DSpace Community:
http://hdl.handle.net/2117/2071
Tue, 02 Sep 2014 13:07:24 GMT2014-09-02T13:07:24Zwebmaster.bupc@upc.eduUniversitat Politècnica de Catalunya. Servei de Biblioteques i DocumentaciónoDeim-based PGD for parametric nonlinear model order reduction
http://hdl.handle.net/2117/22099
Title: Deim-based PGD for parametric nonlinear model order reduction
Authors: Aguado, José V.; Chinesta, Francisco; Leygue, Adrien; Cueto Prendes, Elias; Huerta, Antonio
Abstract: Anewtechniqueforefficientlysolvingparametricnonlinearreducedorder
modelsintheProperGeneralizedDecomposition(PGD)frameworkispresentedhere.
ThistechniqueisbasedontheDiscreteEmpiricalInterpolationMethod(DEIM)[1],and
thusthenonlineartermisinterpolatedusingthereducedbasisinsteadofbeingfully
evaluated.TheDEIMhasalreadybeendemonstratedtoprovidesatisfactoryresultsin
termsofcomputationalcomplexitydecreasewhencombinedwiththeProperOrthogonal
Decomposition(POD).However,inthePODcasethereducedbasisis
aposteriori
known
asitcomesfromseveralpre-computedsnapshots.Onthecontrary,thePGDisan
apriori
modelreductionmethod.ThismakestheDEIM-PGDcouplingratherdelicate,because
differentchoicesarepossibleasitisanalyzedinthisworkMon, 17 Mar 2014 12:13:01 GMThttp://hdl.handle.net/2117/220992014-03-17T12:13:01ZAguado, José V.; Chinesta, Francisco; Leygue, Adrien; Cueto Prendes, Elias; Huerta, AntonionoAnewtechniqueforefficientlysolvingparametricnonlinearreducedorder
modelsintheProperGeneralizedDecomposition(PGD)frameworkispresentedhere.
ThistechniqueisbasedontheDiscreteEmpiricalInterpolationMethod(DEIM)[1],and
thusthenonlineartermisinterpolatedusingthereducedbasisinsteadofbeingfully
evaluated.TheDEIMhasalreadybeendemonstratedtoprovidesatisfactoryresultsin
termsofcomputationalcomplexitydecreasewhencombinedwiththeProperOrthogonal
Decomposition(POD).However,inthePODcasethereducedbasisis
aposteriori
known
asitcomesfromseveralpre-computedsnapshots.Onthecontrary,thePGDisan
apriori
modelreductionmethod.ThismakestheDEIM-PGDcouplingratherdelicate,because
differentchoicesarepossibleasitisanalyzedinthisworkAdvanced harmonic techniques for solving the transient heat equation
http://hdl.handle.net/2117/22098
Title: Advanced harmonic techniques for solving the transient heat equation
Authors: Aguado, José Vicente; Huerta, Antonio; Chinesta, Francisco; Cueto Prendes, Elias; Leygue, Adrien
Abstract: Simulation-based management of processes has always been a
big challenge
because of the difficulty to merge two apparently opposed idea
s: the real time handling
demanded by the process, and the traditionally strong time c
onsumption linked to the sim-
ulation. However, very often processes are monitored or con
trolled by performing relatively
few measures on some specific points of the domain. Then, one s
trategy for accelerating
the simulation might be based on trying to compute the respon
se only where it is needed.
