The Experts below are selected from a list of 297 Experts worldwide ranked by ideXlab platform

Michael J. Simmons - One of the best experts on this subject based on the ideXlab platform.

  • a test for enhancement of cytotype regulation in drosophila melanogaster by the transposase encoding p element 2 3
    Molecular Genetics and Genomics, 2013
    Co-Authors: Peter J Merriman, Michael J. Simmons
    Abstract:

    Transposable P elements are regulated in the germ line by piRNAs, which are small RNAs that associate with the Piwi class of proteins. This regulation, called the P cytotype, is enhanced by genetic interactions between P elements that are primary sources of these RNAs and other P elements. The enhanced regulation is thought to reflect amplification of the primary piRNAs by cleavage of mRNAs derived from the other P elements through a mechanism called the ping-pong cycle. We tested the transposase-encoding P element known as ∆2-3 for its ability to enhance cytotype regulation anchored in P elements inserted at the telomere of the left arm of the X chromosome (TP elements). The ∆2-3 P element lacks the intron between exons 2 and 3 in the structurally complete P element (CP). Unlike the CP element, it does not markedly enhance cytotype regulation anchored in TP elements, nor does it transmit transposase activity through the egg cytoplasm. However, mRNAs from both the CP and ∆2-3 elements are maternally deposited in embryos. These observations suggest that maternally transmitted CP mRNA enhances cytotype regulation by participating in the ping-pong cycle and that it encodes the P transposase in the embryonic germ line, whereas maternally transmitted ∆2-3 mRNA does not, possibly because it is not efficiently directed into the primordial embryonic germ line. Strong transposon regulation may, therefore, require ping-pong cycling with maternally inherited mRNAs in the embryo.

  • cytotype regulation of p transposable elements in drosophila melanogaster repressor polypeptides or pirnas
    Genetics, 2008
    Co-Authors: Philip A Jensen, Jeremy R Stuart, Michael P Goodpaster, Joseph W. Goodman, Michael J. Simmons
    Abstract:

    The telomeric P elements TP5 and TP6 are associated with the P cytotype, a maternally inherited condition that represses P-element-induced hybrid dysgenesis in the Drosophila germ line. To see if cytotype repression by TP5 and TP6 might be mediated by the polypeptides they could encode, hobo transgenes carrying these elements were tested for expression of mRNA in the female germ line and for repression of hybrid dysgenesis. The TP5 and TP6 transgenes expressed more germ-line mRNA than the native telomeric P elements, but they were decidedly inferior to the native elements in their ability to repress hybrid dysgenesis. These paradoxical results are inconsistent with the repressor polypeptide model of cytotype. An alternative model based on the destruction of P transposase mRNA by Piwi-interacting (pi) RNAs was supported by finding reduced P mRNA levels in flies that carried the native telomeric P elements, which are inserted in a known major piRNA locus.

Mathieu Morlighem - One of the best experts on this subject based on the ideXlab platform.

  • Representation of basal melting at the grounding line in ice flow models
    The Cryosphere, 2018
    Co-Authors: Hélène Seroussi, Mathieu Morlighem
    Abstract:

    Abstract. While a lot of attention has been given to the numerical implementation of grounding lines and basal friction in the grounding zone, little has been done about the impact of the numerical treatment of ocean-induced basal melting in this region. Several strategies are currently being employed in the ice sheet modeling community, and the resulting grounding line dynamics may differ strongly, which ultimately adds significant uncertainty to the projected contribution of marine ice sheets to sea level rise. We investigate here several implementations of basal melt parameterization on partially floating elements in a finite-element framework, based on the Marine Ice Sheet–Ocean Model Intercomparison Project (MISOMIP) setup: (1) melt applied only to entirely floating elements, (2) melt applied over all elements that are crossed by the grounding line, and (3) melt integrated partially over the floating portion of a finite element using two different sub-element integration methods. All methods converge towards the same state when the mesh resolution is fine enough. However, (2) and (3) will systematically overestimate the rate of grounding line retreat in coarser resolutions, while (1) converges faster to the solution in most cases. The differences between sub-element parameterizations are exacerbated for experiments with high melting rates in the vicinity of the grounding line and for a Weertman sliding law. As most real-world simulations use horizontal mesh resolutions of several hundreds of meters at best, and high melt rates are generally present close to the grounding lines, we recommend not using (3) to avoid overestimating the rate of grounding line retreat and to carefully assess the impact of mesh resolution and sub-element melt parameterizations on all simulation results.

