The Experts below are selected from a list of 120096 Experts worldwide ranked by ideXlab platform

Tamas Kristof - One of the best experts on this subject based on the ideXlab platform.

  • selective transport through a model calcium channel studied by Local Equilibrium monte carlo simulations coupled to the nernst planck equation
    2014
    Co-Authors: Dezső Boda, Dirk Gillespie, Robert Kovacs, Tamas Kristof
    Abstract:

    Abstract We have recently introduced the Local Equilibrium Monte Carlo (LEMC) technique (Boda, Gillespie, J. Chem. Theor. Comput. 8 (2012) 824-829) in which a non-Equilibrium system is divided into small volume elements and separate Grand Canonical Monte Carlo simulations are performed for each using a Local intensive parameter, which, as soon as Local Equilibrium is assumed, can be identified with the Local electrochemical potential. The simulation provides the concentration profiles of the steady-state diffuse system, where ions are transported through a membrane from one bulk compartment to the other. The dynamics of the ions is described with the Nernst–Planck (NP) transport equation. The NP equation is coupled to the LEMC simulations via an iteration procedure that ensures that conservation of mass (the continuity equation) is satisfied. We apply the method to a simple calcium channel model and demonstrate its efficiency. The computer experiments are inspired by real electrophysiological experiments for the Ryanodine Receptor calcium channel. The diffusion coefficients in the channel are fitted to results of Dynamic Monte Carlo simulations.

  • simulation of steady state diffusion driving force ensured by dual control volumes or Local Equilibrium monte carlo
    2012
    Co-Authors: Zoltan Hato, Dezső Boda, Tamas Kristof
    Abstract:

    We provide a systematic comparative analysis of various simulation methods for studying steady-state diffusive transport of molecular systems. The methods differ in two respects: (1) the actual method with which the dynamics of the system is handled can be a direct simulation technique [molecular dynamics (MD) and dynamic Monte Carlo (DMC)] or can be an indirect transport equation [the Nernst-Planck (NP) equation], while (2) the driving force of the steady-state transport can be maintained with control cells on the two sides of the transport region [dual control volume (DCV) technique] or it can be maintained in the whole simulation domain with the Local Equilibrium Monte Carlo (LEMC) technique, where the space is divided into small subvolumes, different chemical potentials are assigned to each, and grand canonical Monte Carlo simulations are performed for them separately. The various combinations of the transport-methods with the driving-force methods have advantages and disadvantages. The MD+DCV and DMC...

Dirk Gillespie - One of the best experts on this subject based on the ideXlab platform.

  • selective transport through a model calcium channel studied by Local Equilibrium monte carlo simulations coupled to the nernst planck equation
    2014
    Co-Authors: Dezső Boda, Dirk Gillespie, Robert Kovacs, Tamas Kristof
    Abstract:

    Abstract We have recently introduced the Local Equilibrium Monte Carlo (LEMC) technique (Boda, Gillespie, J. Chem. Theor. Comput. 8 (2012) 824-829) in which a non-Equilibrium system is divided into small volume elements and separate Grand Canonical Monte Carlo simulations are performed for each using a Local intensive parameter, which, as soon as Local Equilibrium is assumed, can be identified with the Local electrochemical potential. The simulation provides the concentration profiles of the steady-state diffuse system, where ions are transported through a membrane from one bulk compartment to the other. The dynamics of the ions is described with the Nernst–Planck (NP) transport equation. The NP equation is coupled to the LEMC simulations via an iteration procedure that ensures that conservation of mass (the continuity equation) is satisfied. We apply the method to a simple calcium channel model and demonstrate its efficiency. The computer experiments are inspired by real electrophysiological experiments for the Ryanodine Receptor calcium channel. The diffusion coefficients in the channel are fitted to results of Dynamic Monte Carlo simulations.

  • steady state electrodiffusion from the nernst planck equation coupled to Local Equilibrium monte carlo simulations
    2012
    Co-Authors: Dezso Boda, Dirk Gillespie
    Abstract:

    We propose a procedure to compute the steady-state transport of charged particles based on the Nernst–Planck (NP) equation of electrodiffusion. To close the NP equation and to establish a relation between the concentration and electrochemical potential profiles, we introduce the Local Equilibrium Monte Carlo (LEMC) method. In this method, Grand Canonical Monte Carlo simulations are performed using the electrochemical potential specified for the distinct volume elements. An iteration procedure that self-consistently solves the NP and flux continuity equations with LEMC is shown to converge quickly. This NP+LEMC technique can be used in systems with diffusion of charged or uncharged particles in complex three-dimensional geometries, including systems with low concentrations and small applied voltages that are difficult for other particle simulation techniques.