For this reason this work revisits a classical technique, th
e harmonic analysis, which is
combined with recent model reduction techniques giving pla
ce to an advanced harmonic
technique for solving linear parabolic equations and, in pa
rticular, the transient heat equa-
tion. Thanks to fact that Reciprocity principle applies in t
he frequency domain, the solu-
tion can be computed where it is of interest by performing an i
nexpensive postprocessing
of a pre-computed transfer function. This transfer functio
n, that must be valid for a suffi-
ciently large range of frequencies, is efficiently computed b
y using the Proper Generalized
Decomposition method.Mon, 17 Mar 2014 12:04:32 GMThttp://hdl.handle.net/2117/220982014-03-17T12:04:32ZAguado, José Vicente; Huerta, Antonio; Chinesta, Francisco; Cueto Prendes, Elias; Leygue, AdriennoSimulation-based management of processes has always been a
big challenge
because of the difficulty to merge two apparently opposed idea
s: the real time handling
demanded by the process, and the traditionally strong time c
onsumption linked to the sim-
ulation. However, very often processes are monitored or con
trolled by performing relatively
few measures on some specific points of the domain. Then, one s
trategy for accelerating
the simulation might be based on trying to compute the respon
se only where it is needed.
For this reason this work revisits a classical technique, th
e harmonic analysis, which is
combined with recent model reduction techniques giving pla
ce to an advanced harmonic
technique for solving linear parabolic equations and, in pa
rticular, the transient heat equa-
tion. Thanks to fact that Reciprocity principle applies in t
he frequency domain, the solu-
tion can be computed where it is of interest by performing an i
nexpensive postprocessing
of a pre-computed transfer function. This transfer functio
n, that must be valid for a suffi-
ciently large range of frequencies, is efficiently computed b
y using the Proper Generalized
Decomposition method.Error assessment for timeline-dependent quantities of interest in transient elastodynamics
http://hdl.handle.net/2117/22096
Title: Error assessment for timeline-dependent quantities of interest in transient elastodynamics
Authors: Verdugo, Francesc; Parés Mariné, Núria; Díez, Pedro
Abstract: This work presents a new approach to assess the error in speci c quantities
of interest in the framework of linear elastodynamics. In particular, a new type of quantities
of interest (referred as timeline-dependent quantities) is proposed. These quantities
are scalar time-dependent outputs of the transient solution which are better suited to
time-dependent problems than the standard scalar ones available in the literature. The
proposed methodology furnishes error estimates for both the standard scalar and the new
timeline-dependent quantities of interest. The key ingredient is the modal-based approximation
of the associated adjoint problems which allows e ciently computing and storing
the adjoint solution.Mon, 17 Mar 2014 11:45:00 GMThttp://hdl.handle.net/2117/220962014-03-17T11:45:00ZVerdugo, Francesc; Parés Mariné, Núria; Díez, PedronoThis work presents a new approach to assess the error in speci c quantities
of interest in the framework of linear elastodynamics. In particular, a new type of quantities
of interest (referred as timeline-dependent quantities) is proposed. These quantities
are scalar time-dependent outputs of the transient solution which are better suited to
time-dependent problems than the standard scalar ones available in the literature. The
proposed methodology furnishes error estimates for both the standard scalar and the new
timeline-dependent quantities of interest. The key ingredient is the modal-based approximation
of the associated adjoint problems which allows e ciently computing and storing
the adjoint solution.Numerical simulation of soil-water jet interaction with smoothed particle hydrodynamics
http://hdl.handle.net/2117/22095
Title: Numerical simulation of soil-water jet interaction with smoothed particle hydrodynamics
Authors: GUO, ZHIMING; Shao, Jiaru; Shen, Yongxing; Liu, Moubin
