scholarly journals Non‐equilibrium large‐scale membrane transformations driven by MinDE biochemical reaction cycles

2020 ◽  
Author(s):  
MEIFANG FU ◽  
Henri G. Franquelim ◽  
Simon Kretschmer ◽  
Petra Schwille
Keyword(s):  
Large Scale ◽  
Biochemical Reaction ◽  
Reaction Cycles ◽  
Non Equilibrium

Re-Programming Hydrogel Properties using a Fuel-driven Reaction Cycle

2019 ◽  
Author(s):  
Nishant Singh ◽  
Bruno Lainer ◽  
Georges Formon ◽  
Serena De Piccoli ◽  
Thomas Hermans
Keyword(s):  
Methionine Oxidation ◽  
Guanosine Triphosphate ◽  
Control Reaction ◽  
Reaction Cycle ◽  
Materials Properties ◽  
Assembly Kinetics ◽  
Control Assembly ◽  
Indispensable Tool ◽  
Reaction Cycles ◽  
Non Equilibrium

Nature uses catalysis as an indispensable tool to control assembly and reaction cycles in vital non-equilibrium supramolecular processes. For instance, enzymatic methionine oxidation regulates actin (dis)assembly, and catalytic guanosine triphosphate hydrolysis is found in tubulin (dis)assembly. Here we present a completely artificial reaction cycle which is driven by a chemical fuel that is catalytically obtained from a ‘pre-fuel’. The reaction cycle controls the disassembly and re-assembly of a hydrogel, where the rate of pre-fuel turnover dictates the morphology as well as the mechanical properties. By adding additional fresh aliquots of fuel and removing waste, the hydrogels can be re-programmed time after time. Overall, we show how catalysis can control fuel generation to control reaction / assembly kinetics and materials properties in life-like non-equilibrium systems.

scholarly journals Parasitic Behavior in Competing Chemically Fueled Reaction Cycles

2021 ◽  
Author(s):  
Patrick S. Schwarz ◽  
Sudarshana Laha ◽  
Jacqueline Janssen ◽  
Tabea Huss ◽  
Job Boekhoven ◽  
...  
Keyword(s):  
Dynamic Behavior ◽  
Model Systems ◽  
Reaction Networks ◽  
Reaction Cycles ◽  
Non Equilibrium

Non-equilibrium, fuel-driven reaction cycles serve as model systems of the intricate reaction networks of life. Rich and dynamic behavior is observed when reaction cycles regulate assembly processes, such as phase...

scholarly journals ASHEE-1.0: a compressible, equilibrium–Eulerian model for volcanic ash plumes

2016 ◽  
Vol 9 (2) ◽  
pp. 697-730 ◽  
Author(s):  
M. Cerminara ◽  
T. Esposti Ongaro ◽  
L. C. Berselli
Keyword(s):  
Numerical Simulation ◽  
Large Scale ◽  
Volume Fraction ◽  
Radial Profile ◽  
Air Entrainment ◽  
Compressible Turbulence ◽  
Eulerian Model ◽  
Volcanic Plumes ◽  
Large Eddy ◽  
Non Equilibrium

Abstract. A new fluid-dynamic model is developed to numerically simulate the non-equilibrium dynamics of polydisperse gas–particle mixtures forming volcanic plumes. Starting from the three-dimensional N-phase Eulerian transport equations for a mixture of gases and solid dispersed particles, we adopt an asymptotic expansion strategy to derive a compressible version of the first-order non-equilibrium model, valid for low-concentration regimes (particle volume fraction less than 10−3) and particle Stokes number (St – i.e., the ratio between relaxation time and flow characteristic time) not exceeding about 0.2. The new model, which is called ASHEE (ASH Equilibrium Eulerian), is significantly faster than the N-phase Eulerian model while retaining the capability to describe gas–particle non-equilibrium effects. Direct Numerical Simulation accurately reproduces the dynamics of isotropic, compressible turbulence in subsonic regimes. For gas–particle mixtures, it describes the main features of density fluctuations and the preferential concentration and clustering of particles by turbulence, thus verifying the model reliability and suitability for the numerical simulation of high-Reynolds number and high-temperature regimes in the presence of a dispersed phase. On the other hand, Large-Eddy Numerical Simulations of forced plumes are able to reproduce the averaged and instantaneous flow properties. In particular, the self-similar Gaussian radial profile and the development of large-scale coherent structures are reproduced, including the rate of turbulent mixing and entrainment of atmospheric air. Application to the Large-Eddy Simulation of the injection of the eruptive mixture in a stratified atmosphere describes some of the important features of turbulent volcanic plumes, including air entrainment, buoyancy reversal and maximum plume height. For very fine particles (St → 0, when non-equilibrium effects are negligible) the model reduces to the so-called dusty-gas model. However, coarse particles partially decouple from the gas phase within eddies (thus modifying the turbulent structure) and preferentially concentrate at the eddy periphery, eventually being lost from the plume margins due to the concurrent effect of gravity. By these mechanisms, gas–particle non-equilibrium processes are able to influence the large-scale behavior of volcanic plumes.