Dezső Boda - One of the best experts on this subject based on the ideXlab platform.

  • selective transport through a model calcium channel studied by Local Equilibrium monte carlo simulations coupled to the nernst planck equation
    2014
    Co-Authors: Dezső Boda, Dirk Gillespie, Robert Kovacs, Tamas Kristof
    Abstract:

    Abstract We have recently introduced the Local Equilibrium Monte Carlo (LEMC) technique (Boda, Gillespie, J. Chem. Theor. Comput. 8 (2012) 824-829) in which a non-Equilibrium system is divided into small volume elements and separate Grand Canonical Monte Carlo simulations are performed for each using a Local intensive parameter, which, as soon as Local Equilibrium is assumed, can be identified with the Local electrochemical potential. The simulation provides the concentration profiles of the steady-state diffuse system, where ions are transported through a membrane from one bulk compartment to the other. The dynamics of the ions is described with the Nernst–Planck (NP) transport equation. The NP equation is coupled to the LEMC simulations via an iteration procedure that ensures that conservation of mass (the continuity equation) is satisfied. We apply the method to a simple calcium channel model and demonstrate its efficiency. The computer experiments are inspired by real electrophysiological experiments for the Ryanodine Receptor calcium channel. The diffusion coefficients in the channel are fitted to results of Dynamic Monte Carlo simulations.

  • simulation of steady state diffusion driving force ensured by dual control volumes or Local Equilibrium monte carlo
    2012
    Co-Authors: Zoltan Hato, Dezső Boda, Tamas Kristof
    Abstract:

    We provide a systematic comparative analysis of various simulation methods for studying steady-state diffusive transport of molecular systems. The methods differ in two respects: (1) the actual method with which the dynamics of the system is handled can be a direct simulation technique [molecular dynamics (MD) and dynamic Monte Carlo (DMC)] or can be an indirect transport equation [the Nernst-Planck (NP) equation], while (2) the driving force of the steady-state transport can be maintained with control cells on the two sides of the transport region [dual control volume (DCV) technique] or it can be maintained in the whole simulation domain with the Local Equilibrium Monte Carlo (LEMC) technique, where the space is divided into small subvolumes, different chemical potentials are assigned to each, and grand canonical Monte Carlo simulations are performed for them separately. The various combinations of the transport-methods with the driving-force methods have advantages and disadvantages. The MD+DCV and DMC...

Robin K. Newsom - One of the best experts on this subject based on the ideXlab platform.

  • estimation of turbulence dissipation rate and its variability from sonic anemometer and wind doppler lidar during the xpia field campaign
    2018
    Co-Authors: Nicola Bodini, Julie K. Lundquist, Robin K. Newsom
    Abstract:

    Despite turbulence being a fundamental transport process in the boundary layer, the capability of current numerical models to represent it is undermined by the limits of the adopted assumptions, notably that of Local Equilibrium. Here we leverage the potential of extensive observations in determining the variability of turbulence dissipation rate (e). These observations can provide insights towards the understanding of the scales at which the major assumption of Local Equilibrium between generation and dissipation of turbulence is invalid. Typically, observations of e require time- and labor-intensive measurements from sonic and/or hot-wire anemometers. We explore the capability of wind Doppler lidars to provide measurements of e. We refine and extend an existing method to accommodate different atmospheric stability conditions. To validate our approach, we estimate e from four wind Doppler lidars during the 3-month XPIA campaign at the Boulder Atmospheric Observatory (Colorado), and we assess the uncertainty of the proposed method by data inter-comparison with sonic anemometer measurements of e. Our analysis of this extensive dataset provides understanding of the climatology of turbulence dissipation over the course of the campaign. Further, the variability of e with atmospheric stability, height, and wind speed is also assessed. Finally, we present how e increases as nocturnal turbulence is generated during low-level jet events.

