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Robert E. Dickinson - One of the best experts on this subject based on the ideXlab platform.

  • Reply to comment by Dekker and Rietkerk on “Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation”
    Geophysical Research Letters, 2005
    Co-Authors: Xiaodong Zeng, Samuel S. P. Shen, Xubin Zeng, Robert E. Dickinson
    Abstract:

    [1] Dekker and Rietkerk [2005] (hereinafter referred to as DR) raise some valid points regarding our paper ‘‘Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation’’ [Zeng et al., 2004] (hereinafter referred to as XZ). We appreciate the opportunity to clarify these issues here and hope this dialogue (between scientists working on horizontal interaction and spatial patterns and those who are more interested in the area-averaged land-atmosphere interactions) will shed some new lights on the overall land modeling over arid and semiarid regions. [2] DR argued that XZ ignored well-known spatial processes, leading to spatial pattern formation, no abrupt boundaries, and dramatically changing parameter regions. As a single column model, by definition, horizontal interactions cannot be explicitly included and spatial patterns cannot be produced in XZ. However, this does not mean that the area-averaged effects of these spatial patterns are completely ignored. In fact, horizontal heterogeneity is included in XZ by separately considering processes (e.g., evaporation, transpiration, runoff) over the vegetated and non-vegetated areas in a single column. The use of average soil water over the column also implies an (instantaneous) horizontal water exchange between these two areas. In contrast, models on spatial patterns as reviewed by Rietkerk et al. [2004] would divide this single column into numerous small cells. While the horizontal interaction among different cells is considered in these models, each cell is assumed to be uniformly covered by vegetation (i.e., without considering bare soil fraction). [3] Different mechanisms have been proposed to explain the self-organized spatial patterns, as summarized byRietkerk et al. [2004]. The essence of all these mechanisms is that water is more concentrated into patches of vegetation due to spatial interactions over arid and semiarid regions. Since our single column model contains only the soil water averaged over vegetated and non-vegetated areas, the above effect can be largely represented by the increase of the exponential coefficient in the biomass growth dependence on soil water (i.e., XZ, e0 g in equation (4)). Indeed, Figure 1 shows that, as e0 g increases, the parameter regime of bistability between m1 and m2 shifts towards left, in agreement with Figure 2 of DR. Detailed discussion of the sensitivity of the parameter regime of bistability to all model parameters is given by Zeng et al. [2005]. Further, in Figure 1 vegetated states at different e0 g do not converge to the same state, in agreement with van de Koppel and Rietkerk [2004]. In contrast, it is unclear how DR draw their Figure 2 where the vegetated states with or without spatial interactions intercept with each other at a higher resource input, which is inconsistent with van de Koppel and Rietkerk [2004] and Figure 1 here. [4] We also agree with DR that, visually, vegetation boundaries are not abrupt but go through a diversity of vegetation patterns instead over arid and semiarid regions, and we regret that this point was not explicitly stated in XZ. However, the abrupt change was discussed in terms of biomass in XZ and other references cited in DR. For instance, Figure 1 shows that a small perturbation near the unstable Equilibrium state or a small variation in moisture index near the critical points m1 and m2 may lead to a desert or vegetated state. Note that the vegetated state in our single column model still contains non-vegetated area and may correspond to a particular spatial pattern [e.g., see Rietkerk et al., 2004, Figure 3]. Therefore, even though our model cannot predict specific spatial patterns, it can still predict vegetation boundaries in terms of biomass. [5] In summary, while horizontal interactions and spatial patterns are not explicitly considered in XZ, their effect averaged over an area can be implicitly represented by the adjustment of model coefficients, and the results in XZ on abrupt boundaries in terms of biomass and parameter regimes remain correct. [6] While the model in XZ emphasizes vertical interactions between vegetation and soil water (e.g., inclusion of wilted biomass that is very important over temperate grassland), other models as reviewed by Rietkerk et al. [2004] GEOPHYSICAL RESEARCH LETTERS, VOL. 32, L09403, doi:10.1029/2004GL022339, 2005

  • Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation
    Geophysical Research Letters, 2004
    Co-Authors: Xiaodong Zeng, Samuel S. P. Shen, Xubin Zeng, Robert E. Dickinson
    Abstract:

    [1] In semi-arid areas, Multiple Equilibrium states of an ecosystem (e.g., grassland and desert) are found to coexist, and the transition from grassland to desert is often abrupt at the boundary. A simple ecosystem model is developed to provide the biophysical explanation of this phenomenon. The model has three variables: living biomass, wilted biomass, and soil wetness. The moisture index, which is the ratio of the annual precipitation to potential evaporation, is the only external climate driving force, and the key mechanism is the vegetation-soil interaction. It is found that the maintenance of a grassland requires a minimum moisture index, and the abrupt transition occurs when the moisture index is around this critical value. These results are robust within a wide range for most model parameters, suggesting that the model may be applicable to other temperate grasslands. The characteristics of the wilted biomass also strongly influence the ecosystem's dynamics.

Xiaodong Zeng - One of the best experts on this subject based on the ideXlab platform.

  • Reply to comment by Dekker and Rietkerk on “Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation”
    Geophysical Research Letters, 2005
    Co-Authors: Xiaodong Zeng, Samuel S. P. Shen, Xubin Zeng, Robert E. Dickinson
    Abstract:

    [1] Dekker and Rietkerk [2005] (hereinafter referred to as DR) raise some valid points regarding our paper ‘‘Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation’’ [Zeng et al., 2004] (hereinafter referred to as XZ). We appreciate the opportunity to clarify these issues here and hope this dialogue (between scientists working on horizontal interaction and spatial patterns and those who are more interested in the area-averaged land-atmosphere interactions) will shed some new lights on the overall land modeling over arid and semiarid regions. [2] DR argued that XZ ignored well-known spatial processes, leading to spatial pattern formation, no abrupt boundaries, and dramatically changing parameter regions. As a single column model, by definition, horizontal interactions cannot be explicitly included and spatial patterns cannot be produced in XZ. However, this does not mean that the area-averaged effects of these spatial patterns are completely ignored. In fact, horizontal heterogeneity is included in XZ by separately considering processes (e.g., evaporation, transpiration, runoff) over the vegetated and non-vegetated areas in a single column. The use of average soil water over the column also implies an (instantaneous) horizontal water exchange between these two areas. In contrast, models on spatial patterns as reviewed by Rietkerk et al. [2004] would divide this single column into numerous small cells. While the horizontal interaction among different cells is considered in these models, each cell is assumed to be uniformly covered by vegetation (i.e., without considering bare soil fraction). [3] Different mechanisms have been proposed to explain the self-organized spatial patterns, as summarized byRietkerk et al. [2004]. The essence of all these mechanisms is that water is more concentrated into patches of vegetation due to spatial interactions over arid and semiarid regions. Since our single column model contains only the soil water averaged over vegetated and non-vegetated areas, the above effect can be largely represented by the increase of the exponential coefficient in the biomass growth dependence on soil water (i.e., XZ, e0 g in equation (4)). Indeed, Figure 1 shows that, as e0 g increases, the parameter regime of bistability between m1 and m2 shifts towards left, in agreement with Figure 2 of DR. Detailed discussion of the sensitivity of the parameter regime of bistability to all model parameters is given by Zeng et al. [2005]. Further, in Figure 1 vegetated states at different e0 g do not converge to the same state, in agreement with van de Koppel and Rietkerk [2004]. In contrast, it is unclear how DR draw their Figure 2 where the vegetated states with or without spatial interactions intercept with each other at a higher resource input, which is inconsistent with van de Koppel and Rietkerk [2004] and Figure 1 here. [4] We also agree with DR that, visually, vegetation boundaries are not abrupt but go through a diversity of vegetation patterns instead over arid and semiarid regions, and we regret that this point was not explicitly stated in XZ. However, the abrupt change was discussed in terms of biomass in XZ and other references cited in DR. For instance, Figure 1 shows that a small perturbation near the unstable Equilibrium state or a small variation in moisture index near the critical points m1 and m2 may lead to a desert or vegetated state. Note that the vegetated state in our single column model still contains non-vegetated area and may correspond to a particular spatial pattern [e.g., see Rietkerk et al., 2004, Figure 3]. Therefore, even though our model cannot predict specific spatial patterns, it can still predict vegetation boundaries in terms of biomass. [5] In summary, while horizontal interactions and spatial patterns are not explicitly considered in XZ, their effect averaged over an area can be implicitly represented by the adjustment of model coefficients, and the results in XZ on abrupt boundaries in terms of biomass and parameter regimes remain correct. [6] While the model in XZ emphasizes vertical interactions between vegetation and soil water (e.g., inclusion of wilted biomass that is very important over temperate grassland), other models as reviewed by Rietkerk et al. [2004] GEOPHYSICAL RESEARCH LETTERS, VOL. 32, L09403, doi:10.1029/2004GL022339, 2005

  • Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation
    Geophysical Research Letters, 2004
    Co-Authors: Xiaodong Zeng, Samuel S. P. Shen, Xubin Zeng, Robert E. Dickinson
    Abstract:

    [1] In semi-arid areas, Multiple Equilibrium states of an ecosystem (e.g., grassland and desert) are found to coexist, and the transition from grassland to desert is often abrupt at the boundary. A simple ecosystem model is developed to provide the biophysical explanation of this phenomenon. The model has three variables: living biomass, wilted biomass, and soil wetness. The moisture index, which is the ratio of the annual precipitation to potential evaporation, is the only external climate driving force, and the key mechanism is the vegetation-soil interaction. It is found that the maintenance of a grassland requires a minimum moisture index, and the abrupt transition occurs when the moisture index is around this critical value. These results are robust within a wide range for most model parameters, suggesting that the model may be applicable to other temperate grasslands. The characteristics of the wilted biomass also strongly influence the ecosystem's dynamics.

Judit Ovádi - One of the best experts on this subject based on the ideXlab platform.

  • microtubule assembly derived by dimerization of tppp p25 evaluation of thermodynamic parameters for Multiple Equilibrium system from itc data
    Biochimica et Biophysica Acta, 2012
    Co-Authors: Judit Oláh, Ágnes Zotter, Emma Hlavanda, Sándor Szunyogh, Ferenc Orosz, Krisztián Szigeti, Judit Fidy, Judit Ovádi
    Abstract:

    article Background: The disordered Tubulin Polymerization Promoting Protein/p25 (TPPP/p25) modulates the dy- namics and stability of the microtubule system. In this paper the role of dimerization in its microtubule- related functions is established, and an approach is proposed to evaluate thermodynamic constants for mul- tiple Equilibrium systems from ITC measurements. Methods: For structural studies size exclusion chromatography, SDS-PAGE, chemical cross-linking, circular di- chroism, fluorescence spectroscopy and isothermal titration calorimetry were used; the functional effect was analyzed by tubulin polymerization assay. Numerical simulation of the Multiple Equilibrium was performed with Mathematica software. Results: The dimerization of TPPP/p25 is promoted by elevation of the protein concentration and by GTP ad- dition. The dimeric form displaying enhanced tubulin polymerization promoting activity is stabilized by di- sulfide bond or chemical cross-linking. The GTP binding to the dimeric form (Kd-GTP = 200 μM) is tighter with one order of magnitude than to the monomeric one leading to the enrichment of the dimers. A mathe- matical model elaborated for the Multiple Equilibrium of the TPPP/p25-GTP system was validated by fitting the GTP-dependent changes of ellipticity and fluorescence signal in the course of TPPP/p25 titrations. The evaluation of the Equilibrium constants rendered it possible to determine the thermodynamic parameters of the association of different TPPP/p25 forms with GTP from ITC measurements. Conclusions/General Significance: The dimerization of TPPP/p25 with favorable physiological functional poten- cy is proposed to play significant role in the fine tuning of TPPP/p25-mediated microtubule assembly; the un- folded monomers might be involved in the formation of pathological inclusions characteristic for Parkinson's disease and other synucleinopathies.

