89,844 research outputs found
Simulated single molecule microscopy with SMeagol
SMeagol is a software tool to simulate highly realistic microscopy data based
on spatial systems biology models, in order to facilitate development,
validation, and optimization of advanced analysis methods for live cell single
molecule microscopy data. Availability and Implementation: SMeagol runs on
Matlab R2014 and later, and uses compiled binaries in C for reaction-diffusion
simulations. Documentation, source code, and binaries for recent versions of
Mac OS, Windows, and Ubuntu Linux can be downloaded from
http://smeagol.sourceforge.net.Comment: v2: 14 pages including supplementary text. Pre-copyedited,
author-produced version of an application note published in Bioinformatics
following peer review. The version of record, and additional supplementary
material is available online at:
https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw10
Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damk\"ohler numbers
Mixing fronts, where fluids of different chemical compositions mix with each
other, are typically subjected to velocity gradients, ranging from the pore
scale to the catchment scale due to permeability variations and flow line
geometries. A common trait of these processes is that the mixing interface is
strained by shear. Depending on the P\'eclet number , which represents the
ratio of the characteristic diffusion time to the characteristic advection
time, and the Damk\"ohler number , which represents the ratio of the
characteristic diffusion time to the characteristic reaction time, the local
reaction rates can be strongly impacted by the dynamics of the mixing
interface. This impact has been characterized mostly either in kinetics-limited
or in mixing-limited conditions, that is, for either very low or very high
. Here the coupling of shear flow and chemical reactivity is investigated
for arbitrary Damk\"ohler numbers, for a bimolecular reaction and an initial
interface with separated reactants. Approximate analytical expressions for the
global production rate and reactive mixing scale are derived based on a
reactive lamella approach that allows for a general coupling between stretching
enhanced mixing and chemical reactions. While for , reaction kinetics
and stretching effects are decoupled, a scenario which we name "weak
stretching", for , we uncover a "strong stretching" scenario where new
scaling laws emerge from the interplay between reaction kinetics, diffusion,
and stretching. The analytical results are validated against numerical
simulations. These findings shed light on the effect of flow heterogeneity on
the enhancement of chemical reaction and the creation of spatially localized
hotspots of reactivity for a broad range of systems ranging from kinetic
limited to mixing limited situations
Geometry-controlled kinetics
It has long been appreciated that transport properties can control reaction
kinetics. This effect can be characterized by the time it takes a diffusing
molecule to reach a target -- the first-passage time (FPT). Although essential
to quantify the kinetics of reactions on all time scales, determining the FPT
distribution was deemed so far intractable. Here, we calculate analytically
this FPT distribution and show that transport processes as various as regular
diffusion, anomalous diffusion, diffusion in disordered media and in fractals
fall into the same universality classes. Beyond this theoretical aspect, this
result changes the views on standard reaction kinetics. More precisely, we
argue that geometry can become a key parameter so far ignored in this context,
and introduce the concept of "geometry-controlled kinetics". These findings
could help understand the crucial role of spatial organization of genes in
transcription kinetics, and more generally the impact of geometry on
diffusion-limited reactions.Comment: Submitted versio
Partial differential equations for self-organization in cellular and developmental biology
Understanding the mechanisms governing and regulating the emergence of structure and heterogeneity within cellular systems, such as the developing embryo, represents a multiscale challenge typifying current integrative biology research, namely, explaining the macroscale behaviour of a system from microscale dynamics. This review will focus upon modelling how cell-based dynamics orchestrate the emergence of higher level structure. After surveying representative biological examples and the models used to describe them, we will assess how developments at the scale of molecular biology have impacted on current theoretical frameworks, and the new modelling opportunities that are emerging as a result. We shall restrict our survey of mathematical approaches to partial differential equations and the tools required for their analysis. We will discuss the gap between the modelling abstraction and biological reality, the challenges this presents and highlight some open problems in the field
Rigorous Multicomponent Reactive Separations Modelling : Complete Consideration of Reaction-Diffusion Phenomena
