose a set of standard assumptions for the modelling of Class II and III protoplanetary disks, which includes detailed continuum radiative transfer, thermo-chemical modelling of gas and ice, and line radiative transfer from optical to cm wavelengths. The first paper of this series focuses on
O. Fovet; L. Ruiz; M. Hrachowitz; M. Faucheux; C. Gascuel-Odoux
2015-01-01
While most hydrological models reproduce the general flow dynamics, they frequently fail to adequately mimic system-internal processes. In particular, the relationship between storage and discharge, which often follows annual hysteretic patterns in shallow hard-rock aquifers, is rarely considered in modelling studies. One main reason is that catchment storage is...
Vertical Equating: An Empirical Study of the Consistency of Thurstone and Rasch Model Approaches.
Schratz, Mary K.
To explore the appropriateness of the Rasch model for the vertical equating of a multi-level, multi-form achievement test series, both the Rasch model and the traditional Thurstone procedures were applied to the Listening Comprehension subtest scores of the Stanford Achievement Test. Two adjacent levels of these tests were administered in 1981 to…
Woitke, P.; Min, M.; Pinte, C.; Thi, W. -F; Kamp, I.; Rab, C.; Anthonioz, F.; Antonellini, S.; Baldovin-Saavedra, C.; Carmona, A.; Dominik, C.; Dionatos, O.; Greaves, J.; Güdel, M.; Ilee, J. D.; Liebhart, A.; Ménard, F.; Rigon, L.; Waters, L. B. F. M.; Aresu, G.; Meijerink, R.; Spaans, M.
2016-01-01
We propose a set of standard assumptions for the modelling of Class II and III protoplanetary disks, which includes detailed continuum radiative transfer, thermo-chemical modelling of gas and ice, and line radiative transfer from optical to cm wavelengths. The first paper of this series focuses on t
Self-consistent modelling of hot plasmas within non-extensive Tsallis' thermostatistics
Pain, Jean-Christophe; Gilleron, Franck
2011-01-01
A study of the effects of non-extensivity on the modelling of atomic physics in hot dense plasmas is proposed within Tsallis' statistics. The electronic structure of the plasma is calculated through an average-atom model based on the minimization of the non-extensive free energy.
CONSISTENT USE OF THE KALMAN FILTER IN CHEMICAL TRANSPORT MODELS (CTMS) FOR DEDUCING EMISSIONS
Past research has shown that emissions can be deduced using observed concentrations of a chemical, a Chemical Transport Model (CTM), and the Kalman filter in an inverse modeling application. An expression was derived for the relationship between the "observable" (i.e., the con...
DEFF Research Database (Denmark)
Keck, Rolf-Erik; Veldkamp, Dick; Wedel-Heinen, Jens Jakob
This thesis describes the further development and validation of the dynamic meandering wake model for simulating the flow field and power production of wind farms operating in the atmospheric boundary layer (ABL). The overall objective of the conducted research is to improve the modelling capabil...... intensity. This power drop is comparable to measurements from the North Hoyle and OWEZ wind farms....
Martin, Kelly J; Picioreanu, Cristian; Nerenberg, Robert
2013-09-01
A two-dimensional, particle-based biofilm model coupled with mass transport and computational fluid dynamics was developed to simulate autotrophic denitrification in a spiral-wound membrane biofilm reactor (MBfR), where hydrogen is supplied via hollow-fiber membrane fabric. The spiral-wound configuration consists of alternating layers of plastic spacer net and membrane fabric that create rows of flow channels, with the top and bottom walls comprised of membranes. The transversal filaments of the spacer partially obstruct the channel flow, producing complex mixing and shear patterns that require multidimensional representation. This study investigated the effect of hydrogen and nitrate concentrations, as well as spacer configuration, on biofilm development and denitrification fluxes. The model results indicate that the cavity spacer filaments, which rest on the bottom membranes, cause uneven biofilm growth. Most biofilm resided on the bottom membranes, only in the wake of the filaments where low shear zones formed. In this way, filament configuration may help achieve a desired biofilm thickness. For the conditions tested in this study, the highest nitrate fluxes were attained by minimizing the filament diameter and maximizing the filament spacing. This lowered the shear stress at the top membranes, allowing for more biofilm growth. For the scenarios studied, biomass limitation at the top membranes hindered performance more significantly than diffusion limitation in the thick biofilms at the bottom membranes. The results also highlighted the importance of two-dimensional modeling to capture uneven biofilm growth on a substratum with geometrical complexity. Copyright © 2013 Elsevier Ltd. All rights reserved.
Consistent approach to edge detection using multiscale fuzzy modeling analysis in the human retina
Directory of Open Access Journals (Sweden)
Mehdi Salimian
2012-06-01
Full Text Available Today, many widely used image processing algorithms based on human visual system have been developed. In this paper a smart edge detection based on modeling the performance of simple and complex cells and also modeling and multi-scale image processing in the primary visual cortex is presented. A way to adjust the parameters of Gabor filters (mathematical models of simple cells And the proposed non-linear threshold response are presented in order to Modeling of simple and complex cells. Also, due to multi-scale modeling analysis conducted in the human retina, in the proposed algorithm, all edges of the small and large structures with high precision are detected and localized. Comparing the results of the proposed method for a reliable database with conventional methods shows the higher Performance (about 4-13% and reliability of the proposed method in the detection and localization of edge.
Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie
2014-10-07
Constraint-based models are currently the only methodology that allows the study of metabolism at the whole-genome scale. Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point arithmetic. Here we introduce MONGOOSE, a toolbox for analysing the structure of constraint-based metabolic models in exact arithmetic. We apply MONGOOSE to the analysis of 98 existing metabolic network models and find that the biomass reaction is surprisingly blocked (unable to sustain non-zero flux) in nearly half of them. We propose a principled approach for unblocking these reactions and extend it to the problems of identifying essential and synthetic lethal reactions and minimal media. Our structural insights enable a systematic study of constraint-based metabolic models, yielding a deeper understanding of their possibilities and limitations.
Dynamic Model of the High Temperature Proton Exchange Membrane Fuel Cell Stack Temperature
DEFF Research Database (Denmark)
Andreasen, Søren Juhl; Kær, Søren Knudsen
2009-01-01
consists of a prototype cathode air cooled 30 cell HTPEM fuel cell stack developed at the Institute of Energy Technology at Aalborg University. This fuel cell stack uses PEMEAS Celtec P-1000 membranes and runs on pure hydrogen in a dead-end anode configuration with a purge valve. The cooling of the stack...... elements for start-up, heat conduction through stack insulation, cathode air convection, and heating of the inlet gases in the manifold. Various measurements are presented to validate the model predictions of the stack temperatures....
Jacques, Kevin; Sabariego, Ruth,; Geuzaine, Christophe; GYSELINCK Johan
2015-01-01
This paper deals with the implementation of an energy-consistent ferromagnetic hysteresis model in 2D finite element computations. This vector hysteresis model relies on a strong thermodynamic foundation and ensures the closure of minor hysteresis loops. The model accuracy can be increased by controlling the number of intrinsic cell components while parameters can be easily fitted on common material measurements. Here, the native h-based material model is inverted using the Newton-Raphson met...
Modeling impermeable membranes as acoustic filters for biomedical applications.
Goenaga, Miguel A; Juan, Eduardo J
2006-01-01
The main purpose of this research project was to explore a mathematical expression that could be used by medical device designers to appropriately select impermeable membranes to isolate acoustic transducers from water, dust, earwax or other foreign material. The sound transmission properties of various types of impermeable membranes were analytically evaluated and compared to experimental measurements. Computer simulations were also performed to estimate the effects of three key membrane parameters: thickness (h), density (p) and sound speed (c), on the membrane's overall acoustic response. Results indicated that membrane thickness and density affect sound transmission the most. Membrane sound speed had minimal effect on sound transmission.
Towards Automatic Validation and Healing of Citygml Models for Geometric and Semantic Consistency
Alam, N.; Wagner, D.; Wewetzer, M.; von Falkenhausen, J.; Coors, V.; Pries, M.
2013-09-01
A steadily growing number of application fields for large 3D city models have emerged in recent years. Like in many other domains, data quality is recognized as a key factor for successful business. Quality management is mandatory in the production chain nowadays. Automated domain-specific tools are widely used for validation of business-critical data but still common standards defining correct geometric modeling are not precise enough to define a sound base for data validation of 3D city models. Although the workflow for 3D city models is well-established from data acquisition to processing, analysis and visualization, quality management is not yet a standard during this workflow. Processing data sets with unclear specification leads to erroneous results and application defects. We show that this problem persists even if data are standard compliant. Validation results of real-world city models are presented to demonstrate the potential of the approach. A tool to repair the errors detected during the validation process is under development; first results are presented and discussed. The goal is to heal defects of the models automatically and export a corrected CityGML model.
Gamayunov, K. V.; Khazanov, G. V.; Liemohn, M. W.; Fok, M.-C.; Ridley, A. J.
2009-01-01
Further development of our self-consistent model of interacting ring current (RC) ions and electromagnetic ion cyclotron (EMIC) waves is presented. This model incorporates large scale magnetosphere-ionosphere coupling and treats self-consistently not only EMIC waves and RC ions, but also the magnetospheric electric field, RC, and plasmasphere. Initial simulations indicate that the region beyond geostationary orbit should be included in the simulation of the magnetosphere-ionosphere coupling. Additionally, a self-consistent description, based on first principles, of the ionospheric conductance is required. These initial simulations further show that in order to model the EMIC wave distribution and wave spectral properties accurately, the plasmasphere should also be simulated self-consistently, since its fine structure requires as much care as that of the RC. Finally, an effect of the finite time needed to reestablish a new potential pattern throughout the ionosphere and to communicate between the ionosphere and the equatorial magnetosphere cannot be ignored.
Energy Technology Data Exchange (ETDEWEB)
Keck, R.-E.
2013-07-15
This thesis describes the further development and validation of the dynamic meandering wake model for simulating the flow field and power production of wind farms operating in the atmospheric boundary layer (ABL). The overall objective of the conducted research is to improve the modelling capability of the dynamics wake meandering model to a level where it is sufficiently mature to be applied in industrial applications and for an augmentation of the IEC-standard for wind turbine wake modelling. Based on a comparison of capabilities of the dynamic wake meandering model to the requirement of the wind industry, four areas were identified as high prioritizations for further research: 1. the turbulence distribution in a single wake. 2. multiple wake deficits and build-up of turbulence over a row of turbines. 3. the effect of the atmospheric boundary layer on wake turbulence and wake deficit evolution. 4. atmospheric stability effects on wake deficit evolution and meandering. The conducted research is to a large extent based on detailed wake investigations and reference data generated through computational fluid dynamics simulations, where the wind turbine rotor has been represented by an actuator line model. As a consequence, part of the research also targets the performance of the actuator line model when generating wind turbine wakes in the atmospheric boundary layer. Highlights of the conducted research: 1. A description is given for using the dynamic wake meandering model as a standalone flow-solver for the velocity and turbulence distribution, and power production in a wind farm. The performance of the standalone implementation is validated against field data, higher-order computational fluid dynamics models, as well as the most common engineering wake models in the wind industry. 2. The EllipSys3D actuator line model, including the synthetic methods used to model atmospheric boundary layer shear and turbulence, is verified for modelling the evolution of wind
The Twente lower extremity model : consistent dynamic simulation of the human locomotor apparatus
Klein Horsman, Martijn Dirk
2007-01-01
Orthopedic interventions such as tendon transfers have shown to be successful in the treatment of gait disorders. Still, in many cases dysfunctions remained or worsened. To assist clinicians, an interactive tool will be useful that allows evaluation of if-then scenarios with respect to treatment methods. Comprehensive musculoskeletal models have shown a high potential to serve as such a tool. By varying anatomical model parameters, alterations in anatomy due to surgery can be implemented. Inv...
Toward a self-consistent, high-resolution absolute plate motion model for the Pacific
Wessel, Paul; Harada, Yasushi; Kroenke, Loren W.