Abstract: Smoothed particle hydrodynamics (SPH) is a meshfree, Lagrangian particle method, which has been applied to different areas in sciences and industrial applications. In this work, SPH is used to simulate the soil-water jet interaction and erosion. In the simulation, water is modelled as a viscous fluid with weak compressibility and the soil is assumed to be an elastic-perfectly plastic material. The stress states of soil in the plastic flow regime follow the Drucker-Prager failure criterion. Both the shear and tensile criterions are used for the yield of soil particles if the yield point is reached and the total stress of the particle is scaled. Instead of computing particle pressure from an equation of state, the spherical stress is computed by dividing total stress into spherical stress and deviatoric stress. The interaction of coupling interfaces is strengthened by a penalty function to avoid unphysical penetration between particles from different materials. The obtained numerical results have shown that SPH could be a valuable method for the simulation of complex soil water interaction.Mon, 17 Mar 2014 11:38:12 GMThttp://hdl.handle.net/2117/220952014-03-17T11:38:12ZGUO, ZHIMING; Shao, Jiaru; Shen, Yongxing; Liu, MoubinnoElastic- perfectly plastic flow, Meshfree method, Smoothed particle hydrodynamics (SPH), Soil-water interaction, Water jetSmoothed particle hydrodynamics (SPH) is a meshfree, Lagrangian particle method, which has been applied to different areas in sciences and industrial applications. In this work, SPH is used to simulate the soil-water jet interaction and erosion. In the simulation, water is modelled as a viscous fluid with weak compressibility and the soil is assumed to be an elastic-perfectly plastic material. The stress states of soil in the plastic flow regime follow the Drucker-Prager failure criterion. Both the shear and tensile criterions are used for the yield of soil particles if the yield point is reached and the total stress of the particle is scaled. Instead of computing particle pressure from an equation of state, the spherical stress is computed by dividing total stress into spherical stress and deviatoric stress. The interaction of coupling interfaces is strengthened by a penalty function to avoid unphysical penetration between particles from different materials. The obtained numerical results have shown that SPH could be a valuable method for the simulation of complex soil water interaction.A finite element strategy coupling a gradient-enhanced damage model and cohesive cracks for quasi-brittle materials
http://hdl.handle.net/2117/22094
Title: A finite element strategy coupling a gradient-enhanced damage model and cohesive cracks for quasi-brittle materials
Authors: Tamayo Mas, Elena; Rodríguez Ferran, Antonio
Abstract: A new combined strategy to describe failure of quasi-brittle materials is presented thus allowing the complete description of the process, from initiation of damage to crack propagation. For the early stages of the process, and in order to overcome the well-known problems characterising local descriptions of damage (e.g. mesh-dependence), a gradient-enhanced model based on smoothed displacements is employed. In order to deal with material separation, this continuous description is coupled to a cohesive crack when damage parameter exceeds a critical value. Some difficulties may arise when dealing with the transition from regularised damage models to evolving cracks: crack initiation, crack-path direction, energetic equivalence... In this work, a discrete cohesive crack is introduced when the damage parameter exceeds a critical value. On the one hand, and to determine the crack-path direction, the medial axis of the already damaged profile is computed. That is, a geometric tool widely used in the computer graphics field is used here to track the crack surface. Since this technique is exclusively based on the shape of the regularised damage profile, no mesh sensitivity is observed when determining the crack direction. On the other hand, and to define the cohesive law, an energy balance is imposed thus ensuring that the fracture energy not yet dissipated in the damage zone is transferred to the crack.Mon, 17 Mar 2014 11:30:17 GMThttp://hdl.handle.net/2117/220942014-03-17T11:30:17ZTamayo Mas, Elena; Rodríguez Ferran, AntonionoCohesive cracks, Continuous-discontinuous strategy, Extended finite element method, Medial surface, Regularisation, Smoothed displacementsA new combined strategy to describe failure of quasi-brittle materials is presented thus allowing the complete description of the process, from initiation of damage to crack propagation. For the early stages of the process, and in order to overcome the well-known problems characterising local descriptions of damage (e.g. mesh-dependence), a gradient-enhanced model based on smoothed displacements is employed. In order to deal with material separation, this continuous description is coupled to a cohesive crack when damage parameter exceeds a critical value. Some difficulties may arise when dealing with the transition from regularised damage models to evolving cracks: crack initiation, crack-path direction, energetic equivalence... In this work, a discrete cohesive crack is introduced when the damage parameter exceeds a critical value. On the one hand, and to determine the crack-path direction, the medial axis of the already damaged profile is computed. That is, a geometric tool widely used in the computer graphics field is used here to track the crack surface. Since this technique is exclusively based on the shape of the regularised damage profile, no mesh sensitivity is observed when determining the crack direction. On the other hand, and to define the cohesive law, an energy balance is imposed thus ensuring that the fracture energy not yet dissipated in the damage zone is transferred to the crack.Integración de texto y vídeo en un nuevo recurso para el aprendizaje de matemáticas en línea
http://hdl.handle.net/2117/22026
Title: Integración de texto y vídeo en un nuevo recurso para el aprendizaje de matemáticas en línea
Authors: Calm, Remei; Ripoll, Jordi; Olivé Farré, Carme; Masià, Ramon; Sancho-Vinuesa, Teresa; Parés Mariné, Núria; Pozo Montero, Francesc
Abstract: Las características especiales del aprendizaje en línea conllevan la necesidad de disponer de materiales adaptados. El feedback con los estudiantes denota que la notación matemática y los conocimientos previos son a menudo los grandes escollos a superar para la comprensión de la materia. Todo ello ha guiado nuestro esfuerzo por mejorar la calidad de la enseñanza que impartimos, buscando nuevos recursos educativos que ayuden a paliar los problemas detectados. En este documento se presenta la experiencia de la integración de texto y video en un recurso utilizado en asignaturas de Análisis Matemático. Justificamos su elección y detallamos su uso a lo largo de un semestre. Finalmente, hacemos un análisis estadístico de los datos disponibles, que nos lleva a la conclusión que existe una clara tendencia de mejora de los resultados académicos.Thu, 13 Mar 2014 13:21:03 GMThttp://hdl.handle.net/2117/220262014-03-13T13:21:03ZCalm, Remei; Ripoll, Jordi; Olivé Farré, Carme; Masià, Ramon; Sancho-Vinuesa, Teresa; Parés Mariné, Núria; Pozo Montero, Francescnoaprendizaje a distancia, recursos TIC, videos docentes, resolución dinámica de problemas matemáticosLas características especiales del aprendizaje en línea conllevan la necesidad de disponer de materiales adaptados. El feedback con los estudiantes denota que la notación matemática y los conocimientos previos son a menudo los grandes escollos a superar para la comprensión de la materia. Todo ello ha guiado nuestro esfuerzo por mejorar la calidad de la enseñanza que impartimos, buscando nuevos recursos educativos que ayuden a paliar los problemas detectados. En este documento se presenta la experiencia de la integración de texto y video en un recurso utilizado en asignaturas de Análisis Matemático. Justificamos su elección y detallamos su uso a lo largo de un semestre. Finalmente, hacemos un análisis estadístico de los datos disponibles, que nos lleva a la conclusión que existe una clara tendencia de mejora de los resultados académicos.Spatial and temporal trace metal distribution of a Peruvian basin: recognizing trace metal sources and assessing the potential risk
http://hdl.handle.net/2117/21708
Title: Spatial and temporal trace metal distribution of a Peruvian basin: recognizing trace metal sources and assessing the potential risk
Authors: Yacoub López, Cristina; Blazquez, N.; Pérez Foguet, Agustí; Miralles Esteban, Núria
Abstract: Recent efforts have been made to determine
the environmental impact of mining over the past
11 years in the Jequetepeque River basin, in northern
Peru. We have now analyzed data from two studies to
elucidate the spatial and temporal trace metal distribu-
tions and to assess the sources of contamination.
These two studies were carried out from 2003 to
2008 by a Peruvian government administration and
from 2008 to 2010 by us. We analyzed 249 samples
by principal component analysis, measuring: pH,
electrical conductivity, total dissolved solids, total
suspended solids, chloride, weak-acid-dissociable
cyanide, total cyanide, nitrite and nitrate, ammonium,
sulfate, and trace metals and metalloids (Al, As, Ca,
Cd, Cu, Cr, Fe, Mg, Mn, Ni, Pb, and Zn). Within the
spatial distribution of the basin, the highest Al, As, Cu,
Fe, Ni, and Pb concentrations were found at the closest
point to the mine sites for both periods of time, with
the higher peaks measured during the first years of the
sampling data. Temporal trends showed higher con-
centrations of Cu and Fe in samples taken before
2005, at which point the two mines were closed.