  • Representation of basal melting at the grounding line in ice flow models
    2018
    Co-Authors: Hélène Seroussi, Mathieu Morlighem
    Abstract:

    Abstract. While a lot of attention has been given to the numerical implementation of grounding lines and basal friction in the grounding zone, little has been done about the impact of the numerical treatment of ocean-induced basal melting in this region. Several strategies are currently being employed in the ice sheet modeling community, and the resulting grounding line dynamics may differ strongly, which ultimately add significant uncertainty to the projected contribution of marine ice sheets to sea level rise. We investigate here several implementations of basal melt parameterization on partially floating elements in a finite element framework, based on the Marine Ice Sheet-Ocean Model Intercomparison Project (MISOMIP) setup: (1) melt applied only to entirely floating elements, (2) melt applied over the entire elements that are crossed by the grounding line, and (3) melt integrated partially over the floating portion of a finite element using two different sub-element integration methods. All methods converge towards the same state when the mesh resolution is fine enough. However, (2) and (3) will systematically overestimate the rate of grounding line retreat in coarser resolutions, while (1) converges faster to the solution in most cases. The differences between sub-element parameterizations are exacerbated for experiments with large melting rates in the vicinity of the grounding line and for a Weertman sliding law. As most real-world simulations use horizontal mesh resolutions of several hundreds of meters at best, and large melt rates are generally present close to the grounding lines, we recommend using (1) to avoid overestimating the rate of grounding line retreat.

Eugenio Oñate - One of the best experts on this subject based on the ideXlab platform.

  • 2d particle contact based meshfree method in cdem and its application in geotechnical problems
    Engineering Computations, 2015
    Co-Authors: Chun Feng, Eugenio Oñate
    Abstract:

    Purpose - Continuum-based discrete element method is an explicit numerical method, which is a combination of block discrete element method (DEM) and FEM. When simulating large deformation problems, such as cutting, blasting, water-like material flowing, the distortion of elements will lead to no convergence of the numerical system. To solve the convergence problem, a particle contact-based meshfree method (PCMM) is introduced in. The paper aims to discuss this issue. Design/methodology/approach - PCMM is based on traditional particle DEM, and use particle contacts to generate triangular elements. If three particles are contact with each other, the element will be created. Once elements are created, the macroscopic constitutive law could be introduced in. When large deformation of element occurs, the contact relationship between particles will be changed. Those elements that do not meet the contact condition will be deleted, and new elements that coincide with the relationship will be generated. By the deletion and creation of elements, the convergence problem induced by element distortion will be eliminated. To solve FEM and PCMM coupled problems, a point-edge contact model is introduced in, and normal and tangential springs are adopted to transfer the contact force between particles and blocks. Findings - According to the deletion and recreation of elements based on particle contacts, PCMM could simulate large deformation problems. Some numerical cases (i.e. elastic field testing, uniaxial compression analysis and wave propagation simulation) show the accuracy of PCMM, and others (i.e. soil cutting, contact burst and water-like material flowing) show the rationality of PCMM. Originality/value - In traditional particle DEM, contact relationships are used to calculate contact forces. But in PCMM, contact relationships are adopted to generate elements. Compared to other meshfree methods, in PCMM, the element automatic deletion and recreation technique is used to solve large deformation problems.