2006-03-01
The hot spot hypothesis postulates that linear volcanic trails form as lithospheric plates move relative to stationary or slowly moving plumes. Given geometry and ages from several trails, one can reconstruct absolute plate motions (APM) that provide valuable information about past and present tectonism, paleogeography, and volcanism. Most APM models have been designed by fitting small circles to coeval volcanic chain segments and determining stage rotation poles, opening angles, and time intervals. Unlike relative plate motion (RPM) models, such APM models suffer from oversimplicity, self-inconsistencies, inadequate fits to data, and lack of rigorous uncertainty estimates; in addition, they work only for fixed hot spots. Newer methods are now available that overcome many of these limitations. We present a technique that provides high-resolution APM models derived from stationary or moving hot spots (given prescribed paths). The simplest model assumes stationary hot spots, and an example of such a model is presented. Observations of geometry and chronology on the Pacific plate appear well explained by this type of model. Because it is a one-plate model, it does not discriminate between hot spot drift or true polar wander as explanations for inferred paleolatitudes from the Emperor chain. Whether there was significant relative motion within the hot spots under the Pacific plate during the last ˜70 m.y. is difficult to quantify, given the paucity and geological uncertainty of age determinations. Evidence in support of plume drift appears limited to the period before the 47 Ma Hawaii-Emperor Bend and, apart from the direct paleolatitude determinations, may have been somewhat exaggerated.
2012-06-13
daily low-dose Bacillus anthracis spore inhalation exposures in the rabbit model Roy E. Barnewall 1, Jason E. Comer 1, Brian D. Miller 1, BradfordW...multiple exposure days. Keywords: Bacillus anthracis , inhalation exposures, low-dose, subchronic exposures, spores, anthrax, aerosol system INTRODUCTION... Bacillus Anthracis Spore Inhalation Exposures In The Rabbit Model 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d
Directory of Open Access Journals (Sweden)
Jiateng Guo
2016-02-01
Full Text Available Three-dimensional (3D geological models are important representations of the results of regional geological surveys. However, the process of constructing 3D geological models from two-dimensional (2D geological elements remains difficult and is not necessarily robust. This paper proposes a method of migrating from 2D elements to 3D models. First, the geological interfaces were constructed using the Hermite Radial Basis Function (HRBF to interpolate the boundaries and attitude data. Then, the subsurface geological bodies were extracted from the spatial map area using the Boolean method between the HRBF surface and the fundamental body. Finally, the top surfaces of the geological bodies were constructed by coupling the geological boundaries to digital elevation models. Based on this workflow, a prototype system was developed, and typical geological structures (e.g., folds, faults, and strata were simulated. Geological modes were constructed through this workflow based on realistic regional geological survey data. The model construction process was rapid, and the resulting models accorded with the constraints of the original data. This method could also be used in other fields of study, including mining geology and urban geotechnical investigations.
A consistent hamiltonian treatment of the Thirring-Wess and Schwinger model in the covariant gauge
Martinovič, L'ubomír
2014-06-01
We present a unified hamiltonian treatment of the massless Schwinger model in the Landau gauge and of its non-gauge counterpart-the Thirring-Wess (TW) model. The operator solution of the Dirac equation has the same structure in the both models and identifies free fields as the true dynamical degrees of freedom. The coupled boson field equations (Maxwell and Proca, respectively) can also be solved exactly. The Hamiltonan in Fock representation is derived for the TW model and its diagonalization via a Bogoliubov transformation is suggested. The axial anomaly is derived in both models directly from the operator solution using a hermitian version of the point-splitting regularization. A subtlety of the residual gauge freedom in the covariant gauge is shown to modify the usual definition of the "gauge-invariant" currents. The consequence is that the axial anomaly and the boson mass generation are restricted to the zero-mode sector only. Finally, we discuss quantization of the unphysical gauge-field components in terms of ghost modes in an indefinite-metric space and sketch the next steps within the finite-volume treatment necessary to fully reveal physical content of the model in our hamiltonian formulation.
DEFF Research Database (Denmark)
Fedorova, Marina; Sin, Gürkan; Gani, Rafiqul
2013-01-01
This work focuses on development of computer-aided modeling framework. The framework is a knowledge-based system that is built on a generic modeling language and structured based on workflows for different general modeling tasks. The overall objective of this work is to support the model developers...... and users to generate and test models systematically, efficiently and reliably. In this way, development of products and processes can be faster, cheaper and very efficient. In this contribution, as part of the framework a generic modeling template for the systematic derivation of problem specific catalytic...... membrane fixed bed models is developed. The application of the modeling template is highlighted with a case study related to the modeling of a catalytic membrane reactor coupling dehydrogenation of ethylbenzene with hydrogenation of nitrobenzene....
Hachem, Walid; Mestre, Xavier; Najim, Jamal; Vallet, Pascal
2011-01-01
In array processing, a common problem is to estimate the angles of arrival of $K$ deterministic sources impinging on an array of $M$ antennas, from $N$ observations of the source signal, corrupted by gaussian noise. The problem reduces to estimate a quadratic form (called "localization function") of a certain projection matrix related to the source signal empirical covariance matrix. Recently, a new subspace estimation method (called "G-MUSIC") has been proposed, in the context where the number of available samples $N$ is of the same order of magnitude than the number of sensors $M$. In this context, the traditional subspace methods tend to fail because the empirical covariance matrix of the observations is a poor estimate of the source signal covariance matrix. The G-MUSIC method is based on a new consistent estimator of the localization function in the regime where $M$ and $N$ tend to $+\\infty$ at the same rate. However, the consistency of the angles estimator was not adressed. The purpose of this paper is ...
Pervaporation : membranes and models for the dehydration of ethanol
Spitzen, Johannes Wilhelmus Franciscus
1988-01-01
In this thesis the dehydration of ethanol/water mixtures by pervaporation using homogeneous membranes is studied. Both the general transport mechanism as well as the development of highly selective membranes for ethanol/water separation are investigated.
Woitke, P; Pinte, C; Thi, W -F; Kamp, I; Rab, C; Anthonioz, F; Antonellini, S; Baldovin-Saavedra, C; Carmona, A; Dominik, C; Dionatos, O; Greaves, J; Güdel, M; Ilee, J D; Liebhart, A; Ménard, F; Rigon, L; Waters, L B F M; Aresu, G; Meijerink, R; Spaans, M
2015-01-01
We propose a set of standard assumptions for the modelling of Class II and III protoplanetary disks, which includes detailed continuum radiative transfer, thermo-chemical modelling of gas and ice, and line radiative transfer from optical to cm wavelengths. We propose new standard dust opacities for disk models, we present a simplified treatment of PAHs sufficient to reproduce the PAH emission features, and we suggest using a simple treatment of dust settling. We roughly adjust parameters to obtain a model that predicts typical Class II T Tauri star continuum and line observations. We systematically study the impact of each model parameter (disk mass, disk extension and shape, dust settling, dust size and opacity, gas/dust ratio, etc.) on all continuum and line observables, in particular on the SED, mm-slope, continuum visibilities, and emission lines including [OI] 63um, high-J CO lines, (sub-)mm CO isotopologue lines, and CO fundamental ro-vibrational lines. We find that evolved dust properties (large grains...
Consistent parameter fixing in the quark-meson model with vacuum fluctuations
Carignano, Stefano; Buballa, Michael; Elkamhawy, Wael
2016-08-01
We revisit the renormalization prescription for the quark-meson model in an extended mean-field approximation, where vacuum quark fluctuations are included. At a given cutoff scale the model parameters are fixed by fitting vacuum quantities, typically including the sigma-meson mass mσ and the pion decay constant fπ. In most publications the latter is identified with the expectation value of the sigma field, while for mσ the curvature mass is taken. When quark loops are included, this prescription is however inconsistent, and the correct identification involves the renormalized pion decay constant and the sigma pole mass. In the present article we investigate the influence of the parameter-fixing scheme on the phase structure of the model at finite temperature and chemical potential. Despite large differences between the model parameters in the two schemes, we find that in homogeneous matter the effect on the phase diagram is relatively small. For inhomogeneous phases, on the other hand, the choice of the proper renormalization prescription is crucial. In particular, we show that if renormalization effects on the pion decay constant are not considered, the model does not even present a well-defined renormalized limit when the cutoff is sent to infinity.
Shell Effect of Superheavy Nuclei in Self-consistent Mean-Field Models
Institute of Scientific and Technical Information of China (English)
RENZhong-Zhou; TAIFei; XUChang; CHENDing-Han; ZHANGHu-Yong; CAIXiang-Zhou; SHENWen-Qing
2004-01-01
We analyze in detail the numerical results of superheavy nuclei in deformed relativistic mean-field model and deformed Skyrme-Hartree-Fock model. The common points and differences of both models are systematically compared and discussed. Their consequences on the stability of superheavy nuclei are explored and explained. The theoreticalresults are compared with new data of superheavy nuclei from GSI and from Dubna and reasonable agreement is reached.Nuclear shell effect in superheavy region is analyzed and discussed. The spherical shell effect disappears in some cases due to the appearance of deformation or superdeformation in the ground states of nuclei, where valence nucleons occupysignificantly the intruder levels of nuclei. It is shown for the first time that the significant occupation of vaJence nucleons on the intruder states plays an important role for the ground state properties of superheavy nuclei. Nuclei are stable in the deformed or superdeformed configurations. We further point out that one cannot obtain the octupole deformation of even-even nuclei in the present relativistic mean-field model with the σ，ω and ρ mesons because there is no parityviolating interaction and the conservation of parity of even-even nuclei is a basic assumption of the present relativistic mean-field model.
Directory of Open Access Journals (Sweden)
Ravie c. Muniyandi
2010-01-01
Full Text Available Problem statement: Membrane computing formalism has provided better modeling capabilities for biological systems in comparison to conventional mathematical models. Model checking could be used to reason about the biological system in detail and with precision by verifying formally whether membrane computing model meets the properties of the system. Approach: This study was carried to investigate the preservation of properties of two biological systems that had been modeled and simulated in membrane computing by a method of model checking using PRISM. The two biological systems were prey-predator population and signal processing in the legend-receptor networks of protein TGF-ß. Results: The model checking of membrane computing model of the biological systems with five different properties showed that the properties of the biological systems could be preserved in the membrane computing model. Conclusion: Membrane computing model not only provides a better approach in representing and simulating a biological system but also able to sustain the basic properties of the system.
Consistent treatment of viscoelastic effects at junctions in one-dimensional blood flow models
Müller, Lucas O.; Leugering, Günter; Blanco, Pablo J.
2016-06-01
While the numerical discretization of one-dimensional blood flow models for vessels with viscoelastic wall properties is widely established, there is still no clear approach on how to couple one-dimensional segments that compose a network of viscoelastic vessels. In particular for Voigt-type viscoelastic models, assumptions with regard to boundary conditions have to be made, which normally result in neglecting the viscoelastic effect at the edge of vessels. Here we propose a coupling strategy that takes advantage of a hyperbolic reformulation of the original model and the inherent information of the resulting system. We show that applying proper coupling conditions is fundamental for preserving the physical coherence and numerical accuracy of the solution in both academic and physiologically relevant cases.
A Hybrid EAV-Relational Model for Consistent and Scalable Capture of Clinical Research Data.
Khan, Omar; Lim Choi Keung, Sarah N; Zhao, Lei; Arvanitis, Theodoros N
2014-01-01
Many clinical research databases are built for specific purposes and their design is often guided by the requirements of their particular setting. Not only does this lead to issues of interoperability and reusability between research groups in the wider community but, within the project itself, changes and additions to the system could be implemented using an ad hoc approach, which may make the system difficult to maintain and even more difficult to share. In this paper, we outline a hybrid Entity-Attribute-Value and relational model approach for modelling data, in light of frequently changing requirements, which enables the back-end database schema to remain static, improving the extensibility and scalability of an application. The model also facilitates data reuse. The methods used build on the modular architecture previously introduced in the CURe project.