Risk assessment was quantified by the hazard quotient
as related to water ingestion. The risk for human
health posed by the concentrations of several trace
metals and metalloids was found to be highly adverse
(As and Cr), significant (Al, Cd, Cu, Fe, and Pb), or
minimal (Ni and ZnMon, 24 Feb 2014 09:14:26 GMThttp://hdl.handle.net/2117/217082014-02-24T09:14:26ZYacoub López, Cristina; Blazquez, N.; Pérez Foguet, Agustí; Miralles Esteban, NúrianoHazard quotient
Mine pollution
Principal component analysis
Trace metalsRecent efforts have been made to determine
the environmental impact of mining over the past
11 years in the Jequetepeque River basin, in northern
Peru. We have now analyzed data from two studies to
elucidate the spatial and temporal trace metal distribu-
tions and to assess the sources of contamination.
These two studies were carried out from 2003 to
2008 by a Peruvian government administration and
from 2008 to 2010 by us. We analyzed 249 samples
by principal component analysis, measuring: pH,
electrical conductivity, total dissolved solids, total
suspended solids, chloride, weak-acid-dissociable
cyanide, total cyanide, nitrite and nitrate, ammonium,
sulfate, and trace metals and metalloids (Al, As, Ca,
Cd, Cu, Cr, Fe, Mg, Mn, Ni, Pb, and Zn). Within the
spatial distribution of the basin, the highest Al, As, Cu,
Fe, Ni, and Pb concentrations were found at the closest
point to the mine sites for both periods of time, with
the higher peaks measured during the first years of the
sampling data. Temporal trends showed higher con-
centrations of Cu and Fe in samples taken before
2005, at which point the two mines were closed.
Risk assessment was quantified by the hazard quotient
as related to water ingestion. The risk for human
health posed by the concentrations of several trace
metals and metalloids was found to be highly adverse
(As and Cr), significant (Al, Cd, Cu, Fe, and Pb), or
minimal (Ni and ZnModelling of mixed damage on fibre reinforced composite laminates subjected to low velocity impact
http://hdl.handle.net/2117/21064
Title: Modelling of mixed damage on fibre reinforced composite laminates subjected to low velocity impact
Authors: Curiel Sosa, Jose Luis; Phaneendra, S.; Muñoz Romero, JoséThu, 19 Dec 2013 11:04:35 GMThttp://hdl.handle.net/2117/210642013-12-19T11:04:35ZCuriel Sosa, Jose Luis; Phaneendra, S.; Muñoz Romero, JosénoDiffusion-reaction model for Drosophila embryo development
http://hdl.handle.net/2117/21063
Title: Diffusion-reaction model for Drosophila embryo development
Authors: Allena, Rachele; Muñoz Romero, José; Aubry, Denis
Abstract: During the early stages of gastrulation in Drosophila embryo, the epithelial cells composing the single tissue layer of the egg undergo large strains and displacements. These movements have been usually modeled by decomposing the total deformation gradient in an (imposed or strain/stress dependent) active part and a passive response. Although the influence of the chemical and genetic activity in the mechanical response of the cell has been experimentally observed, the effects of the mechanical deformation on the latter has been far less studied, and much less modeled. Here, we propose a model which couples morphogen transport and the cell mechanics during embryogenesis. A diffusion-reaction equation is introduced as an additional mechanical regulator of morphogenesis. Consequently, the active deformations are not directly
2 imposed in the analytical formulation, but they rather depend on the morphogen concentration, which is introduced as a new variable. In this work, we show that similar strain patterns to those observed during biological experiments can be reproduced by properly combining the two phenomena. Additionally, we use a novel technique to parameterize the embryo geometry by solving two Laplace problems with specific boundary conditions. We apply the method to two morphogenetic movements: ventral furrow invagination and germ band extension. The matching between our results and the observed experimental deformations