This paper gives the first step of the development of a rigorous multicomponent reactive separation model. Such a model is highly essential to further the optimization of acid gases removal plants (CO2 capture, gas treating, etc.) in terms of size and energy consumption, since chemical solvents are conventionally used.Firstly, two main modelling approaches are presented: the equilibrium-based and the rate-based approaches. Secondly, an extended rate-based model with rigorous modelling methodology for diffusion-reaction phenomena is proposed. The film theory and the generalized Maxwell-Stefan equations are used in order to characterize multicomponent interactions. The complete chain of chemical reactions is taken into account. The reactions can be kinetically controlled or at chemical equilibrium, and they are considered for both liquid film and liquid bulk. Thirdly, the method of numerical resolution is described. Coupling the generalized Maxwell-Stefan equations with chemical equilibrium equations leads to a highly non-linear Differential-Algebraic Equations system known as DAE index 3. The set of equations is discretized with finite-differences as its integration by Gear method is complex. The resulting algebraic system is resolved by the Newton- Raphson method. Finally, the present model and the associated methods of numerical resolution are validated for the example of esterification of methanol. This archetype non-electrolytic system permits an interesting analysis of reaction impact on mass transfer, especially near the phase interface. The numerical resolution of the model by Newton-Raphson method gives good results in terms of calculation time and convergence. The simulations show that the impact of reactions at chemical equilibrium and that of kinetically controlled reactions with high kinetics on mass transfer is relatively similar. Moreover, the Fick’s law is less adapted for multicomponent mixtures where some abnormalities such as counter-diffusion take place
Anion Exchange Kinetics of Nanodimensional Layered Metal Hydroxides: Use of Isoconversional Analysis
Anion exchange reactions of nanodimensional layered metal hydroxide compounds are utilized to create materials with targeted physical and chemical properties and also as a means for controlled release of intercalated anions. The kinetics of this important class of reaction are generally characterized by model-based approaches. In this work, a different approach based on isothermal, isoconversional analysis was utilized to determine effective activation energies with respect to extent of reaction. Two different layered metal hydroxide materials were chosen for reaction with chloride anions, using a temperature range of 30−60 °C. The concentrations of anions released into solution and the changes in polycrystalline solid phases were evaluated using model-based (Avrami-Erofe’ev nucleation−growth model) and model-free (integral isoconversional) methods. The results demonstrate the utility of the isoconversional approach for identifying when fitting to a single model is not appropriate, particularly for characterizing the temperature dependence of the reaction kinetics
Ion and mixed conducting oxides as catalysts
This paper gives a survey of the catalytic properties of solid oxides which display oxygen ion or mixed (i.e. ionic + electronic) conductivity. Particular consideration is given to the oxidation-reduction reactions of gas phase components, but attention is also devoted to oxygen exchange between gas and oxide. An attempt has been made to relate and explain the observed phenomena such as catalytic activity and selectivity in terms of the electrical conducting properties of the oxides, which depend on their crystal and defect structures.\ud
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In a number of cases possible applications of these materials in (electro)catalytic reactors, sensors, fuel cells, oxygen pumps, etc. are indicated
Quantifying protein diffusion and capture on filaments
The functional relevance of regulating proteins is often limited to specific
binding sites such as the ends of microtubules or actin-filaments. A
localization of proteins on these functional sites is of great importance. We
present a quantitative theory for a diffusion and capture process, where
proteins diffuse on a filament and stop diffusing when reaching the filament's
end. It is found that end-association after one-dimensional diffusion is the
main source for tip-localization of such proteins. As a consequence, diffusion
and capture is highly efficient in enhancing the reaction velocity of enzymatic
reactions, where proteins and filament ends are to each other as enzyme and
substrate. We show that the reaction velocity can effectively be described
within a Michaelis-Menten framework. Together one-dimensional diffusion and
capture beats the (three-dimensional) Smoluchowski diffusion limit for the rate
of protein association to filament ends.Comment: 13 pages, 7 figure
Derivation of a dual porosity model for the uptake of nutrients by root hairs
Root hairs are thought to play an important role in mediating nutrient uptake by plants. We develop a mathematical model for the nutrient transport and uptake in the root hair zone of a single root in the soil. Nutrients are assumed to diffuse both in the soil fluid phase and within the soil particles. Nutrients can also be bound to the soil particle surfaces by reversible reactions. Using homogenization techniques we derive a macroscopic dual porosity model for nutrient diffusion and reaction in the soil which includes the effect of all root hair surfaces
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