Mason, R Preston; Jacob, Robert F; Shrivastava, Sandeep; Sherratt, Samuel C R; Chattopadhyay, Amitabha
2016-12-01
Cholesterol crystalline domains characterize atherosclerotic membranes, altering vascular signaling and function. Omega-3 fatty acids reduce membrane lipid peroxidation and subsequent cholesterol domain formation. We evaluated non-peroxidation-mediated effects of eicosapentaenoic acid (EPA), other TG-lowering agents, docosahexaenoic acid (DHA), and other long-chain fatty acids on membrane fluidity, bilayer width, and cholesterol domain formation in model membranes. In membranes prepared at 1.5:1 cholesterol-to-phospholipid (C/P) mole ratio (creating pre-existing domains), EPA, glycyrrhizin, arachidonic acid, and alpha linolenic acid promoted the greatest reductions in cholesterol domains (by 65.5%, 54.9%, 46.8%, and 45.2%, respectively) compared to controls; other treatments had modest effects. EPA effects on cholesterol domain formation were dose-dependent. In membranes with 1:1 C/P (predisposing domain formation), DHA, but not EPA, dose-dependently increased membrane fluidity. DHA also induced cholesterol domain formation without affecting temperature-induced changes in-bilayer unit cell periodicity relative to controls (d-space; 57Å-55Å over 15-30°C). Together, these data suggest simultaneous formation of distinct cholesterol-rich ordered domains and cholesterol-poor disordered domains in the presence of DHA. By contrast, EPA had no effect on cholesterol domain formation and produced larger d-space values relative to controls (60Å-57Å; pmembrane bilayer width, membrane fluidity, and cholesterol crystalline domain formation; suggesting omega-3 fatty acids with differing chain length or unsaturation may differentially influence membrane lipid dynamics and structural organization as a result of distinct phospholipid/sterol interactions.
Derivation of adsorption parameters for nanofiltration membranes using a 1-pK Basic Stern model
de Lint, W.B.S.; Benes, Nieck Edwin; Higler, A.P.; Verweij, H.
2002-01-01
The ion retention and flux of nanofiltration (NF) membranes are to a large extent determined by the membrane surface charge. This surface charge is in turn strongly influenced by adsorption of ions from the solution onto the membrane material. A 1-pK adsorption model with a Basic Stern electrostatic
Institute of Scientific and Technical Information of China (English)
Mohamed BALAH; Hamdan Naser AL-GHAMEDY
2004-01-01
The paper presents an approach for the formulation of general laminated shells based on a third order shear deformation theory. These shells undergo finite (unlimited in size) rotations and large overall motions but with small strains. A singularity-free parametrization of the rotation field is adopted. The constitutive equations, derived with respect to laminate curvilinear coordinates,are applicable to shell elements with an arbitrary number of orthotropic layers and where the material principal axes can vary from layer to layer. A careful consideration of the consistent linearization procedure pertinent to the proposed parametrization of finite rotations leads to symmetric tangent stiffness matrices. The matrix formulation adopted here makes it possible to implement the present formulation within the framework of the finite element method as a straightforward task.
Polymer Electrolyte Membrane (PEM) Fuel Cells Modeling and Optimization
Zhang, Zhuqian; Wang, Xia; Shi, Zhongying; Zhang, Xinxin; Yu, Fan
2006-11-01
Performance of polymer electrolyte membrane (PEM) fuel cells is dependent on operating parameters and designing parameters. Operating parameters mainly include temperature, pressure, humidity and the flow rate of the inlet reactants. Designing parameters include reactants distributor patterns and dimensions, electrodes dimensions, and electrodes properties such as porosity, permeability and so on. This work aims to investigate the effects of various designing parameters on the performance of PEM fuel cells, and the optimum values will be determined under a given operating condition.A three-dimensional steady-state electrochemical mathematical model was established where the mass, fluid and thermal transport processes are considered as well as the electrochemical reaction. A Powell multivariable optimization algorithm will be applied to investigate the optimum values of designing parameters. The objective function is defined as the maximum potential of the electrolyte fluid phase at the membrane/cathode interface at a typical value of the cell voltage. The robustness of the optimum design of the fuel cell under different cell potentials will be investigated using a statistical sensitivity analysis. By comparing with the reference case, the results obtained here provide useful tools for a better design of fuel cells.
Modelling and Fabrication of Micro-SOFC Membrane Structure
Directory of Open Access Journals (Sweden)
Brigita ABAKEVIČIENĖ
2014-06-01
Full Text Available Fabrication process of micro-SOFC membrane structure using the bulk micromachining of silicon technique with SiO2 and Si3N4 sacrificial layers is presented in this study. The process involves back side photolithography, magnetron sputtering of platinum thin films, thermal evaporation of YSZ electrolyte, deep reactive ion etching of silicon, and, finally, release of free-standing membrane using CF4/O2 plasma etching.X-ray analysis shows the cubic phase of YSZ electrolyte and platinum electrodes. Modelling of normal stress distribution in the micro-SOFC structure with the Si3N4 sacrificial layer shows that at high temperatures the substrate expands less than the coating, causing tensile stresses in the substrate area next to the coating and compressive stresses in the coating, as the substrate material has a lower coefficient of thermal expansion than the layered Pt/YSZ/Pt coating. DOI: http://dx.doi.org/10.5755/j01.ms.20.2.5585
Modelling and Fabrication of Micro-SOFC Membrane Structure
Directory of Open Access Journals (Sweden)
Brigita ABAKEVIČIENĖ
2014-06-01
Full Text Available Fabrication process of micro-SOFC membrane structure using the bulk micromachining of silicon technique with SiO2 and Si3N4 sacrificial layers is presented in this study. The process involves back side photolithography, magnetron sputtering of platinum thin films, thermal evaporation of YSZ electrolyte, deep reactive ion etching of silicon, and, finally, release of free-standing membrane using CF4/O2 plasma etching.X-ray analysis shows the cubic phase of YSZ electrolyte and platinum electrodes. Modelling of normal stress distribution in the micro-SOFC structure with the Si3N4 sacrificial layer shows that at high temperatures the substrate expands less than the coating, causing tensile stresses in the substrate area next to the coating and compressive stresses in the coating, as the substrate material has a lower coefficient of thermal expansion than the layered Pt/YSZ/Pt coating. DOI: http://dx.doi.org/10.5755/j01.ms.20.2.5585
Membrane trafficking in the yeast Saccharomyces cerevisiae model.
Feyder, Serge; De Craene, Johan-Owen; Bär, Séverine; Bertazzi, Dimitri L; Friant, Sylvie
2015-01-09
The yeast Saccharomyces cerevisiae is one of the best characterized eukaryotic models. The secretory pathway was the first trafficking pathway clearly understood mainly thanks to the work done in the laboratory of Randy Schekman in the 1980s. They have isolated yeast sec mutants unable to secrete an extracellular enzyme and these SEC genes were identified as encoding key effectors of the secretory machinery. For this work, the 2013 Nobel Prize in Physiology and Medicine has been awarded to Randy Schekman; the prize is shared with James Rothman and Thomas Südhof. Here, we present the different trafficking pathways of yeast S. cerevisiae. At the Golgi apparatus newly synthesized proteins are sorted between those transported to the plasma membrane (PM), or the external medium, via the exocytosis or secretory pathway (SEC), and those targeted to the vacuole either through endosomes (vacuolar protein sorting or VPS pathway) or directly (alkaline phosphatase or ALP pathway). Plasma membrane proteins can be internalized by endocytosis (END) and transported to endosomes where they are sorted between those targeted for vacuolar degradation and those redirected to the Golgi (recycling or RCY pathway). Studies in yeast S. cerevisiae allowed the identification of most of the known effectors, protein complexes, and trafficking pathways in eukaryotic cells, and most of them are conserved among eukaryotes.
Membrane Trafficking in the Yeast Saccharomyces cerevisiae Model
Directory of Open Access Journals (Sweden)
Serge Feyder
2015-01-01
Full Text Available The yeast Saccharomyces cerevisiae is one of the best characterized eukaryotic models. The secretory pathway was the first trafficking pathway clearly understood mainly thanks to the work done in the laboratory of Randy Schekman in the 1980s. They have isolated yeast sec mutants unable to secrete an extracellular enzyme and these SEC genes were identified as encoding key effectors of the secretory machinery. For this work, the 2013 Nobel Prize in Physiology and Medicine has been awarded to Randy Schekman; the prize is shared with James Rothman and Thomas Südhof. Here, we present the different trafficking pathways of yeast S. cerevisiae. At the Golgi apparatus newly synthesized proteins are sorted between those transported to the plasma membrane (PM, or the external medium, via the exocytosis or secretory pathway (SEC, and those targeted to the vacuole either through endosomes (vacuolar protein sorting or VPS pathway or directly (alkaline phosphatase or ALP pathway. Plasma membrane proteins can be internalized by endocytosis (END and transported to endosomes where they are sorted between those targeted for vacuolar degradation and those redirected to the Golgi (recycling or RCY pathway. Studies in yeast S. cerevisiae allowed the identification of most of the known effectors, protein complexes, and trafficking pathways in eukaryotic cells, and most of them are conserved among eukaryotes.
Acidic phospholipid bicelles: a versatile model membrane system.
Struppe, J; Whiles, J A; Vold, R R
2000-01-01
With the aim of establishing acidic bicellar solutions as a useful membrane model system, we have used deuterium NMR spectroscopy to investigate the properties of dimyristoyl/dihexanoylphosphatidylcholine (DMPC/DHPC) bicelles containing 25% (w/w in H(2)O) of either dimyristoylphosphatidylserine (DMPS) or dimyristoylphosphatidylglycerol (DMPG). The addition of the acidic lipid component to this lyotropic liquid crystalline system reduces its range of stability because of poor miscibility of the two dimyristoylated phospholipids. Compared to the neutral bicelles, which are stable at pH 4 to pH 7, acidic bicelles are stable only from pH 5.5 to pH 7. Solid-state deuterium NMR analysis of d(54)-DMPC showed similar ordering in neutral and acidic bicelles. Fully deuterated DMPS or DMPG is ordered in a way similar to that of DMPC. Study of the binding of the myristoylated N-terminal 14-residue peptide mu-GSSKSKPKDPSQRR from pp60(nu-src) to both neutral and acidic bicelles shows the utility of these novel membrane mimetics. PMID:10620292
Defective membrane remodeling in neuromuscular diseases: insights from animal models.
Directory of Open Access Journals (Sweden)
Belinda S Cowling
Full Text Available Proteins involved in membrane remodeling play an essential role in a plethora of cell functions including endocytosis and intracellular transport. Defects in several of them lead to human diseases. Myotubularins, amphiphysins, and dynamins are all proteins implicated in membrane trafficking and/or remodeling. Mutations in myotubularin, amphiphysin 2 (BIN1, and dynamin 2 lead to different forms of centronuclear myopathy, while mutations in myotubularin-related proteins cause Charcot-Marie-Tooth neuropathies. In addition to centronuclear myopathy, dynamin 2 is also mutated in a dominant form of Charcot-Marie-Tooth neuropathy. While several proteins from these different families are implicated in similar diseases, mutations in close homologues or in the same protein in the case of dynamin 2 lead to diseases affecting different tissues. This suggests (1 a common molecular pathway underlying these different neuromuscular diseases, and (2 tissue-specific regulation of these proteins. This review discusses the pathophysiology of the related neuromuscular diseases on the basis of animal models developed for proteins of the myotubularin, amphiphysin, and dynamin families. A better understanding of the common mechanisms between these neuromuscular disorders will lead to more specific health care and therapeutic approaches.
National Research Council Canada - National Science Library
Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie
2014-01-01
.... Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point arithmetic...
Modeling of etch profile evolution including wafer charging effects using self consistent ion fluxes
Energy Technology Data Exchange (ETDEWEB)
Hoekstra, R.J.; Kushner, M.J. [Univ. of Illinois, Urbana, IL (United States). Dept. of Electrical and Computer Engineering
1996-12-31
As high density plasma reactors become more predominate in industry, the need has intensified for computer aided design tools which address both equipment issues such as ion flux uniformity onto the water and process issues such etch feature profile evolution. A hierarchy of models has been developed to address these issues with the goal of producing a comprehensive plasma processing design capability. The Hybrid Plasma Equipment Model (HPEM) produces ion and neutral densities, and electric fields in the reactor. The Plasma Chemistry Monte Carlo Model (PCMC) determines the angular and energy distributions of ion and neutral fluxes to the wafer using species source functions, time dependent bulk electric fields, and sheath potentials from the HPEM. These fluxes are then used by the Monte Carlo Feature Profile Model (MCFP) to determine the time evolution of etch feature profiles. Using this hierarchy, the effects of physical modifications of the reactor, such as changing wafer clamps or electrode structures, on etch profiles can be evaluated. The effects of wafer charging on feature evolution are examined by calculating the fields produced by the charge deposited by ions and electrons within the features. The effect of radial variations and nonuniformity in angular and energy distribution of the reactive fluxes on feature profiles and feature charging will be discussed for p-Si etching in inductively-coupled plasma (ICP) sustained in chlorine gas mixtures. The effects of over- and under-wafer topography on etch profiles will also be discussed.