confirms that diffusion-reaction of morphogens can actually be controlling large morphogenetic movements.Thu, 19 Dec 2013 10:50:57 GMThttp://hdl.handle.net/2117/210632013-12-19T10:50:57ZAllena, Rachele; Muñoz Romero, José; Aubry, DenisnoDuring the early stages of gastrulation in Drosophila embryo, the epithelial cells composing the single tissue layer of the egg undergo large strains and displacements. These movements have been usually modeled by decomposing the total deformation gradient in an (imposed or strain/stress dependent) active part and a passive response. Although the influence of the chemical and genetic activity in the mechanical response of the cell has been experimentally observed, the effects of the mechanical deformation on the latter has been far less studied, and much less modeled. Here, we propose a model which couples morphogen transport and the cell mechanics during embryogenesis. A diffusion-reaction equation is introduced as an additional mechanical regulator of morphogenesis. Consequently, the active deformations are not directly
2 imposed in the analytical formulation, but they rather depend on the morphogen concentration, which is introduced as a new variable. In this work, we show that similar strain patterns to those observed during biological experiments can be reproduced by properly combining the two phenomena. Additionally, we use a novel technique to parameterize the embryo geometry by solving two Laplace problems with specific boundary conditions. We apply the method to two morphogenetic movements: ventral furrow invagination and germ band extension. The matching between our results and the observed experimental deformations confirms that diffusion-reaction of morphogens can actually be controlling large morphogenetic movements.Stability of anchored sheet wall in cohesive-frictional soils by FE limit analysis
http://hdl.handle.net/2117/21062
Title: Stability of anchored sheet wall in cohesive-frictional soils by FE limit analysis
Authors: Muñoz Romero, José; Lyamin, Andrei; Huerta, AntonioThu, 19 Dec 2013 10:37:37 GMThttp://hdl.handle.net/2117/210622013-12-19T10:37:37ZMuñoz Romero, José; Lyamin, Andrei; Huerta, AntonionoPGD-based “Computational Vademecum” for efficient design, optimization and control
http://hdl.handle.net/2117/21044
Title: PGD-based “Computational Vademecum” for efficient design, optimization and control
Authors: Chinesta, Francisco; Leygue, Adrien; Bordeu, F.; Cueto Prendes, Elias; González, David; Alfaro, Icíar; Ammar, Amine; Huerta, Antonio; Díez, Pedro
Abstract: D
espite the impressive progresses
attained by simulation capabilities and
techniques, some challenging problems
remain today intractable. These prob-
lems, that are common to many branches
of science and engineering, are of differ-
ent nature. Among them, we can cite
those related to high-dimensional models,
on which mesh-based approaches fail due
to the exponential increase of degrees of
freedom. Other challenging scenarios
concern problems requiring many direct
solutions (optimization, inverse identifica-
tion, uncertainty quantification
!
) or those
needing very fast solutions (real time
simulation, simulation based control
!
).Wed, 18 Dec 2013 13:20:22 GMThttp://hdl.handle.net/2117/210442013-12-18T13:20:22ZChinesta, Francisco; Leygue, Adrien; Bordeu, F.; Cueto Prendes, Elias; González, David; Alfaro, Icíar; Ammar, Amine; Huerta, Antonio; Díez, PedronoD
espite the impressive progresses
attained by simulation capabilities and
techniques, some challenging problems
remain today intractable. These prob-
lems, that are common to many branches
of science and engineering, are of differ-
ent nature. Among them, we can cite
those related to high-dimensional models,
on which mesh-based approaches fail due
to the exponential increase of degrees of
freedom. Other challenging scenarios
concern problems requiring many direct
solutions (optimization, inverse identifica-
tion, uncertainty quantification
!
) or those
needing very fast solutions (real time
simulation, simulation based control
!