  • Microtubule assembly-derived by dimerization of TPPP/p25. Evaluation of thermodynamic parameters for Multiple Equilibrium system from ITC data.
    Biochimica et biophysica acta, 2012
    Co-Authors: Judit Oláh, Ágnes Zotter, Emma Hlavanda, Sándor Szunyogh, Ferenc Orosz, Krisztián Szigeti, Judit Fidy, Judit Ovádi
    Abstract:

    article Background: The disordered Tubulin Polymerization Promoting Protein/p25 (TPPP/p25) modulates the dy- namics and stability of the microtubule system. In this paper the role of dimerization in its microtubule- related functions is established, and an approach is proposed to evaluate thermodynamic constants for mul- tiple Equilibrium systems from ITC measurements. Methods: For structural studies size exclusion chromatography, SDS-PAGE, chemical cross-linking, circular di- chroism, fluorescence spectroscopy and isothermal titration calorimetry were used; the functional effect was analyzed by tubulin polymerization assay. Numerical simulation of the Multiple Equilibrium was performed with Mathematica software. Results: The dimerization of TPPP/p25 is promoted by elevation of the protein concentration and by GTP ad- dition. The dimeric form displaying enhanced tubulin polymerization promoting activity is stabilized by di- sulfide bond or chemical cross-linking. The GTP binding to the dimeric form (Kd-GTP = 200 μM) is tighter with one order of magnitude than to the monomeric one leading to the enrichment of the dimers. A mathe- matical model elaborated for the Multiple Equilibrium of the TPPP/p25-GTP system was validated by fitting the GTP-dependent changes of ellipticity and fluorescence signal in the course of TPPP/p25 titrations. The evaluation of the Equilibrium constants rendered it possible to determine the thermodynamic parameters of the association of different TPPP/p25 forms with GTP from ITC measurements. Conclusions/General Significance: The dimerization of TPPP/p25 with favorable physiological functional poten- cy is proposed to play significant role in the fine tuning of TPPP/p25-mediated microtubule assembly; the un- folded monomers might be involved in the formation of pathological inclusions characteristic for Parkinson's disease and other synucleinopathies.

Xubin Zeng - One of the best experts on this subject based on the ideXlab platform.

  • Reply to comment by Dekker and Rietkerk on “Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation”
    Geophysical Research Letters, 2005
    Co-Authors: Xiaodong Zeng, Samuel S. P. Shen, Xubin Zeng, Robert E. Dickinson
    Abstract:

    [1] Dekker and Rietkerk [2005] (hereinafter referred to as DR) raise some valid points regarding our paper ‘‘Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation’’ [Zeng et al., 2004] (hereinafter referred to as XZ). We appreciate the opportunity to clarify these issues here and hope this dialogue (between scientists working on horizontal interaction and spatial patterns and those who are more interested in the area-averaged land-atmosphere interactions) will shed some new lights on the overall land modeling over arid and semiarid regions. [2] DR argued that XZ ignored well-known spatial processes, leading to spatial pattern formation, no abrupt boundaries, and dramatically changing parameter regions. As a single column model, by definition, horizontal interactions cannot be explicitly included and spatial patterns cannot be produced in XZ. However, this does not mean that the area-averaged effects of these spatial patterns are completely ignored. In fact, horizontal heterogeneity is included in XZ by separately considering processes (e.g., evaporation, transpiration, runoff) over the vegetated and non-vegetated areas in a single column. The use of average soil water over the column also implies an (instantaneous) horizontal water exchange between these two areas. In contrast, models on spatial patterns as reviewed by Rietkerk et al. [2004] would divide this single column into numerous small cells. While the horizontal interaction among different cells is considered in these models, each cell is assumed to be uniformly covered by vegetation (i.e., without considering bare soil fraction). [3] Different mechanisms have been proposed to explain the self-organized spatial patterns, as summarized byRietkerk et al. [2004]. The essence of all these mechanisms is that water is more concentrated into patches of vegetation due to spatial interactions over arid and semiarid regions. Since our single column model contains only the soil water averaged over vegetated and non-vegetated areas, the above effect can be largely represented by the increase of the exponential coefficient in the biomass growth dependence on soil water (i.e., XZ, e0 g in equation (4)). Indeed, Figure 1 shows that, as e0 g increases, the parameter regime of bistability between m1 and m2 shifts towards left, in agreement with Figure 2 of DR. Detailed discussion of the sensitivity of the parameter regime of bistability to all model parameters is given by Zeng et al. [2005]. Further, in Figure 1 vegetated states at different e0 g do not converge to the same state, in agreement with van de Koppel and Rietkerk [2004]. In contrast, it is unclear how DR draw their Figure 2 where the vegetated states with or without spatial interactions intercept with each other at a higher resource input, which is inconsistent with van de Koppel and Rietkerk [2004] and Figure 1 here. [4] We also agree with DR that, visually, vegetation boundaries are not abrupt but go through a diversity of vegetation patterns instead over arid and semiarid regions, and we regret that this point was not explicitly stated in XZ. However, the abrupt change was discussed in terms of biomass in XZ and other references cited in DR. For instance, Figure 1 shows that a small perturbation near the unstable Equilibrium state or a small variation in moisture index near the critical points m1 and m2 may lead to a desert or vegetated state. Note that the vegetated state in our single column model still contains non-vegetated area and may correspond to a particular spatial pattern [e.g., see Rietkerk et al., 2004, Figure 3]. Therefore, even though our model cannot predict specific spatial patterns, it can still predict vegetation boundaries in terms of biomass. [5] In summary, while horizontal interactions and spatial patterns are not explicitly considered in XZ, their effect averaged over an area can be implicitly represented by the adjustment of model coefficients, and the results in XZ on abrupt boundaries in terms of biomass and parameter regimes remain correct. [6] While the model in XZ emphasizes vertical interactions between vegetation and soil water (e.g., inclusion of wilted biomass that is very important over temperate grassland), other models as reviewed by Rietkerk et al. [2004] GEOPHYSICAL RESEARCH LETTERS, VOL. 32, L09403, doi:10.1029/2004GL022339, 2005

  • Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation
    Geophysical Research Letters, 2004
    Co-Authors: Xiaodong Zeng, Samuel S. P. Shen, Xubin Zeng, Robert E. Dickinson
    Abstract:

    [1] In semi-arid areas, Multiple Equilibrium states of an ecosystem (e.g., grassland and desert) are found to coexist, and the transition from grassland to desert is often abrupt at the boundary. A simple ecosystem model is developed to provide the biophysical explanation of this phenomenon. The model has three variables: living biomass, wilted biomass, and soil wetness. The moisture index, which is the ratio of the annual precipitation to potential evaporation, is the only external climate driving force, and the key mechanism is the vegetation-soil interaction. It is found that the maintenance of a grassland requires a minimum moisture index, and the abrupt transition occurs when the moisture index is around this critical value. These results are robust within a wide range for most model parameters, suggesting that the model may be applicable to other temperate grasslands. The characteristics of the wilted biomass also strongly influence the ecosystem's dynamics.

Samuel S. P. Shen - One of the best experts on this subject based on the ideXlab platform.

  • Reply to comment by Dekker and Rietkerk on “Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation”
    Geophysical Research Letters, 2005
    Co-Authors: Xiaodong Zeng, Samuel S. P. Shen, Xubin Zeng, Robert E. Dickinson
    Abstract:

    [1] Dekker and Rietkerk [2005] (hereinafter referred to as DR) raise some valid points regarding our paper ‘‘Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation’’ [Zeng et al., 2004] (hereinafter referred to as XZ). We appreciate the opportunity to clarify these issues here and hope this dialogue (between scientists working on horizontal interaction and spatial patterns and those who are more interested in the area-averaged land-atmosphere interactions) will shed some new lights on the overall land modeling over arid and semiarid regions. [2] DR argued that XZ ignored well-known spatial processes, leading to spatial pattern formation, no abrupt boundaries, and dramatically changing parameter regions. As a single column model, by definition, horizontal interactions cannot be explicitly included and spatial patterns cannot be produced in XZ. However, this does not mean that the area-averaged effects of these spatial patterns are completely ignored. In fact, horizontal heterogeneity is included in XZ by separately considering processes (e.g., evaporation, transpiration, runoff) over the vegetated and non-vegetated areas in a single column. The use of average soil water over the column also implies an (instantaneous) horizontal water exchange between these two areas. In contrast, models on spatial patterns as reviewed by Rietkerk et al. [2004] would divide this single column into numerous small cells. While the horizontal interaction among different cells is considered in these models, each cell is assumed to be uniformly covered by vegetation (i.e., without considering bare soil fraction). [3] Different mechanisms have been proposed to explain the self-organized spatial patterns, as summarized byRietkerk et al. [2004]. The essence of all these mechanisms is that water is more concentrated into patches of vegetation due to spatial interactions over arid and semiarid regions. Since our single column model contains only the soil water averaged over vegetated and non-vegetated areas, the above effect can be largely represented by the increase of the exponential coefficient in the biomass growth dependence on soil water (i.e., XZ, e0 g in equation (4)). Indeed, Figure 1 shows that, as e0 g increases, the parameter regime of bistability between m1 and m2 shifts towards left, in agreement with Figure 2 of DR. Detailed discussion of the sensitivity of the parameter regime of bistability to all model parameters is given by Zeng et al. [2005]. Further, in Figure 1 vegetated states at different e0 g do not converge to the same state, in agreement with van de Koppel and Rietkerk [2004]. In contrast, it is unclear how DR draw their Figure 2 where the vegetated states with or without spatial interactions intercept with each other at a higher resource input, which is inconsistent with van de Koppel and Rietkerk [2004] and Figure 1 here. [4] We also agree with DR that, visually, vegetation boundaries are not abrupt but go through a diversity of vegetation patterns instead over arid and semiarid regions, and we regret that this point was not explicitly stated in XZ. However, the abrupt change was discussed in terms of biomass in XZ and other references cited in DR. For instance, Figure 1 shows that a small perturbation near the unstable Equilibrium state or a small variation in moisture index near the critical points m1 and m2 may lead to a desert or vegetated state. Note that the vegetated state in our single column model still contains non-vegetated area and may correspond to a particular spatial pattern [e.g., see Rietkerk et al., 2004, Figure 3]. Therefore, even though our model cannot predict specific spatial patterns, it can still predict vegetation boundaries in terms of biomass. [5] In summary, while horizontal interactions and spatial patterns are not explicitly considered in XZ, their effect averaged over an area can be implicitly represented by the adjustment of model coefficients, and the results in XZ on abrupt boundaries in terms of biomass and parameter regimes remain correct. [6] While the model in XZ emphasizes vertical interactions between vegetation and soil water (e.g., inclusion of wilted biomass that is very important over temperate grassland), other models as reviewed by Rietkerk et al. [2004] GEOPHYSICAL RESEARCH LETTERS, VOL. 32, L09403, doi:10.1029/2004GL022339, 2005

  • Multiple Equilibrium states and the abrupt transitions in a dynamical system of soil water interacting with vegetation
    Geophysical Research Letters, 2004
    Co-Authors: Xiaodong Zeng, Samuel S. P. Shen, Xubin Zeng, Robert E. Dickinson
    Abstract:

    [1] In semi-arid areas, Multiple Equilibrium states of an ecosystem (e.g., grassland and desert) are found to coexist, and the transition from grassland to desert is often abrupt at the boundary. A simple ecosystem model is developed to provide the biophysical explanation of this phenomenon. The model has three variables: living biomass, wilted biomass, and soil wetness. The moisture index, which is the ratio of the annual precipitation to potential evaporation, is the only external climate driving force, and the key mechanism is the vegetation-soil interaction. It is found that the maintenance of a grassland requires a minimum moisture index, and the abrupt transition occurs when the moisture index is around this critical value. These results are robust within a wide range for most model parameters, suggesting that the model may be applicable to other temperate grasslands. The characteristics of the wilted biomass also strongly influence the ecosystem's dynamics.