Application of a Mass-Consistent Wind Model to Chinook Windstorms
1988-06-01
Meteor., 6, 837--344. Endlich, R. M., F. L. Ludwig, C. M. Bhunralkar, and M. A. Estoque , 1380: A practical method for estimating wind character34szics at...Project 8349, Menlo Park, CA. 94025. Endlich, R. M., F. L. Ludwig, C. M. Bhunralkar, and M. A. Estoque , 1982: A diagnostic model for estimating winds
Baraffe, [No Value; Alibert, Y; Mera, D; Charbrier, G; Beaulieu, JP
1998-01-01
We have computed stellar evolutionary models for stars in a mass range characteristic of Cepheid variables (3
Hovakeemian, Sara G; Liu, Runhui; Gellman, Samuel H; Heerklotz, Heiko
2015-09-14
Most antimicrobial peptides act upon target microorganisms by permeabilizing their membranes. The mode of action is often assessed by vesicle leakage experiments that use model membranes, with the assumption that biological activity correlates with the permeabilization of the lipid bilayer. The current work aims to extend the interpretation of vesicle leakage results and examine the correlation between vesicle leakage and antimicrobial activity. To this end, we used a lifetime-based leakage assay with calcein-loaded vesicles to study the membrane permeabilizing properties of a novel antifungal polymer poly-NM, two of its analogs, and a series of detergents. In conjunction, the biological activities of these compounds against Candida albicans were assessed and correlated with data from vesicle leakage. Poly-NM induces all-or-none leakage in polar yeast lipid vesicles at the polymer's MIC, 3 μg mL(-1). At this and higher concentrations, complete leakage after an initial lag time was observed. Concerted activity tests imply that this polymer acts independently of the detergent octyl glucoside (OG) for both vesicle leakage and activity against C. albicans spheroplasts. In addition, poly-NM was found to have negligible activity against zwitterionic vesicles and red blood cells. Our results provide a consistent, detailed picture of the mode of action of poly-NM: this polymer induces membrane leakage by electrostatic lipid clustering. In contrast, poly-MM:CO, a nylon-3 polymer comprised of both cationic and hydrophobic segments, seems to act by a different mechanism that involves membrane asymmetry stress. Vesicle leakage for this polymer is transient (limited to nylon-3 polymers we examined act via similar mechanisms; it is surprising that their mechanisms are so distinct. Some, but not all mechanisms of vesicle permeabilization allow for antimicrobial activity.
Partitioning of amino-acid analogues in a five-slab membrane model
Energy Technology Data Exchange (ETDEWEB)
Sengupta, D [University of Heidelberg; Smith, Jeremy C [ORNL; Ullmann, G. Matthias [University of Bayreuth
2008-09-01
The positional preferences of the twenty amino-acid residues in a phospholipid bilayer are investigated by calculating the solvation free energy of the corresponding side chain analogues using a five-slab continuum electrostatic model. The side-chain analogues of the aromatic residues tryptophan and tyrosine are found to partition in the head-group region, due to compensation between the increase of the non-polar component of the solvation free energy at the boundary with the aqueous region and the decrease in the electrostatic component. The side chain analogue of phenylalanine differs from the other aromatic molecules by being able to partition in both the head-group region and the membrane core. This finding is consistent with experimental findings of the position of phenylalanine in membrane helices. Interestingly, the charged side-chain analogues of arginine and lysine are shown to prefer the head-group region in an orientation that allows the charged moiety to interact with the aqueous layer. The orientation adopted is similar to the 'snorkelling' effect seen in lysine and arginine residues in membrane helices. In contrast, the preference of the charged side-chain analogues of histidine (protonated) and aspartate (deprotonated) for the aqueous layer is shown to be due to a steep decrease in the electrostatic component of the solvation free energy at the boundary to the aqueous region. The calculations allow an understanding of the origins of side chain positioning in membranes and are thus useful in understanding membrane-protein:lipid thermodynamics.
Multiscale modeling of droplet interface bilayer membrane networks.
Freeman, Eric C; Farimani, Amir B; Aluru, Narayana R; Philen, Michael K
2015-11-01
Droplet interface bilayer (DIB) networks are considered for the development of stimuli-responsive membrane-based materials inspired by cellular mechanics. These DIB networks are often modeled as combinations of electrical circuit analogues, creating complex networks of capacitors and resistors that mimic the biomolecular structures. These empirical models are capable of replicating data from electrophysiology experiments, but these models do not accurately capture the underlying physical phenomena and consequently do not allow for simulations of material functionalities beyond the voltage-clamp or current-clamp conditions. The work presented here provides a more robust description of DIB network behavior through the development of a hierarchical multiscale model, recognizing that the macroscopic network properties are functions of their underlying molecular structure. The result of this research is a modeling methodology based on controlled exchanges across the interfaces of neighboring droplets. This methodology is validated against experimental data, and an extension case is provided to demonstrate possible future applications of droplet interface bilayer networks.
Woitke, P.; Min, M.; Pinte, C.; Thi, W.-F.; Kamp, I.; Rab, C.; Anthonioz, F.; Antonellini, S.; Baldovin-Saavedra, C.; Carmona, A.; Dominik, C.; Dionatos, O.; Greaves, J.; Güdel, M.; Ilee, J. D.; Liebhart, A.; Ménard, F.; Rigon, L.; Waters, L. B. F. M.; Aresu, G.; Meijerink, R.; Spaans, M.
2016-02-01
We propose a set of standard assumptions for the modelling of Class II and III protoplanetary disks, which includes detailed continuum radiative transfer, thermo-chemical modelling of gas and ice, and line radiative transfer from optical to cm wavelengths. The first paper of this series focuses on the assumptions about the shape of the disk, the dust opacities, dust settling, and polycyclic aromatic hydrocarbons (PAHs). In particular, we propose new standard dust opacities for disk models, we present a simplified treatment of PAHs in radiative equilibrium which is sufficient to reproduce the PAH emission features, and we suggest using a simple yet physically justified treatment of dust settling. We roughly adjust parameters to obtain a model that predicts continuum and line observations that resemble typical multi-wavelength continuum and line observations of Class II T Tauri stars. We systematically study the impact of each model parameter (disk mass, disk extension and shape, dust settling, dust size and opacity, gas/dust ratio, etc.) on all mainstream continuum and line observables, in particular on the SED, mm-slope, continuum visibilities, and emission lines including [OI] 63 μm, high-J CO lines, (sub-)mm CO isotopologue lines, and CO fundamental ro-vibrational lines. We find that evolved dust properties, i.e. large grains, often needed to fit the SED, have important consequences for disk chemistry and heating/cooling balance, leading to stronger near- to far-IR emission lines in general. Strong dust settling and missing disk flaring have similar effects on continuum observations, but opposite effects on far-IR gas emission lines. PAH molecules can efficiently shield the gas from stellar UV radiation because of their strong absorption and negligible scattering opacities in comparison to evolved dust. The observable millimetre-slope of the SED can become significantly more gentle in the case of cold disk midplanes, which we find regularly in our T Tauri models
Zervas, P. L.; Sarimveis, H.; Palyvos, J. A.; Markatos, N. C. G.
Hybrid renewable energy systems are expected to become competitive to conventional power generation systems in the near future and, thus, optimization of their operation is of particular interest. In this work, a hybrid power generation system is studied consisting of the following main components: photovoltaic array (PV), electrolyser, metal hydride tanks, and proton exchange membrane fuel cells (PEMFC). The key advantage of the hybrid system compared to stand-alone photovoltaic systems is that it can store efficiently solar energy by transforming it to hydrogen, which is the fuel supplied to the fuel cell. However, decision making regarding the operation of this system is a rather complicated task. A complete framework is proposed for managing such systems that is based on a rolling time horizon philosophy.
Genome scale models of yeast: towards standardized evaluation and consistent omic integration
DEFF Research Database (Denmark)
Sanchez, Benjamin J.; Nielsen, Jens
2015-01-01
Genome scale models (GEMs) have enabled remarkable advances in systems biology, acting as functional databases of metabolism, and as scaffolds for the contextualization of high-throughput data. In the case of Saccharomyces cerevisiae (budding yeast), several GEMs have been published...... and are currently used for metabolic engineering and elucidating biological interactions. Here we review the history of yeast's GEMs, focusing on recent developments. We study how these models are typically evaluated, using both descriptive and predictive metrics. Additionally, we analyze the different ways...... in which all levels of omics data (from gene expression to flux) have been integrated in yeast GEMs. Relevant conclusions and current challenges for both GEM evaluation and omic integration are highlighted....
Advancing Nucleosynthesis in Self-consistent, Multidimensional Models of Core-Collapse Supernovae
Harris, J Austin; Chertkow, Merek A; Bruenn, Stephen W; Lentz, Eric J; Messer, O E Bronson; Mezzacappa, Anthony; Blondin, John M; Marronetti, Pedro; Yakunin, Konstantin N
2014-01-01
We investigate core-collapse supernova (CCSN) nucleosynthesis in polar axisymmetric simulations using the multidimensional radiation hydrodynamics code CHIMERA. Computational costs have traditionally constrained the evolution of the nuclear composition in CCSN models to, at best, a 14-species $\\alpha$-network. Such a simplified network limits the ability to accurately evolve detailed composition, neutronization and the nuclear energy generation rate. Lagrangian tracer particles are commonly used to extend the nuclear network evolution by incorporating more realistic networks in post-processing nucleosynthesis calculations. Limitations such as poor spatial resolution of the tracer particles, estimation of the expansion timescales, and determination of the "mass-cut" at the end of the simulation impose uncertainties inherent to this approach. We present a detailed analysis of the impact of these uncertainties on post-processing nucleosynthesis calculations and implications for future models.
Thermodynamically consistent modeling for dissolution/growth of bubbles in an incompressible solvent
Bothe, Dieter
2014-01-01
We derive mathematical models of the elementary process of dissolution/growth of bubbles in a liquid under pressure control. The modeling starts with a fully compressible version, both for the liquid and the gas phase so that the entropy principle can be easily evaluated. This yields a full PDE system for a compressible two-phase fluid with mass transfer of the gaseous species. Then the passage to an incompressible solvent in the liquid phase is discussed, where a carefully chosen equation of state for the liquid mixture pressure allows for a limit in which the solvent density is constant. We finally provide a simplification of the PDE system in case of a dilute solution.
Directory of Open Access Journals (Sweden)
Sam Walcott
2015-11-01
Full Text Available Muscle contracts due to ATP-dependent interactions of myosin motors with thin filaments composed of the proteins actin, troponin, and tropomyosin. Contraction is initiated when calcium binds to troponin, which changes conformation and displaces tropomyosin, a filamentous protein that wraps around the actin filament, thereby exposing myosin binding sites on actin. Myosin motors interact with each other indirectly via tropomyosin, since myosin binding to actin locally displaces tropomyosin and thereby facilitates binding of nearby myosin. Defining and modeling this local coupling between myosin motors is an open problem in muscle modeling and, more broadly, a requirement to understanding the connection between muscle contraction at the molecular and macro scale. It is challenging to directly observe this coupling, and such measurements have only recently been made. Analysis of these data suggests that two myosin heads are required to activate the thin filament. This result contrasts with a theoretical model, which reproduces several indirect measurements of coupling between myosin, that assumes a single myosin head can activate the thin filament. To understand this apparent discrepancy, we incorporated the model into stochastic simulations of the experiments, which generated simulated data that were then analyzed identically to the experimental measurements. By varying a single parameter, good agreement between simulation and experiment was established. The conclusion that two myosin molecules are required to activate the thin filament arises from an assumption, made during data analysis, that the intensity of the fluorescent tags attached to myosin varies depending on experimental condition. We provide an alternative explanation that reconciles theory and experiment without assuming that the intensity of the fluorescent tags varies.