).High-order mesh generation on CAD geometries
http://hdl.handle.net/2117/21005
Title: High-order mesh generation on CAD geometries
Authors: Gargallo Peiró, Abel; Roca Navarro, Xevi; Peraire Guitart, Jaume; Sarrate Ramos, Josep
Abstract: We present a technique to extend Jacobian-based distortion (quality) measures
for planar triangles to high-order isoparametric elements of any interpolation degree on CAD parameterized surfaces. The resulting distortion (quality) measures are expressed in terms of the parametric coordinates of the nodes. These extended distortion (quality) measures can be used to check the quality and validity of a high-order surface mesh. We also apply them to simultaneously smooth and untangle high-order surface meshes by minimizing
the extended distortion measure. The minimization is performed in terms of the
parametric coordinates of the nodes. Thus, the nodes always lie on the surface. Finally,
we include several examples to illustrate the application of the proposed technique.Mon, 16 Dec 2013 13:23:38 GMThttp://hdl.handle.net/2117/210052013-12-16T13:23:38ZGargallo Peiró, Abel; Roca Navarro, Xevi; Peraire Guitart, Jaume; Sarrate Ramos, Josepnohigh-order quality, high-order mesh generation, mesh optimization, curved elements, parameterized surfacesWe present a technique to extend Jacobian-based distortion (quality) measures
for planar triangles to high-order isoparametric elements of any interpolation degree on CAD parameterized surfaces. The resulting distortion (quality) measures are expressed in terms of the parametric coordinates of the nodes. These extended distortion (quality) measures can be used to check the quality and validity of a high-order surface mesh. We also apply them to simultaneously smooth and untangle high-order surface meshes by minimizing
the extended distortion measure. The minimization is performed in terms of the
parametric coordinates of the nodes. Thus, the nodes always lie on the surface. Finally,
we include several examples to illustrate the application of the proposed technique.Preserving isotropic element size functions in adaptivity, quadrilateral and hexahedral mesh generation
http://hdl.handle.net/2117/21003
Title: Preserving isotropic element size functions in adaptivity, quadrilateral and hexahedral mesh generation
Authors: Ruiz-Gironés, Eloi; Roca Navarro, Xevi; Sarrate Ramos, Josep
Abstract: In electric circuit theory, it is of great interest to compute the effective resistance between any pair of vertices of a network, as well as the Kirchhoff Index. During the last decade these parametres have been applied in Organic Chemistry as natural structural indexes different from the usual ones in order to achieve an improvement in the discrimination between different molecules which have similar structural behaviours. Moreover, a wide range of generalized Kirchhoff Indexes for some networks have been introduced. The objective of the present work is to obtain the Kirchhoff Index for a wide range of composite networks known as cluster networks.Mon, 16 Dec 2013 13:01:19 GMThttp://hdl.handle.net/2117/210032013-12-16T13:01:19ZRuiz-Gironés, Eloi; Roca Navarro, Xevi; Sarrate Ramos, JosepnoKirchhoff Index, effective resistances, combinatorial laplacian, clusterIn electric circuit theory, it is of great interest to compute the effective resistance between any pair of vertices of a network, as well as the Kirchhoff Index. During the last decade these parametres have been applied in Organic Chemistry as natural structural indexes different from the usual ones in order to achieve an improvement in the discrimination between different molecules which have similar structural behaviours. Moreover, a wide range of generalized Kirchhoff Indexes for some networks have been introduced. The objective of the present work is to obtain the Kirchhoff Index for a wide range of composite networks known as cluster networks.Slope effects on SWAT modeling in a mountainous basin
http://hdl.handle.net/2117/20941
Title: Slope effects on SWAT modeling in a mountainous basin
Authors: Yacoub López, Cristina; Pérez Foguet, Agustí
Abstract: The soil and water assessment tool (SWAT) is a distributed basin model that includes the option of defining spatial discretization in terms of terrain slope. Influence of terrain slope in runoff results from mountain basins is a determining factor in its simulation results; however, its use as a criterion for basin discretization and for the parameter calibration has not yet been analyzed. In this study, this influence is analyzed for calibrations using two different cases. Ten discretization cases were carried out to evaluate the relative importance of slope discretization compared with other discretization criteria. Data from 1999–2005 were used for model calibration, and those from 2006–2009, for model validation. Parameter identification and specification