Prediction of Non-Equilibrium Heat Conduction Using Parallel Computation of the Phonon Boltzmann Transport Equation

2014 ◽  
Author(s):  
Syed A. Ali ◽  
Gautham Kollu ◽  
Sandip Mazumder ◽  
P. Sadayappan
Keyword(s):  
Heat Conduction ◽  
Transport Equation ◽  
Parallel Computation ◽  
Large Scale ◽  
Phonon Scattering ◽  
Boltzmann Transport Equation ◽  
Computational Time ◽  
Spectral Space ◽  
Boltzmann Transport ◽  
Non Equilibrium

Non-equilibrium heat conduction, as occurring in modern-day sub-micron semiconductor devices, can be predicted effectively using the Boltzmann Transport Equation (BTE) for phonons. In this article, strategies and algorithms for large-scale parallel computation of the phonon BTE are presented. An unstructured finite volume method for spatial discretization is coupled with the control angle discrete ordinates method for angular discretization. The single-time relaxation approximation is used to treat phonon-phonon scattering. Both dispersion and polarization of the phonons are accounted for. Three different parallelization strategies are explored: (a) band-based, (b) direction-based, and (c) hybrid band/cell-based. Subsequent to validation studies in which silicon thin-film thermal conductivity was successfully predicted, transient simulations of non-equilibrium thermal transport were conducted in a three-dimensional device-like silicon structure, discretized using 604,054 tetrahedral cells. The angular space was discretized using 400 angles, and the spectral space was discretized into 40 spectral intervals (bands). This resulted in ∼9.7×109 unknowns, which are approximately 3 orders of magnitude larger than previously reported computations in this area. Studies showed that direction-based and hybrid band/cell-based parallelization strategies resulted in similar total computational time. However, the parallel efficiency of the hybrid band/cell-based strategy — about 88% — was found to be superior to that of the direction-based strategy, and is recommended as the preferred strategy for even larger scale computations.

WinBEST-KIT: Biochemical reaction simulator that can define and customize algebraic equations and events as GUI components

2019 ◽  
Vol 17 (06) ◽  
pp. 1950036
Author(s):  
Tatsuya Sekiguchi ◽  
Hiroyuki Hamada ◽  
Masahiro Okamoto
Keyword(s):  
Large Scale ◽  
System Biology Markup Language ◽  
Biochemical Reaction ◽  
Engineering System ◽  
Algebraic Equations ◽  
Biochemical Engineering ◽  
Biochemical Reaction Networks ◽  
Kinetic Mechanisms ◽  
Mathematical Equations ◽  
Definition Of

We previously developed Windows-based Biochemical Engineering System analyzing Tool-KIT (WinBEST-KIT), a biochemical reaction simulator for analyzing large-scale and complicated biochemical reaction networks. One particularly notable feature is the ability for users to define original mathematical equations for representing unknown kinetic mechanisms and customize them as GUI components for representing reaction steps. Many simulators support System Biology Markup Language SBML; however, since the definition of the algebraic equations (AssignmentRule) and the events are made through an interface that is distinct from the definition of the reaction steps, there are tough works to define them. Accordingly, we have developed a new version of WinBEST-KIT that allows users to define the algebraic equations and the events through the same interface as those used in the definition of the reaction steps and customize them as GUI components appearing in the symbol selection area. The customized algebraic equations and events can thus be visually arranged at any time and any place. It also allows users to easily understand the roles of the algebraic equations and the events. We have also implemented other useful features, including importing/exporting of SBML format files, exporting to MATLAB, and merging the existing models into the model currently being created. The current version of WinBEST-KIT is freely available at http://winbest-kit.org/ .

scholarly journals Non-equilibrium response and slow equilibration in hard disk systems

2021 ◽  
Vol 249 ◽  
pp. 14004
Author(s):  
Daigo Mugita ◽  
Masaharu Isobe
Keyword(s):  
Large Scale ◽  
Initial Conditions ◽  
Local Density ◽  
Orientational Order ◽  
Hard Disk ◽  
Equilibrium Response ◽  
Equilibration Process ◽  
Liquid States ◽  
Large Scale Simulations ◽  
Non Equilibrium

The relaxation from a non-equilibrium state to the equilibrium depends on the methodologies and initial conditions. To investigate the microscopic mechanisms of equilibration systematically, we focus on the non-equilibrium response during the equilibration process induced by a disturbance of the homogeneous expansion of the simple hard disk systems. Large scale simulations by event-driven molecular dynamics revealed that an anomalous slow equilibration toward the liquid states emerges when starting from the co-existence phase. The origin of the slow decay mechanism is investigated using the probability distribution of local density and orientational order parameter.Their inhomogeneities seem to cause the anomalous slow equilibration.

scholarly journals Re-Programming Hydrogel Properties using a Fuel-driven Reaction Cycle

2019 ◽  
Author(s):  
Nishant Singh ◽  
Bruno Lainer ◽  
Georges Formon ◽  
Serena De Piccoli ◽  
Thomas Hermans
Keyword(s):  
Methionine Oxidation ◽  
Guanosine Triphosphate ◽  
Control Reaction ◽  
Reaction Cycle ◽  
Materials Properties ◽  
Assembly Kinetics ◽  
Control Assembly ◽  
Indispensable Tool ◽  
Reaction Cycles ◽  
Non Equilibrium

Nature uses catalysis as an indispensable tool to control assembly and reaction cycles in vital non-equilibrium supramolecular processes. For instance, enzymatic methionine oxidation regulates actin (dis)assembly, and catalytic guanosine triphosphate hydrolysis is found in tubulin (dis)assembly. Here we present a completely artificial reaction cycle which is driven by a chemical fuel that is catalytically obtained from a ‘pre-fuel’. The reaction cycle controls the disassembly and re-assembly of a hydrogel, where the rate of pre-fuel turnover dictates the morphology as well as the mechanical properties. By adding additional fresh aliquots of fuel and removing waste, the hydrogels can be re-programmed time after time. Overall, we show how catalysis can control fuel generation to control reaction / assembly kinetics and materials properties in life-like non-equilibrium systems.

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