Self-Consistent, Axisymmetric Two-Integral Models of Elliptical Galaxies with Embedded Nuclear Discs
Bosch, van den, PPJ Paul; de, Zeeuw, W.
1996-01-01
Recently, observations with the Hubble Space Telescope have revealed small stellar discs embedded in the nuclei of a number of ellipticals and S0s. In this paper we construct two-integral axisymmetric models for such systems. We calculate the even part of the phase-space distribution function, and specify the odd part by means of a simple parameterization. We investigate the photometric as well as the kinematic signatures of nuclear discs, including their velocity profiles (VPs), and study th...
Energy regeneration model of self-consistent field of electron beams into electric power*
Kazmin, B. N.; Ryzhov, D. R.; Trifanov, I. V.; Snezhko, A. A.; Savelyeva, M. V.
2016-04-01
We consider physic-mathematical models of electric processes in electron beams, conversion of beam parameters into electric power values and their transformation into users’ electric power grid (onboard spacecraft network). We perform computer simulation validating high energy efficiency of the studied processes to be applied in the electric power technology to produce the power as well as electric power plants and propulsion installation in the spacecraft.
Flood damage: a model for consistent, complete and multipurpose scenarios
Directory of Open Access Journals (Sweden)
S. Menoni
2016-12-01
implemented in ex post damage assessments, also with the objective of better programming financial resources that will be needed for these types of events in the future. On the other hand, integrated interpretations of flood events are fundamental to adapting and optimizing flood mitigation strategies on the basis of thorough forensic investigation of each event, as corroborated by the implementation of the model in a case study.
A consistent model for leptogenesis, dark matter and the IceCube signal
Energy Technology Data Exchange (ETDEWEB)
Fiorentin, M. Re [School of Physics and Astronomy, University of Southampton,SO17 1BJ Southampton (United Kingdom); Niro, V. [Departamento de Física Teórica, Universidad Autónoma de Madrid,Cantoblanco, E-28049 Madrid (Spain); Instituto de Física Teórica UAM/CSIC,Calle Nicolás Cabrera 13-15, Cantoblanco, E-28049 Madrid (Spain); Fornengo, N. [Dipartimento di Fisica, Università di Torino,via P. Giuria, 1, 10125 Torino (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Torino,via P. Giuria, 1, 10125 Torino (Italy)
2016-11-04
We discuss a left-right symmetric extension of the Standard Model in which the three additional right-handed neutrinos play a central role in explaining the baryon asymmetry of the Universe, the dark matter abundance and the ultra energetic signal detected by the IceCube experiment. The energy spectrum and neutrino flux measured by IceCube are ascribed to the decays of the lightest right-handed neutrino N{sub 1}, thus fixing its mass and lifetime, while the production of N{sub 1} in the primordial thermal bath occurs via a freeze-in mechanism driven by the additional SU(2){sub R} interactions. The constraints imposed by IceCube and the dark matter abundance allow nonetheless the heavier right-handed neutrinos to realize a standard type-I seesaw leptogenesis, with the B−L asymmetry dominantly produced by the next-to-lightest neutrino N{sub 2}. Further consequences and predictions of the model are that: the N{sub 1} production implies a specific power-law relation between the reheating temperature of the Universe and the vacuum expectation value of the SU(2){sub R} triplet; leptogenesis imposes a lower bound on the reheating temperature of the Universe at 7×10{sup 9} GeV. Additionally, the model requires a vanishing absolute neutrino mass scale m{sub 1}≃0.
Consistent negative response of US crops to high temperatures in observations and crop models
Schauberger, Bernhard; Archontoulis, Sotirios; Arneth, Almut; Balkovic, Juraj; Ciais, Philippe; Deryng, Delphine; Elliott, Joshua; Folberth, Christian; Khabarov, Nikolay; Müller, Christoph; Pugh, Thomas A. M.; Rolinski, Susanne; Schaphoff, Sibyll; Schmid, Erwin; Wang, Xuhui; Schlenker, Wolfram; Frieler, Katja
2017-04-01
High temperatures are detrimental to crop yields and could lead to global warming-driven reductions in agricultural productivity. To assess future threats, the majority of studies used process-based crop models, but their ability to represent effects of high temperature has been questioned. Here we show that an ensemble of nine crop models reproduces the observed average temperature responses of US maize, soybean and wheat yields. Each day above 30°C diminishes maize and soybean yields by up to 6% under rainfed conditions. Declines observed in irrigated areas, or simulated assuming full irrigation, are weak. This supports the hypothesis that water stress induced by high temperatures causes the decline. For wheat a negative response to high temperature is neither observed nor simulated under historical conditions, since critical temperatures are rarely exceeded during the growing season. In the future, yields are modelled to decline for all three crops at temperatures above 30°C. Elevated CO2 can only weakly reduce these yield losses, in contrast to irrigation.
Consistent negative response of US crops to high temperatures in observations and crop models
Schauberger, Bernhard; Archontoulis, Sotirios; Arneth, Almut; Balkovic, Juraj; Ciais, Philippe; Deryng, Delphine; Elliott, Joshua; Folberth, Christian; Khabarov, Nikolay; Müller, Christoph; Pugh, Thomas A. M.; Rolinski, Susanne; Schaphoff, Sibyll; Schmid, Erwin; Wang, Xuhui; Schlenker, Wolfram; Frieler, Katja
2017-01-01
High temperatures are detrimental to crop yields and could lead to global warming-driven reductions in agricultural productivity. To assess future threats, the majority of studies used process-based crop models, but their ability to represent effects of high temperature has been questioned. Here we show that an ensemble of nine crop models reproduces the observed average temperature responses of US maize, soybean and wheat yields. Each day >30 °C diminishes maize and soybean yields by up to 6% under rainfed conditions. Declines observed in irrigated areas, or simulated assuming full irrigation, are weak. This supports the hypothesis that water stress induced by high temperatures causes the decline. For wheat a negative response to high temperature is neither observed nor simulated under historical conditions, since critical temperatures are rarely exceeded during the growing season. In the future, yields are modelled to decline for all three crops at temperatures >30 °C. Elevated CO2 can only weakly reduce these yield losses, in contrast to irrigation.
Jha, Sanjeev Kumar
2013-01-01
A downscaling approach based on multiple-point geostatistics (MPS) is presented. The key concept underlying MPS is to sample spatial patterns from within training images, which can then be used in characterizing the relationship between different variables across multiple scales. The approach is used here to downscale climate variables including skin surface temperature (TSK), soil moisture (SMOIS), and latent heat flux (LH). The performance of the approach is assessed by applying it to data derived from a regional climate model of the Murray-Darling basin in southeast Australia, using model outputs at two spatial resolutions of 50 and 10 km. The data used in this study cover the period from 1985 to 2006, with 1985 to 2005 used for generating the training images that define the relationships of the variables across the different spatial scales. Subsequently, the spatial distributions for the variables in the year 2006 are determined at 10 km resolution using the 50 km resolution data as input. The MPS geostatistical downscaling approach reproduces the spatial distribution of TSK, SMOIS, and LH at 10 km resolution with the correct spatial patterns over different seasons, while providing uncertainty estimates through the use of multiple realizations. The technique has the potential to not only bridge issues of spatial resolution in regional and global climate model simulations but also in feature sharpening in remote sensing applications through image fusion, filling gaps in spatial data, evaluating downscaled variables with available remote sensing images, and aggregating/disaggregating hydrological and groundwater variables for catchment studies.
Fioc, M; Fioc, Michel; Rocca-Volmerange, Brigitte
1999-01-01
We provide here the documentation of the new version of the spectral evolution model PEGASE. PEGASE computes synthetic spectra of galaxies in the UV to near-IR range from 0 to 20 Gyr, for a given stellar IMF and evolutionary scenario (star formation law, infall, galactic winds). The radiation emitted by stars from the main sequence to the pre-supernova or white dwarf stage is calculated, as well as the extinction by dust. A simple modeling of the nebular emission (continuum and lines) is also proposed. PEGASE may be used to model starbursts as well as old galaxies. The main improvements of PEGASE.2 relative to PEGASE.1 (Fioc & Rocca-Volmerange 1997) are the following: (1)The stellar evolutionary tracks of the Padova group for metallicities between 0.0001 and 0.1 have been included; (2)The evolution of the metallicity of the interstellar medium (ISM) due to SNII, SNIa and AGB stars is followed. Stars are formed with the same metallicity as the ISM (instead of a solar metallicity in PEGASE.1), providing thu...
The Bioenvironmental modeling of Bahar city based on Climate-consistent Architecture
Directory of Open Access Journals (Sweden)
Parna Kazemian
2014-07-01
Full Text Available The identification of the climate of a particularplace and the analysis of the climatic needs in terms of human comfort and theuse of construction materials is one of the prerequisites of aclimate-consistent design. In studies on climate and weather, usingillustrative reports, first a picture of the state of climate is offered. Then,based on the obtained results, the range of changes is determined, and thecause-effect relationships at different scales are identified. Finally, by ageneral examination of the obtained information, on the one hand, the range ofchanges is identified, and, on the other hand, their practical uses in thefuture are selected. In the present paper, the bioclimatic conditions of Baharcity, according to the 29-year-long statistics of the synoptic station between1976 and 2005 was examined, using Olgyay and Mahoney indexes. It should beadded that, because of the short distance between Bahar and Hamedan, they havea single synoptic station. The results indicate that Bahar city has dominantlycold weather during most of the months. Therefore, based on the implications ofeach method, the principles of the suggestive architectural designing can beintegrated and improved in order to achieve sustainable development.
A self-consistent impedance method for electromagnetic surface impedance modeling
Thiel, David V.; Mittra, Raj
2001-01-01
A two-dimensional, self-consistent impedance method has been derived and used to calculate the electromagnetic surface impedance above buried objects at very low frequencies. The earth half space is discretized using an array of impedance elements. Inhomogeneities in the complex permittivity of the earth are reflected in variations in these impedance elements. The magnetic field is calculated for each cell in the solution space using a difference equation derived from Faraday's and Ampere's laws. It is necessary to include an air layer above the earth's surface to allow the scattered magnetic field to be calculated at the surface. The source field is applied above the earth's surface as a Dirichlet boundary condition, whereas the Neumann condition is employed at all other boundaries in the solution space. This, in turn, enables users to use both finite and infinite magnetic field sources as excitations. The technique is shown to be computationally efficient and yields reasonably accurate results when applied to a number of one- and two-dimensional earth structures with a known surface impedance distribution.
Self-consistent physical parameters for 5 intermediate-age SMC stellar clusters from CMD modelling
Dias, Bruno; Barbuy, Beatriz; Santiago, Basilio; Ortolani, Sergio; Balbinot, Eduardo
2013-01-01
Context. Stellar clusters in the Small Magellanic Cloud (SMC) are useful probes to study the chemical and dynamical evolution of this neighbouring dwarf galaxy, enabling inspection of a large period covering over 10 Gyr. Aims. The main goals of this work are the derivation of age, metallicity, distance modulus, reddening, core radius and central density profile for six sample clusters, in order to place them in the context of the Small Cloud evolution. The studied clusters are: AM 3, HW 1, HW 34, HW 40, Lindsay 2, and Lindsay 3, where HW 1, HW 34, and Lindsay 2 are studied for the first time. Methods. Optical Colour-Magnitude Diagrams (V, B-V CMDs) and radial density profiles were built from images obtained with the 4.1m SOAR telescope, reaching V~23. The determination of structural parameters were carried out applying King profile fitting. The other parameters were derived in a self-consistent way by means of isochrone fitting, which uses the likelihood statistics to identify the synthetic CMDs that best rep...
A self-consistent 3D model of fluctuations in the helium-ionizing background
Davies, Frederick B.; Furlanetto, Steven R.; Dixon, Keri L.