  • estimation of turbulence dissipation rate and its variability from sonic anemometer and wind doppler lidar during the xpia field campaign
    2018
    Co-Authors: Nicola Bodini, Julie K. Lundquist, Robin K. Newsom
    Abstract:

    Abstract. Despite turbulence being a fundamental transport process in the boundary layer, the capability of current numerical models to represent it is undermined by the limits of the adopted assumptions, notably that of Local Equilibrium. Here we leverage the potential of extensive observations in determining the variability in turbulence dissipation rate ( ϵ ). These observations can provide insights towards the understanding of the scales at which the major assumption of Local Equilibrium between generation and dissipation of turbulence is invalid. Typically, observations of ϵ require time- and labor-intensive measurements from sonic and/or hot-wire anemometers. We explore the capability of wind Doppler lidars to provide measurements of ϵ . We refine and extend an existing method to accommodate different atmospheric stability conditions. To validate our approach, we estimate ϵ from four wind Doppler lidars during the 3-month XPIA campaign at the Boulder Atmospheric Observatory (Colorado), and we assess the uncertainty of the proposed method by data intercomparison with sonic anemometer measurements of ϵ . Our analysis of this extensive dataset provides understanding of the climatology of turbulence dissipation over the course of the campaign. Further, the variability in ϵ with atmospheric stability, height, and wind speed is also assessed. Finally, we present how ϵ increases as nocturnal turbulence is generated during low-level jet events.

Julie K. Lundquist - One of the best experts on this subject based on the ideXlab platform.

  • estimation of turbulence dissipation rate and its variability from sonic anemometer and wind doppler lidar during the xpia field campaign
    2018
    Co-Authors: Nicola Bodini, Julie K. Lundquist, Robin K. Newsom
    Abstract:

    Despite turbulence being a fundamental transport process in the boundary layer, the capability of current numerical models to represent it is undermined by the limits of the adopted assumptions, notably that of Local Equilibrium. Here we leverage the potential of extensive observations in determining the variability of turbulence dissipation rate (e). These observations can provide insights towards the understanding of the scales at which the major assumption of Local Equilibrium between generation and dissipation of turbulence is invalid. Typically, observations of e require time- and labor-intensive measurements from sonic and/or hot-wire anemometers. We explore the capability of wind Doppler lidars to provide measurements of e. We refine and extend an existing method to accommodate different atmospheric stability conditions. To validate our approach, we estimate e from four wind Doppler lidars during the 3-month XPIA campaign at the Boulder Atmospheric Observatory (Colorado), and we assess the uncertainty of the proposed method by data inter-comparison with sonic anemometer measurements of e. Our analysis of this extensive dataset provides understanding of the climatology of turbulence dissipation over the course of the campaign. Further, the variability of e with atmospheric stability, height, and wind speed is also assessed. Finally, we present how e increases as nocturnal turbulence is generated during low-level jet events.

  • estimation of turbulence dissipation rate and its variability from sonic anemometer and wind doppler lidar during the xpia field campaign
    2018
    Co-Authors: Nicola Bodini, Julie K. Lundquist, Robin K. Newsom
    Abstract:

    Abstract. Despite turbulence being a fundamental transport process in the boundary layer, the capability of current numerical models to represent it is undermined by the limits of the adopted assumptions, notably that of Local Equilibrium. Here we leverage the potential of extensive observations in determining the variability in turbulence dissipation rate ( ϵ ). These observations can provide insights towards the understanding of the scales at which the major assumption of Local Equilibrium between generation and dissipation of turbulence is invalid. Typically, observations of ϵ require time- and labor-intensive measurements from sonic and/or hot-wire anemometers. We explore the capability of wind Doppler lidars to provide measurements of ϵ . We refine and extend an existing method to accommodate different atmospheric stability conditions. To validate our approach, we estimate ϵ from four wind Doppler lidars during the 3-month XPIA campaign at the Boulder Atmospheric Observatory (Colorado), and we assess the uncertainty of the proposed method by data intercomparison with sonic anemometer measurements of ϵ . Our analysis of this extensive dataset provides understanding of the climatology of turbulence dissipation over the course of the campaign. Further, the variability in ϵ with atmospheric stability, height, and wind speed is also assessed. Finally, we present how ϵ increases as nocturnal turbulence is generated during low-level jet events.