were performed with the combined latin hypercube and one-factor-at-a-time (LH-OAT) and the shuffled complex evolution-uncertainty analysis methods (SCE-UA), respectively. All cases resulted in very good statistical values, with the Nash-Sutcliffe efficiency coefficient of 0.82–0.85, a bias of 2–10%, and the observations standard deviation ratio of 0.4–0.3. More realistic calibrated parameters were found when terrain slope variation was not included in the spatial discretization criteria. The inclusion of slope did not significantly improve simulations results when a good set of parameters was used, but it did enhance the calibration when a reduced number of subbasins was used.Mon, 09 Dec 2013 14:31:24 GMThttp://hdl.handle.net/2117/209412013-12-09T14:31:24ZYacoub López, Cristina; Pérez Foguet, AgustínoAutocalibration, Hydrological parameters, Sensitivity analysis, Spatial discretization, Uncertainty.The soil and water assessment tool (SWAT) is a distributed basin model that includes the option of defining spatial discretization in terms of terrain slope. Influence of terrain slope in runoff results from mountain basins is a determining factor in its simulation results; however, its use as a criterion for basin discretization and for the parameter calibration has not yet been analyzed. In this study, this influence is analyzed for calibrations using two different cases. Ten discretization cases were carried out to evaluate the relative importance of slope discretization compared with other discretization criteria. Data from 1999–2005 were used for model calibration, and those from 2006–2009, for model validation. Parameter identification and specification were performed with the combined latin hypercube and one-factor-at-a-time (LH-OAT) and the shuffled complex evolution-uncertainty analysis methods (SCE-UA), respectively. All cases resulted in very good statistical values, with the Nash-Sutcliffe efficiency coefficient of 0.82–0.85, a bias of 2–10%, and the observations standard deviation ratio of 0.4–0.3. More realistic calibrated parameters were found when terrain slope variation was not included in the spatial discretization criteria. The inclusion of slope did not significantly improve simulations results when a good set of parameters was used, but it did enhance the calibration when a reduced number of subbasins was used.Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables
http://hdl.handle.net/2117/20940
Title: Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables
Authors: Hashemian, B.; Millán, Raul Daniel; Arroyo Balaguer, Marino
Abstract: Collective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability to automatically characterize molecular collective behavior. Unfortunately, these methods fail to provide a differentiable function mapping high-dimensional configurations to their low-dimensional representation, as required in enhanced sampling methods. We introduce a methodology that, starting from an ensemble representative of molecular flexibility, builds smooth and nonlinear data-driven collective variables (SandCV) from the output of nonlinear manifold learning algorithms. We demonstrate the method with a standard benchmark molecule, alanine dipeptide, and show how it can be non-intrusively combined with off-the-shelf enhanced sampling methods, here the adaptive biasing force method. We illustrate how enhanced sampling simulations with SandCV can explore regions that were poorly sampled in the original molecular ensemble. We further explore the transferability of SandCV from a simpler system, alanine dipeptide in vacuum, to a more complex system, alanine dipeptide in explicit water.Mon, 09 Dec 2013 13:02:47 GMThttp://hdl.handle.net/2117/209402013-12-09T13:02:47ZHashemian, B.; Millán, Raul Daniel; Arroyo Balaguer, MarinonoCollective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability to automatically characterize molecular collective behavior. Unfortunately, these methods fail to provide a differentiable function mapping high-dimensional configurations to their low-dimensional representation, as required in enhanced sampling methods. We introduce a methodology that, starting from an ensemble representative of molecular flexibility, builds smooth and nonlinear data-driven collective variables (SandCV) from the output of nonlinear manifold learning algorithms. We demonstrate the method with a standard benchmark molecule, alanine dipeptide, and show how it can be non-intrusively combined with off-the-shelf enhanced sampling methods, here the adaptive biasing force method. We illustrate how enhanced sampling simulations with SandCV can explore regions that were poorly sampled in the original molecular ensemble. We further explore the transferability of SandCV from a simpler system, alanine dipeptide in vacuum, to a more complex system, alanine dipeptide in explicit water.