2017-03-01
Large variations in the effective optical depth of the He II Lyα forest have been observed at z ≳ 2.7, but the physical nature of these variations is uncertain: either the Universe is still undergoing the process of He II reionization, or the Universe is highly ionized but the He II-ionizing background fluctuates significantly on large scales. In an effort to build upon our understanding of the latter scenario, we present a novel model for the evolution of ionizing background fluctuations. Previous models have assumed the mean free path of ionizing photons to be spatially uniform, ignoring the dependence of that scale on the local ionization state of the intergalactic medium (IGM). This assumption is reasonable when the mean free path is large compared to the average distance between the primary sources of He II-ionizing photons, ≳ L⋆ quasars. However, when this is no longer the case, the background fluctuations become more severe, and an accurate description of the average propagation of ionizing photons through the IGM requires additionally accounting for the fluctuations in opacity. We demonstrate the importance of this effect by constructing 3D semi-analytic models of the helium-ionizing background from z = 2.5-3.5 that explicitly include a spatially varying mean free path of ionizing photons. The resulting distribution of effective optical depths at large scales in the He II Lyα forest is very similar to the latest observations with HST/COS at 2.5 ≲ z ≲ 3.5.
Consistency of different tropospheric models and mapping functions for precise GNSS processing
Graffigna, Victoria; Hernández-Pajares, Manuel; García-Rigo, Alberto; Gende, Mauricio
2017-04-01
The TOmographic Model of the IONospheric electron content (TOMION) software implements a simultaneous precise geodetic and ionospheric modeling, which can be used to test new approaches for real-time precise GNSS modeling (positioning, ionospheric and tropospheric delays, clock errors, among others). In this work, the software is used to estimate the Zenith Tropospheric Delay (ZTD) emulating real time and its performance is evaluated through a comparative analysis with a built-in GIPSY estimation and IGS final troposphere product, exemplified in a two-day experiment performed in East Australia. Furthermore, the troposphere mapping function was upgraded from Niell to Vienna approach. On a first scenario, only forward processing was activated and the coordinates of the Wide Area GNSS network were loosely constrained, without fixing the carrier phase ambiguities, for both reference and rover receivers. On a second one, precise point positioning (PPP) was implemented, iterating for a fixed coordinates set for the second day. Comparisons between TOMION, IGS and GIPSY estimates have been performed and for the first one, IGS clocks and orbits were considered. The agreement with GIPSY results seems to be 10 times better than with the IGS final ZTD product, despite having considered IGS products for the computations. Hence, the subsequent analysis was carried out with respect to the GIPSY computations. The estimates show a typical bias of 2cm for the first strategy and of 7mm for PPP, in the worst cases. Moreover, Vienna mapping function showed in general a fairly better agreement than Niell one for both strategies. The RMS values' were found to be around 1cm for all studied situations, with a slightly fitter performance for the Niell one. Further improvement could be achieved for such estimations with coefficients for the Vienna mapping function calculated from raytracing as well as integrating meteorological comparative parameters.
Rate of strong consistency of quasi maximum likelihood estimate in generalized linear models
Institute of Scientific and Technical Information of China (English)
YUE Li; CHEN Xiru
2004-01-01
Under the assumption that in the generalized linear model (GLM) the expectation of the response variable has a correct specification and some other smooth conditions,it is shown that with probability one the quasi-likelihood equation for the GLM has a solution when the sample size n is sufficiently large. The rate of this solution tending to the true value is determined. In an important special case, this rate is the same as specified in the LIL for iid partial sums and thus cannot be improved anymore.
Strong consistency of maximum quasi-likelihood estimates in generalized linear models
Institute of Scientific and Technical Information of China (English)
YiN; Changming; ZHAO; Lincheng
2005-01-01
In a generalized linear model with q × 1 responses, bounded and fixed p × qregressors Zi and general link function, under the most general assumption on the mini-mum eigenvalue of∑ni＝1n ZiZ'i, the moment condition on responses as weak as possibleand other mild regular conditions, we prove that with probability one, the quasi-likelihoodequation has a solutionβn for all large sample size n, which converges to the true regres-sion parameterβo. This result is an essential improvement over the relevant results in literature.
Energy Technology Data Exchange (ETDEWEB)
Pain, J.C. [CEA/DIF, B.P. 12, 91680 Bruyeres-le-Chatel Cedex (France)]. E-mail: jean-christophe.pain@cea.fr; Dejonghe, G. [CEA/DIF, B.P. 12, 91680 Bruyeres-le-Chatel Cedex (France); Blenski, T. [CEA/DSM/DRECAM/SPAM, Centre d' Etudes de Saclay, 91191 Gif-sur-Yvette Cedex (France)
2006-05-15
We propose a thermodynamically consistent model involving detailed screened ions, described by superconfigurations, in plasmas. In the present work, the electrons, bound and free, are treated quantum-mechanically so that resonances are carefully taken into account in the self-consistent calculation of the electronic structure of each superconfiguration. The procedure is in some sense similar to the one used in Inferno code developed by D.A. Liberman; however, here we perform this calculation in the ion-sphere model for each superconfiguration. The superconfiguration approximation allows rapid calculation of necessary averages over all possible configurations representing excited states of bound electrons. The model enables a fully quantum-mechanical self-consistent calculation of the electronic structure of ions and provides the relevant thermodynamic quantities (e.g., internal energy, Helmholtz free energy and pressure), together with an improved treatment of pressure ionization. It should therefore give a better insight into the impact of plasma effects on photoabsorption spectra.
Directory of Open Access Journals (Sweden)
Parneet Paul
2016-01-01
Full Text Available Advanced wastewater treatment using membranes are popular environmental system processes since they allow reuse and recycling. However, fouling is a key limiting factor and so proprietary systems such as Avanti’s RPU-185 Flexidisks membrane bioreactor (MBR use novel rotating membranes to assist in ameliorating it. In earlier research, this rotating process was studied by creating a simulation model based on first principles and traditional fouling mechanisms. In order to directly compare the potential benefits of this rotational system, this follow-up study was carried out using Avanti’s newly developed static (non-rotating Flexidisks MBR system. The results from operating the static pilot unit were simulated and modelled using the rotational fouling model developed earlier however with rotational switching functions turned off and rotational parameters set to a static mode. The study concluded that a rotating MBR system could increase flux throughput when compared against a similar static system. It is thought that although the slowly rotating spindle induces a weak crossflow shear, it is still able to even out cake build up across the membrane surface, thus reducing the likelihood of localised critical flux being exceeded at the micro level and lessening the potential of rapid trans-membrane pressure increases at the macro level.
Paul, Parneet; Jones, Franck Anderson
2016-01-05
Advanced wastewater treatment using membranes are popular environmental system processes since they allow reuse and recycling. However, fouling is a key limiting factor and so proprietary systems such as Avanti's RPU-185 Flexidisks membrane bioreactor (MBR) use novel rotating membranes to assist in ameliorating it. In earlier research, this rotating process was studied by creating a simulation model based on first principles and traditional fouling mechanisms. In order to directly compare the potential benefits of this rotational system, this follow-up study was carried out using Avanti's newly developed static (non-rotating) Flexidisks MBR system. The results from operating the static pilot unit were simulated and modelled using the rotational fouling model developed earlier however with rotational switching functions turned off and rotational parameters set to a static mode. The study concluded that a rotating MBR system could increase flux throughput when compared against a similar static system. It is thought that although the slowly rotating spindle induces a weak crossflow shear, it is still able to even out cake build up across the membrane surface, thus reducing the likelihood of localised critical flux being exceeded at the micro level and lessening the potential of rapid trans-membrane pressure increases at the macro level.
A New Algorithm for Self-Consistent 3-D Modeling of Collisions in Dusty Debris Disks
Stark, Christopher C
2009-01-01
We present a new "collisional grooming" algorithm that enables us to model images of debris disks where the collision time is less than the Poynting Robertson time for the dominant grain size. Our algorithm uses the output of a collisionless disk simulation to iteratively solve the mass flux equation for the density distribution of a collisional disk containing planets in 3 dimensions. The algorithm can be run on a single processor in ~1 hour. Our preliminary models of disks with resonant ring structures caused by terrestrial mass planets show that the collision rate for background particles in a ring structure is enhanced by a factor of a few compared to the rest of the disk, and that dust grains in or near resonance have even higher collision rates. We show how collisions can alter the morphology of a resonant ring structure by reducing the sharpness of a resonant ring's inner edge and by smearing out azimuthal structure. We implement a simple prescription for particle fragmentation and show how Poynting-Ro...
A consistent model for \\pi N transition distribution amplitudes and backward pion electroproduction
Lansberg, J P; Semenov-Tian-Shansky, K; Szymanowski, L
2011-01-01
The extension of the concept of generalized parton distributions leads to the introduction of baryon to meson transition distribution amplitudes (TDAs), non-diagonal matrix elements of the nonlocal three quark operator between a nucleon and a meson state. We present a general framework for modelling nucleon to pion ($\\pi N$) TDAs. Our main tool is the spectral representation for \\pi N TDAs in terms of quadruple distributions. We propose a factorized Ansatz for quadruple distributions with input from the soft-pion theorem for \\pi N TDAs. The spectral representation is complemented with a D-term like contribution from the nucleon exchange in the cross channel. We then study backward pion electroproduction in the QCD collinear factorization approach in which the non-perturbative part of the amplitude involves \\pi N TDAs. Within our two component model for \\pi N TDAs we update previous leading-twist estimates of the unpolarized cross section. Finally, we compute the transverse target single spin asymmetry as a fu...
A consistent model for leptogenesis, dark matter and the IceCube signal
Fiorentin, M Re; Fornengo, N
2016-01-01
We discuss a left-right symmetric extension of the Standard Model in which the three additional right-handed neutrinos play a central role in explaining the baryon asymmetry of the Universe, the dark matter abundance and the ultra energetic signal detected by the IceCube experiment. The energy spectrum and neutrino flux measured by IceCube are ascribed to the decays of the lightest right-handed neutrino $N_1$, thus fixing its mass and lifetime, while the production of $N_1$ in the primordial thermal bath occurs via a freeze-in mechanism driven by the additional $SU(2)_R$ interactions. The constraints imposed by IceCube and the dark matter abundance allow nonetheless the heavier right-handed neutrinos to realize a standard type-I seesaw leptogenesis, with the $B-L$ asymmetry dominantly produced by the next-to-lightest neutrino $N_2$. Further consequences and predictions of the model are that: the $N_1$ production implies a specific power-law relation between the reheating temperature of the Universe and the va...
Thermal X-ray emission from a baryonic jet: a self-consistent multicolour spectral model
Khabibullin, Ildar; Sazonov, Sergey
2015-01-01
We present a publicly-available spectral model for thermal X-ray emission from a baryonic jet in an X-ray binary system, inspired by the microquasar SS 433. The jet is assumed to be strongly collimated (half-opening angle $\\Theta\\sim 1\\deg$) and mildly relativistic (bulk velocity $\\beta=V_{b}/c\\sim 0.03-0.3$). Its X-ray spectrum is found by integrating over thin slices of constant temperature, radiating in optically thin coronal regime. The temperature profile along the jet and corresponding differential emission measure distribution are calculated with full account for gas cooling due to expansion and radiative losses. Since the model predicts both the spectral shape and luminosity of the jet's emission, its normalisation is not a free parameter if the source distance is known. We also explore the possibility of using simple X-ray observables (such as flux ratios in different energy bands) to constrain physical parameters of the jet (e.g. gas temperature and density at its base) without broad-band fitting of...
A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling
Shapiro, B.; Jin, Q.
2015-12-01
Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.
Bilayer Thickness Mismatch Controls Domain Size in Model Membranes
Energy Technology Data Exchange (ETDEWEB)
Heberle, Frederick A [ORNL; Petruzielo, Robin S [ORNL; Pan, Jianjun [ORNL; Drazba, Paul [ORNL; Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Feigenson, Gerald [Cornell University; Katsaras, John [ORNL
2013-01-01
The observation of lateral phase separation in lipid bilayers has received considerable attention, especially in connection to lipid raft phenomena in cells. It is widely accepted that rafts play a central role in cellular processes, notably signal transduction. While micrometer-sized domains are observed with some model membrane mixtures, rafts much smaller than 100 nm beyond the reach of optical microscopy are now thought to exist, both in vitro and in vivo. We have used small-angle neutron scattering, a probe free technique, to measure the size of nanoscopic membrane domains in unilamellar vesicles with unprecedented accuracy. These experiments were performed using a four-component model system containing fixed proportions of cholesterol and the saturated phospholipid 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), mixed with varying amounts of the unsaturated phospholipids 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dioleoylsn- glycero-3-phosphocholine (DOPC). We find that liquid domain size increases with the extent of acyl chain unsaturation (DOPC:POPC ratio). Furthermore, we find a direct correlation between domain size and the mismatch in bilayer thickness of the coexisting liquid-ordered and liquid-disordered phases, suggesting a dominant role for line tension in controlling domain size. While this result is expected from line tension theories, we provide the first experimental verification in free-floating bilayers. Importantly, we also find that changes in bilayer thickness, which accompany changes in the degree of lipid chain unsaturation, are entirely confined to the disordered phase. Together, these results suggest how the size of functional domains in homeothermic cells may be regulated through changes in lipid composition.