  • 2D particle contact-based meshfree method in CDEM and its application in geotechnical problems
    Engineering Computations, 2015
    Co-Authors: Chun Feng, Eugenio Oñate
    Abstract:

    Continuum-based discrete element method is an explicit numerical method, which is a combination of block discrete element method (DEM) and FEM. When simulating large deformation problems, such as cutting, blasting, water-like material flowing, the distortion of elements will lead to no convergence of the numerical system. To solve the convergence problem, a particle contact-based meshfree method (PCMM) is introduced in. The paper aims to discuss this issue.\ud PCMM is based on traditional particle DEM, and use particle contacts to generate triangular elements. If three particles are contact with each other, the element will be created. Once elements are created, the macroscopic constitutive law could be introduced in. When large deformation of element occurs, the contact relationship between particles will be changed. Those elements that do not meet the contact condition will be deleted, and new elements that coincide with the relationship will be generated. By the deletion and creation of elements, the convergence problem induced by element distortion will be eliminated. To solve FEM and PCMM coupled problems, a point-edge contact model is introduced in, and normal and tangential springs are adopted to transfer the contact force between particles and blocks.\ud According to the deletion and recreation of elements based on particle contacts, PCMM could simulate large deformation problems. Some numerical cases (i.e. elastic field testing, uniaxial compression analysis and wave propagation simulation) show the accuracy of PCMM, and others (i.e. soil cutting, contact burst and water-like material flowing) show the rationality of PCMM.\ud In traditional particle DEM, contact relationships are used to calculate contact forces. But in PCMM, contact relationships are adopted to generate elements. Compared to other meshfree methods, in PCMM, the element automatic deletion and recreation technique is used to solve large deformation problems.Peer ReviewedPostprint (published version

Hélène Seroussi - One of the best experts on this subject based on the ideXlab platform.

  • Representation of basal melting at the grounding line in ice flow models
    The Cryosphere, 2018
    Co-Authors: Hélène Seroussi, Mathieu Morlighem
    Abstract:

    Abstract. While a lot of attention has been given to the numerical implementation of grounding lines and basal friction in the grounding zone, little has been done about the impact of the numerical treatment of ocean-induced basal melting in this region. Several strategies are currently being employed in the ice sheet modeling community, and the resulting grounding line dynamics may differ strongly, which ultimately adds significant uncertainty to the projected contribution of marine ice sheets to sea level rise. We investigate here several implementations of basal melt parameterization on partially floating elements in a finite-element framework, based on the Marine Ice Sheet–Ocean Model Intercomparison Project (MISOMIP) setup: (1) melt applied only to entirely floating elements, (2) melt applied over all elements that are crossed by the grounding line, and (3) melt integrated partially over the floating portion of a finite element using two different sub-element integration methods. All methods converge towards the same state when the mesh resolution is fine enough. However, (2) and (3) will systematically overestimate the rate of grounding line retreat in coarser resolutions, while (1) converges faster to the solution in most cases. The differences between sub-element parameterizations are exacerbated for experiments with high melting rates in the vicinity of the grounding line and for a Weertman sliding law. As most real-world simulations use horizontal mesh resolutions of several hundreds of meters at best, and high melt rates are generally present close to the grounding lines, we recommend not using (3) to avoid overestimating the rate of grounding line retreat and to carefully assess the impact of mesh resolution and sub-element melt parameterizations on all simulation results.

  • Representation of basal melting at the grounding line in ice flow models
    2018
    Co-Authors: Hélène Seroussi, Mathieu Morlighem
    Abstract:

    Abstract. While a lot of attention has been given to the numerical implementation of grounding lines and basal friction in the grounding zone, little has been done about the impact of the numerical treatment of ocean-induced basal melting in this region. Several strategies are currently being employed in the ice sheet modeling community, and the resulting grounding line dynamics may differ strongly, which ultimately add significant uncertainty to the projected contribution of marine ice sheets to sea level rise. We investigate here several implementations of basal melt parameterization on partially floating elements in a finite element framework, based on the Marine Ice Sheet-Ocean Model Intercomparison Project (MISOMIP) setup: (1) melt applied only to entirely floating elements, (2) melt applied over the entire elements that are crossed by the grounding line, and (3) melt integrated partially over the floating portion of a finite element using two different sub-element integration methods. All methods converge towards the same state when the mesh resolution is fine enough. However, (2) and (3) will systematically overestimate the rate of grounding line retreat in coarser resolutions, while (1) converges faster to the solution in most cases. The differences between sub-element parameterizations are exacerbated for experiments with large melting rates in the vicinity of the grounding line and for a Weertman sliding law. As most real-world simulations use horizontal mesh resolutions of several hundreds of meters at best, and large melt rates are generally present close to the grounding lines, we recommend using (1) to avoid overestimating the rate of grounding line retreat.