Modeling of interactions between nanoparticles and cell membranes
Ban, Young-Min
Rapid development of nanotechnology and ability to manufacture materials and devices with nanometer feature size leads to exciting innovations in many areas including the medical and electronic fields. However, the possible health and environmental impacts of manufactured nanomaterials are not fully known. Recent experimental reports suggest that some of the manufactured nanomaterials, such as fullerenes and carbon nanotubes, are highly toxic even in small concentrations. The goal of the current work is to understand the mechanisms responsible for the toxicity of nanomaterials. In the current study coarse-grained molecular dynamics simulations are employed to investigate the interactions between NPs and cellular membranes at a molecular level. One of the possible toxicity mechanisms of the nanomaterials is membrane disruption. Possibility of membrane disruption exposed to the manufactured nanomaterials are examined by considering chemical reactions and non-reactive physical interactions as chemical as well as physical mechanisms. Mechanisms of transport of carbon-based nanoparticles (fullerene and its derivative) across a phospholipid bilayer are investigated. The free energy profile is obtained using constrained simulations. It is shown that the considered nanoparticles are hydrophobic and therefore they tend to reside in the interior of the lipid bilayer. In addition, the dynamics of the membrane fluctuations is significantly affected by the nanoparticles at the bilayer-water interface. The hydrophobic interaction between the particles and membrane core induces the strong coupling between the nanoparticle motion and membrane deformation. It is observed that the considered nanoparticles affect several physical properties of the membrane. The nanoparticles embedded into the membrane interior lead to the membrane softening, which becomes more significant with increase in CNT length and concentration. The lateral pressure profile and membrane energy in the membrane
DEFF Research Database (Denmark)
Staunstrup, Jørgen
1998-01-01
This paper proposes that Interface Consistency is an important issue for the development of modular designs. Byproviding a precise specification of component interfaces it becomes possible to check that separately developedcomponents use a common interface in a coherent matter thus avoiding a very...... significant source of design errors. Awide range of interface specifications are possible, the simplest form is a syntactical check of parameter types.However, today it is possible to do more sophisticated forms involving semantic checks....
Ataman, Meric; Hernandez Gardiol, Daniel F; Fengos, Georgios; Hatzimanikatis, Vassily
2017-07-01
Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the complexity of these large metabolic networks often hinders their utility in various practical applications. Although reduced models are commonly used for modeling and in integrating experimental data, they are often inconsistent across different studies and laboratories due to different criteria and detail, which can compromise transferability of the findings and also integration of experimental data from different groups. In this study, we have developed a systematic semi-automatic approach to reduce genome-scale models into core models in a consistent and logical manner focusing on the central metabolism or subsystems of interest. The method minimizes the loss of information using an approach that combines graph-based search and optimization methods. The resulting core models are shown to be able to capture key properties of the genome-scale models and preserve consistency in terms of biomass and by-product yields, flux and concentration variability and gene essentiality. The development of these "consistently-reduced" models will help to clarify and facilitate integration of different experimental data to draw new understanding that can be directly extendable to genome-scale models.
On the (in)consistency of a multi-model ensemble of the past 30 years land surface state.
Dutra, Emanuel; Schellekens, Jaap; Beck, Hylke; Balsamo, Gianpaolo
2016-04-01
Global land-surface and hydrological models are a fundamental tool in understanding the land-surface state and evolution either coupled to atmospheric models for climate and weather predictions or in stand-alone mode. In this study we take a recently developed dataset consisting in stand-alone simulations by 10 global hydrological and land surface models sharing the same atmospheric forcing for the period 1979-2012 (the eart2Observe dataset). This multi-model ensemble provides the first freely available dataset with such a spatial/temporal scale that allows for a characterization of the multi-model characteristics such as inter-model consistency and error-spread relationship. We will present a metric for the ensemble consistency using the concept of potential predictability, that can be interpreted as a proxy for the multi-model agreement. Initial results point to regions of low inter-model agreement in the polar and tropical regions, the latter also present when comparing globally available precipitation datasets. In addition to this, the discharge ensemble spread around the ensemble mean was compared to the error of the ensemble mean for several large-scale and small scale basins. This showed a general under-estimation of the ensemble spread, particularly in tropical basins, suggesting that the current dataset lacks the representation of the precipitation uncertainty in the input meteorological data.
Directory of Open Access Journals (Sweden)
Meric Ataman
2017-07-01
Full Text Available Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the complexity of these large metabolic networks often hinders their utility in various practical applications. Although reduced models are commonly used for modeling and in integrating experimental data, they are often inconsistent across different studies and laboratories due to different criteria and detail, which can compromise transferability of the findings and also integration of experimental data from different groups. In this study, we have developed a systematic semi-automatic approach to reduce genome-scale models into core models in a consistent and logical manner focusing on the central metabolism or subsystems of interest. The method minimizes the loss of information using an approach that combines graph-based search and optimization methods. The resulting core models are shown to be able to capture key properties of the genome-scale models and preserve consistency in terms of biomass and by-product yields, flux and concentration variability and gene essentiality. The development of these "consistently-reduced" models will help to clarify and facilitate integration of different experimental data to draw new understanding that can be directly extendable to genome-scale models.
Network modeling of membrane-based artificial cellular systems
Freeman, Eric C.; Philen, Michael K.; Leo, Donald J.
2013-04-01
Computational models are derived for predicting the behavior of artificial cellular networks for engineering applications. The systems simulated involve the use of a biomolecular unit cell, a multiphase material that incorporates a lipid bilayer between two hydrophilic compartments. These unit cells may be considered building blocks that enable the fabrication of complex electrochemical networks. These networks can incorporate a variety of stimuli-responsive biomolecules to enable a diverse range of multifunctional behavior. Through the collective properties of these biomolecules, the system demonstrates abilities that recreate natural cellular phenomena such as mechanotransduction, optoelectronic response, and response to chemical gradients. A crucial step to increase the utility of these biomolecular networks is to develop mathematical models of their stimuli-responsive behavior. While models have been constructed deriving from the classical Hodgkin-Huxley model focusing on describing the system as a combination of traditional electrical components (capacitors and resistors), these electrical elements do not sufficiently describe the phenomena seen in experiment as they are not linked to the molecular scale processes. From this realization an advanced model is proposed that links the traditional unit cell parameters such as conductance and capacitance to the molecular structure of the system. Rather than approaching the membrane as an isolated parallel plate capacitor, the model seeks to link the electrical properties to the underlying chemical characteristics. This model is then applied towards experimental cases in order that a more complete picture of the underlying phenomena responsible for the desired sensing mechanisms may be constructed. In this way the stimuli-responsive characteristics may be understood and optimized.
Gauge propagator and physical consistency of the CPT-even part of the standard model extension
Casana, Rodolfo; Ferreira, Manoel M., Jr.; Gomes, Adalto R.; Pinheiro, Paulo R. D.
2009-12-01
In this work, we explicitly evaluate the gauge propagator of the Maxwell theory supplemented by the CPT-even term of the standard model extension. First, we specialize our evaluation for the parity-odd sector of the tensor Wμνρσ, using a parametrization that retains only the three nonbirefringent coefficients. From the poles of the propagator, it is shown that physical modes of this electrodynamics are stable, noncausal and unitary. In the sequel, we carry out the parity-even gauge propagator using a parametrization that allows to work with only the isotropic nonbirefringent element. In this case, we show that the physical modes of the parity-even sector of the tensor W are causal, stable and unitary for a limited range of the isotropic coefficient.
Consistency and normality of Huber-Dutter estimators for partial linear model
Institute of Scientific and Technical Information of China (English)
2008-01-01
For partial linear model Y = Xτβ0 + g0(T) + with unknown β0 ∈ Rd and an unknown smooth function g0, this paper considers the Huber-Dutter estimators of β0, scale σ for the errors and the function g0 approximated by the smoothing B-spline functions, respectively. Under some regularity conditions, the Huber-Dutter estimators of β0 and σ are shown to be asymptotically normal with the rate of convergence n-1/2 and the B-spline Huber-Dutter estimator of g0 achieves the optimal rate of convergence in nonparametric regression. A simulation study and two examples demonstrate that the Huber-Dutter estimator of β0 is competitive with its M-estimator without scale parameter and the ordinary least square estimator.
Consistency and normality of Huber-Dutter estimators for partial linear model
Institute of Scientific and Technical Information of China (English)
TONG XingWei; CUI HengJian; YU Peng
2008-01-01
For partial linear model Y = Xτβ0 + g0(T) + ∈ with unknown/β0 ∈ Rd and an unknown smooth function g0,this paper considers the Huber-Dutter estimators of/β0,scale σ for the errors and the function g0 approximated by the smoothing B-spline functions,respectively.Under some regularity conditions,the Huber-Dutter estimators of/β0 and σ are shown to be asymptotically normal with the rate of convergence n-1/2 and the B-spline Huber-Dutter estimator of go achieves the optimal rate of convergence in nonparametric regression.A simulation study and two examples demonstrate that the Huber-Dutter estimator of/β0 is competitive with its M-estimator without scale parameter and the ordinary least square estimator.
Quesada, José Manuel; Capote, Roberto; Soukhovitski, Efrem S.; Chiba, Satoshi
2016-03-01
An extension for odd-A actinides of a previously derived dispersive coupledchannel optical model potential (OMP) for 238U and 232Th nuclei is presented. It is used to fit simultaneously all the available experimental databases including neutron strength functions for nucleon scattering on 232Th, 233,235,238U and 239Pu nuclei. Quasi-elastic (p,n) scattering data on 232Th and 238U to the isobaric analogue states of the target nucleus are also used to constrain the isovector part of the optical potential. For even-even (odd) actinides almost all low-lying collective levels below 1 MeV (0.5 MeV) of excitation energy are coupled. OMP parameters show a smooth energy dependence and energy independent geometry.
Gustafsson, Leif; Sternad, Mikael
2007-10-01
Population models concern collections of discrete entities such as atoms, cells, humans, animals, etc., where the focus is on the number of entities in a population. Because of the complexity of such models, simulation is usually needed to reproduce their complete dynamic and stochastic behaviour. Two main types of simulation models are used for different purposes, namely micro-simulation models, where each individual is described with its particular attributes and behaviour, and macro-simulation models based on stochastic differential equations, where the population is described in aggregated terms by the number of individuals in different states. Consistency between micro- and macro-models is a crucial but often neglected aspect. This paper demonstrates how the Poisson Simulation technique can be used to produce a population macro-model consistent with the corresponding micro-model. This is accomplished by defining Poisson Simulation in strictly mathematical terms as a series of Poisson processes that generate sequences of Poisson distributions with dynamically varying parameters. The method can be applied to any population model. It provides the unique stochastic and dynamic macro-model consistent with a correct micro-model. The paper also presents a general macro form for stochastic and dynamic population models. In an appendix Poisson Simulation is compared with Markov Simulation showing a number of advantages. Especially aggregation into state variables and aggregation of many events per time-step makes Poisson Simulation orders of magnitude faster than Markov Simulation. Furthermore, you can build and execute much larger and more complicated models with Poisson Simulation than is possible with the Markov approach.
Towards a Self Consistent Model of the Thermal Structure of the Venus Atmosphere
Limaye, Sanjay; Vandaele, Ann C.; Wilson, Colin
Nearly three decades ago, an international effort led to the adoption of the Venus International Reference Atmosphere (VIRA) was published in 1985 after the significant data returned by the Pioneer Venus Orbiter and Probes and the earlier Venera missions (Kliore et al., 1985). The vertical thermal structure is one component of the reference model which relied primarily on the three Pioneer Venus Small Probes, the Large Probe profiles as well as several hundred retrieved temperature profiles from the Pioneer Venus Orbiter radio occultation data collected during 1978 - 1982. Since then a huge amount of thermal structure data has been obtained from multiple instruments on ESA’s Venus Express (VEX) orbiter mission. The VEX data come from retrieval of temperature profiles from SPICAV/SOIR stellar/solar occultations, VeRa radio occultations and from the passive remote sensing by the VIRTIS instrument. The results of these three experiments vary in their intrinsic properties - altitude coverage, spatial and temporal sampling and resolution and accuracy An international team has been formed with support from the International Space Studies Institute (Bern, Switzerland) to consider the observations of the Venus atmospheric structure obtained since the data used for the COSPAR Venus International Reference Atmosphere (Kliore et al., 1985). We report on the progress made by the comparison of the newer data with VIRA model and also between different experiments where there is overlap. Kliore, A.J., V.I. Moroz, and G.M. Keating, Eds. 1985, VIRA: Venus International Reference Atmosphere, Advances in Space Research, Volume 5, Number 11, 307 pages.
Directory of Open Access Journals (Sweden)
Marco Del Giudice
Full Text Available BACKGROUND: Schizophrenia is a mental disorder marked by an evolutionarily puzzling combination of high heritability, reduced reproductive success, and a remarkably stable prevalence. Recently, it has been proposed that sexual selection may be crucially involved in the evolution of schizophrenia. In the sexual selection model (SSM of schizophrenia and schizotypy, schizophrenia represents the negative extreme of a sexually selected indicator of genetic fitness and condition. Schizotypal personality traits are hypothesized to increase the sensitivity of the fitness indicator, thus conferring mating advantages on high-fitness individuals but increasing the risk of schizophrenia in low-fitness individuals; the advantages of successful schzotypy would be mediated by enhanced courtship-related traits such as verbal creativity. Thus, schizotypy-increasing alleles would be maintained by sexual selection, and could be selectively neutral or even beneficial, at least in some populations. However, most empirical studies find that the reduction in fertility experienced by schizophrenic patients is not compensated for by increased fertility in their unaffected relatives. This finding has been interpreted as indicating strong negative selection on schizotypy-increasing alleles, and providing evidence against sexual selection on schizotypy. METHODOLOGY: A simple mathematical model is presented, showing that reduced fertility in the families of schizophrenic patients can coexist with selective neutrality of schizotypy-increasing alleles, or even with positive selection on schizotypy in the general population. If the SSM is correct, studies of patients' families can be expected to underestimate the true fertility associated with schizotypy. SIGNIFICANCE: This paper formally demonstrates that reduced fertility in the families of schizophrenic patients does not constitute evidence against sexual selection on schizotypy-increasing alleles. Futhermore, it suggests
A new method for modeling rough membrane surface and calculation of interfacial interactions.
Zhao, Leihong; Zhang, Meijia; He, Yiming; Chen, Jianrong; Hong, Huachang; Liao, Bao-Qiang; Lin, Hongjun
2016-01-01
Membrane fouling control necessitates the establishment of an effective method to assess interfacial interactions between foulants and rough surface membrane. This study proposed a new method which includes a rigorous mathematical equation for modeling membrane surface morphology, and combination of surface element integration (SEI) method and the composite Simpson's approach for assessment of interfacial interactions. The new method provides a complete solution to quantitatively calculate interfacial interactions between foulants and rough surface membrane. Application of this method in a membrane bioreactor (MBR) showed that, high calculation accuracy could be achieved by setting high segment number, and moreover, the strength of three energy components and energy barrier was remarkably impaired by the existence of roughness on the membrane surface, indicating that membrane surface morphology exerted profound effects on membrane fouling in the MBR. Good agreement between calculation prediction and fouling phenomena was found, suggesting the feasibility of this method.
Random walk model of subdiffusion in a system with a thin membrane.
Kosztołowicz, Tadeusz
2015-02-01
We consider in this paper subdiffusion in a system with a thin membrane. The subdiffusion parameters are the same in both parts of the system separated by the membrane. Using the random walk model with discrete time and space variables the probabilities (Green's functions) P(x,t) describing a particle's random walk are found. The membrane, which can be asymmetrical, is characterized by the two probabilities of stopping a random walker by the membrane when it tries to pass through the membrane in both opposite directions. Green's functions are transformed to the system in which the variables are continuous, and then the membrane permeability coefficients are given by special formulas which involve the probabilities mentioned above. From the obtained Green's functions, we derive boundary conditions at the membrane. One of the conditions demands the continuity of a flux at the membrane, but the other one is rather unexpected and contains the Riemann-Liouville fractional time derivative P(x(N)(-),t)=λ(1)P(x(N)(+),t)+λ(2)∂(α/2)P(x(N)(+),t)/∂t(α/2), where λ(1),λ(2) depending on membrane permeability coefficients (λ(1)=1 for a symmetrical membrane), α is a subdiffusion parameter, and x(N) is the position of the membrane. This boundary condition shows that the additional "memory effect," represented by the fractional derivative, is created by the membrane. This effect is also created by the membrane for a normal diffusion case in which α=1.
Toward A Self Consistent MHD Model of Chromospheres and Winds From Late Type Evolved Stars
Airapetian, V S; Carpenter, K G
2014-01-01
We present the first magnetohydrodynamic model of the stellar chromospheric heating and acceleration of the outer atmospheres of cool evolved stars, using alpha Tau as a case study. We used a 1.5D MHD code with a generalized Ohm's law that accounts for the effects of partial ionization in the stellar atmosphere to study Alfven wave dissipation and wave reflection. We have demonstrated that due to inclusion of the effects of ion-neutral collisions in magnetized weakly ionized chromospheric plasma on resistivity and the appropriate grid resolution, the numerical resistivity becomes 1-2 orders of magnitude smaller than the physical resistivity. The motions introduced by non-linear transverse Alfven waves can explain non-thermally broadened and non-Gaussian profiles of optically thin UV lines forming in the stellar chromosphere of alpha Tau and other late-type giant and supergiant stars. The calculated heating rates in the stellar chromosphere due to resistive (Joule) dissipation of electric currents, induced by ...
Complementarity of DM searches in a consistent simplified model: the case of Z{sup ′}
Energy Technology Data Exchange (ETDEWEB)
Jacques, Thomas [SISSA and INFN,via Bonomea 265, 34136 Trieste (Italy); Katz, Andrey [Theory Division, CERN,CH-1211 Geneva 23 (Switzerland); Département de Physique Théorique and Center for Astroparticle Physics (CAP),Université de Genève, 24 quai Ansermet, CH-1211 Genève 4 (Switzerland); Morgante, Enrico; Racco, Davide [Département de Physique Théorique and Center for Astroparticle Physics (CAP),Université de Genève, 24 quai Ansermet, CH-1211 Genève 4 (Switzerland); Rameez, Mohamed [Département de Physique Nucléaire et Corpusculaire,Université de Genève, 24 quai Ansermet, CH-1211 Genève 4 (Switzerland); Riotto, Antonio [Département de Physique Théorique and Center for Astroparticle Physics (CAP),Université de Genève, 24 quai Ansermet, CH-1211 Genève 4 (Switzerland)
2016-10-14
We analyze the constraints from direct and indirect detection on fermionic Majorana Dark Matter (DM). Because the interaction with the Standard Model (SM) particles is spin-dependent, a priori the constraints that one gets from neutrino telescopes, the LHC, direct and indirect detection experiments are comparable. We study the complementarity of these searches in a particular example, in which a heavy Z{sup ′} mediates the interactions between the SM and the DM. We find that for heavy dark matter indirect detection provides the strongest bounds on this scenario, while IceCube bounds are typically stronger than those from direct detection. The LHC constraints are dominant for smaller dark matter masses. These light masses are less motivated by thermal relic abundance considerations. We show that the dominant annihilation channels of the light DM in the Sun and the Galactic Center are either bb̄ or tt̄, while the heavy DM annihilation is completely dominated by Zh channel. The latter produces a hard neutrino spectrum which has not been previously analyzed. We study the neutrino spectrum yielded by DM and recast IceCube constraints to allow proper comparison with constraints from direct and indirect detection experiments and LHC exclusions.
Complementarity of DM Searches in a Consistent Simplified Model: the Case of Z'
Jacques, Thomas; Morgante, Enrico; Racco, Davide; Rameez, Mohamed; Riotto, Antonio
2016-01-01
We analyze the constraints from direct and indirect detection on fermionic Majorana Dark Matter (DM). Because the interaction with the Standard Model (SM) particles is spin-dependent, a priori the constraints that one gets from neutrino telescopes, the LHC and direct detection experiments are comparable. We study the complementarity of these searches in a particular example, in which a heavy $Z'$ mediates the interactions between the SM and the DM. We find that in most cases IceCube provides the strongest bounds on this scenario, while the LHC constraints are only meaningful for smaller dark matter masses. These light masses are less motivated by thermal relic abundance considerations. We show that the dominant annihilation channels of the light DM in the Sun are either $b \\bar b$ or $t \\bar t$, while the heavy DM annihilation is completely dominated by $Zh$ channel. The latter produces a hard neutrino spectrum which has not been previously analyzed. We study the neutrino spectrum yielded by DM and recast Ice...
Self-consistent, axisymmetric two-integral models of elliptical galaxies with embedded nuclear discs
Van den Bosch, F C; van den Bosch, Frank C; de Zeeuw, P Tim
1996-01-01
Recently, observations with the Hubble Space Telescope have revealed small stellar discs embedded in the nuclei of a number of ellipticals and S0s. In this paper we construct two-integral axisymmetric models for such systems. We calculate the even part of the phase-space distribution function, and specify the odd part by means of a simple parameterization. We investigate the photometric as well as the kinematic signatures of nuclear discs, including their velocity profiles (VPs), and study the influence of seeing convolution. The rotation curve of a nuclear disc gives an excellent measure of the central mass-to-light ratio whenever the VPs clearly reveal the narrow, rapidly rotating component associated with the nuclear disc. Steep cusps and seeing convolution both result in central VPs that are dominated by the bulge light, and these VPs barely show the presence of the nuclear disc, impeding measurements of the central rotation velocities of the disc stars. However, if a massive BH is present, the disc compo...
Pisnichenko, I A
2007-01-01
The regional climate model prepared from Eta WS (workstation) forecast model has been integrated over South America with the horizontal resolution of 40 km for the period of 1961-1977. The model was forced at its lateral boundaries by the outputs of HadAMP. The data of HadAMP represent the simulation of modern climate with the resolution about150 km. In order to prepare climate regional model from the Eta forecast model was added new blocks and multiple modifications and corrections was made in the original model. The running of climate Eta model was made on the supercomputer SX-6. The detailed analysis of the results of dynamical downscaling experiment includes an investigation of a consistency between the regional and AGCM models as well as of ability of the regional model to resolve important features of climate fields on the finer scale than that resolved by AGCM. In this work we show the results of our investigation of the consistency of the output fields of the Eta model and HadAMP. We have analysed geo...
Bordin, Lorenzo; Creminelli, Paolo; Mirbabayi, Mehrdad; Noreña, Jorge
2017-03-01
We argue that isotropic scalar fluctuations in solid inflation are adiabatic in the super-horizon limit. During the solid phase this adiabatic mode has peculiar features: constant energy-density slices and comoving slices do not coincide, and their curvatures, parameterized respectively by ζ and Script R, both evolve in time. The existence of this adiabatic mode implies that Maldacena's squeezed limit consistency relation holds after angular average over the long mode. The correlation functions of a long-wavelength spherical scalar mode with several short scalar or tensor modes is fixed by the scaling behavior of the correlators of short modes, independently of the solid inflation action or dynamics of reheating.
Hacarlioglu, Pelin
2007-01-01
This dissertation describes the preparation of a novel inorganic membrane for hydrogen permeation and its application in a membrane reactor for the study of the methane steam reforming reaction. The investigations include both experimental studies of the membrane permeation mechanism and theoretical modeling of mass transfer through the membrane and simulation of the membrane reactor with 1-D and 2-D models. A hydrothermally stable and hydrogen selective membrane composed of silica and a...