Chun Feng - One of the best experts on this subject based on the ideXlab platform.

  • 2d particle contact based meshfree method in cdem and its application in geotechnical problems
    Engineering Computations, 2015
    Co-Authors: Chun Feng, Eugenio Oñate
    Abstract:

    Purpose - Continuum-based discrete element method is an explicit numerical method, which is a combination of block discrete element method (DEM) and FEM. When simulating large deformation problems, such as cutting, blasting, water-like material flowing, the distortion of elements will lead to no convergence of the numerical system. To solve the convergence problem, a particle contact-based meshfree method (PCMM) is introduced in. The paper aims to discuss this issue. Design/methodology/approach - PCMM is based on traditional particle DEM, and use particle contacts to generate triangular elements. If three particles are contact with each other, the element will be created. Once elements are created, the macroscopic constitutive law could be introduced in. When large deformation of element occurs, the contact relationship between particles will be changed. Those elements that do not meet the contact condition will be deleted, and new elements that coincide with the relationship will be generated. By the deletion and creation of elements, the convergence problem induced by element distortion will be eliminated. To solve FEM and PCMM coupled problems, a point-edge contact model is introduced in, and normal and tangential springs are adopted to transfer the contact force between particles and blocks. Findings - According to the deletion and recreation of elements based on particle contacts, PCMM could simulate large deformation problems. Some numerical cases (i.e. elastic field testing, uniaxial compression analysis and wave propagation simulation) show the accuracy of PCMM, and others (i.e. soil cutting, contact burst and water-like material flowing) show the rationality of PCMM. Originality/value - In traditional particle DEM, contact relationships are used to calculate contact forces. But in PCMM, contact relationships are adopted to generate elements. Compared to other meshfree methods, in PCMM, the element automatic deletion and recreation technique is used to solve large deformation problems.

  • 2D particle contact-based meshfree method in CDEM and its application in geotechnical problems
    Engineering Computations, 2015
    Co-Authors: Chun Feng, Eugenio Oñate
    Abstract:

    Continuum-based discrete element method is an explicit numerical method, which is a combination of block discrete element method (DEM) and FEM. When simulating large deformation problems, such as cutting, blasting, water-like material flowing, the distortion of elements will lead to no convergence of the numerical system. To solve the convergence problem, a particle contact-based meshfree method (PCMM) is introduced in. The paper aims to discuss this issue.\ud PCMM is based on traditional particle DEM, and use particle contacts to generate triangular elements. If three particles are contact with each other, the element will be created. Once elements are created, the macroscopic constitutive law could be introduced in. When large deformation of element occurs, the contact relationship between particles will be changed. Those elements that do not meet the contact condition will be deleted, and new elements that coincide with the relationship will be generated. By the deletion and creation of elements, the convergence problem induced by element distortion will be eliminated. To solve FEM and PCMM coupled problems, a point-edge contact model is introduced in, and normal and tangential springs are adopted to transfer the contact force between particles and blocks.\ud According to the deletion and recreation of elements based on particle contacts, PCMM could simulate large deformation problems. Some numerical cases (i.e. elastic field testing, uniaxial compression analysis and wave propagation simulation) show the accuracy of PCMM, and others (i.e. soil cutting, contact burst and water-like material flowing) show the rationality of PCMM.\ud In traditional particle DEM, contact relationships are used to calculate contact forces. But in PCMM, contact relationships are adopted to generate elements. Compared to other meshfree methods, in PCMM, the element automatic deletion and recreation technique is used to solve large deformation problems.Peer ReviewedPostprint (published version