The influence of physical state on shikimic acid ozonolysis: a case for in situ microspectroscopy

NASA Astrophysics Data System (ADS)

Steimer, S. S.; Lampimäki, M.; Coz, E.; Grzinic, G.; Ammann, M.

2014-10-01

Atmospheric soluble organic aerosol material can become solid or semi-solid. Due to increasing viscosity and decreasing diffusivity, this can impact important processes such as gas uptake and reactivity within aerosols containing such substances. This work explores the dependence of shikimic acid ozonolysis on humidity and thereby viscosity. Shikimic acid, a proxy for oxygenated reactive organic material, reacts with O3 in a Criegee-type reaction. We used an environmental microreactor embedded in a scanning transmission X-ray microscope (STXM) to probe this oxidation process. This technique facilitates in situ measurements with single micron-sized particles and allows to obtain near-edge X-ray absorption fine structure (NEXAFS) spectra with high spatial resolution. Thus, the chemical evolution of the interior of the particles can be followed under reaction conditions. The experiments show that the overall degradation rate of shikimic acid is depending on the relative humidity in a way that is controlled by the decreasing diffusivity of ozone with decreasing humidity. This decreasing diffusivity is most likely linked to the increasing viscosity of the shikimic acid-water mixture. The degradation rate was also depending on particle size, most congruent with a reacto-diffusion limited kinetic case where the reaction progresses only in a shallow layer within the bulk. No gradient in the shikimic acid concentration was observed within the bulk material at any humidity indicating that the diffusivity of shikimic acid is still high enough to allow its equilibration throughout the particles on the timescale of hours at higher humidity and that the thickness of the oxidized layer under dry conditions, where the particles are solid, is beyond the resolution of STXM.

Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Del Razo, Mauricio; Pan, Wenxiao; Qian, Hong

2014-05-30

The currently existing theory of fluorescence correlation spectroscopy (FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in bulk solutions. For mesoscopic reaction-diffusion systems with nonlinear chemical reactions among a small number of molecules, a situation often encountered in single-cell biochemistry, it is expected that FCS time correlation functions of a reaction-diffusion system can deviate from the classic results of Elson and Magde [Biopolymers (1974) 13:1-27]. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems there are no closedmore » solutions; therefore, stochastic Monte-Carlo simulations are carried out. We show that the deviation is small for a simple bimolecular reaction; the most significant deviations occur when the number of molecules is small and of the same order. Extending Delbrück-Gillespie’s theory for stochastic nonlinear reactions with rapidly stirring to reaction-diffusion systems provides a mesoscopic model for chemical and biochemical reactions at nanometric and mesoscopic level such as a single biological cell.« less

Intraparticle diffusion limitations in the hydrogenation of monounsaturated edible oils and their fatty acid methyl esters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jonker, G.H.; Veldsink, J.W.; Beenackers, A.A.C.M.

1998-12-01

Intraparticle diffusion limitation in the hydrogenation and isomerization of fatty acid methyl esters (FAMEs) and edible oils (triacylglycerol, TAG) in porous nickel catalyst was investigated both under reactive and under inert conditions. Under reactive conditions, the diffusion coefficients were determined from the best fits of the model simulations applying the intrinsic reacting kinetics of monounsaturated FAME hydrogenation to experiments under diffusion limited conditions. Due to the absence of reaction (hydrogenation of double bonds), the obtained effective H{sub z} diffusion coefficient (D{sub e}) with the HPLC technique is volume averaged and thereby determined by the larger intercrystalline pores (<30% of themore » total pore volume) only. Moreover, D{sub e} measured under reaction conditions reflected the influence of the micropores, resulting in a 10-fold lower value.« less

Part-2: Analytical Expressions of Concentrations of Glucose, Oxygen, and Gluconic Acid in a Composite Membrane for Closed-Loop Insulin Delivery for the Non-steady State Conditions.

PubMed

Mehala, N; Rajendran, L; Meena, V

2017-02-01

A mathematical model developed by Abdekhodaie and Wu (J Membr Sci 335:21-31, 2009), which describes a dynamic process involving an enzymatic reaction and diffusion of reactants and product inside glucose-sensitive composite membrane has been discussed. This theoretical model depicts a system of non-linear non-steady state reaction diffusion equations. These equations have been solved using new approach of homotopy perturbation method and analytical solutions pertaining to the concentrations of glucose, oxygen, and gluconic acid are derived. These analytical results are compared with the numerical results, and limiting case results for steady state conditions and a good agreement is observed. The influence of various kinetic parameters involved in the model has been presented graphically. Theoretical evaluation of the kinetic parameters like the maximal reaction velocity (V max ) and Michaelis-Menten constants for glucose and oxygen (K g and K ox ) is also reported. This predicted model is very much useful for designing the glucose-responsive composite membranes for closed-loop insulin delivery.

Convective instabilities in traveling fronts of addition polymerization

NASA Technical Reports Server (NTRS)

Pojman, John A.; Jones, Chris E.; Khan, Akhtar M.

1993-01-01

An autocatalytic reaction in an unstirred vessel can support a constant velocity wavefront resulting from the coupling of diffusion to the chemical reaction. A flare front is a common example in which heat is the autocatalytic species that diffuses into unreacted regions stimulating a reaction that produces more heat. Traveling fronts were studied in synthetic polymerization reactions under high pressure by workers in the former USSR. More recently, propagating fronts of methacrylic acid polymerization were studied under ambient conditions, both with video techniques and by NMR.

Experimental generation and computational modeling of intracellular pH gradients in cardiac myocytes.

PubMed

Swietach, Pawel; Leem, Chae-Hun; Spitzer, Kenneth W; Vaughan-Jones, Richard D

2005-04-01

It is often assumed that pH(i) is spatially uniform within cells. A double-barreled microperfusion system was used to apply solutions of weak acid (acetic acid, CO(2)) or base (ammonia) to localized regions of an isolated ventricular myocyte (guinea pig). A stable, longitudinal pH(i) gradient (up to 1 pH(i) unit) was observed (using confocal imaging of SNARF-1 fluorescence). Changing the fractional exposure of the cell to weak acid/base altered the gradient, as did changing the concentration and type of weak acid/base applied. A diffusion-reaction computational model accurately simulated this behavior of pH(i). The model assumes that H(i)(+) movement occurs via diffusive shuttling on mobile buffers, with little free H(+) diffusion. The average diffusion constant for mobile buffer was estimated as 33 x 10(-7) cm(2)/s, consistent with an apparent H(i)(+) diffusion coefficient, D(H)(app), of 14.4 x 10(-7) cm(2)/s (at pH(i) 7.07), a value two orders of magnitude lower than for H(+) ions in water but similar to that estimated recently from local acid injection via a cell-attached glass micropipette. We conclude that, because H(i)(+) mobility is so low, an extracellular concentration gradient of permeant weak acid readily induces pH(i) nonuniformity. Similar concentration gradients for weak acid (e.g., CO(2)) occur across border zones during regional myocardial ischemia, raising the possibility of steep pH(i) gradients within the heart under some pathophysiological conditions.

Delay-induced wave instabilities in single-species reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Otto, Andereas; Wang, Jian; Radons, Günter

2017-11-01

The Turing (wave) instability is only possible in reaction-diffusion systems with more than one (two) components. Motivated by the fact that a time delay increases the dimension of a system, we investigate the presence of diffusion-driven instabilities in single-species reaction-diffusion systems with delay. The stability of arbitrary one-component systems with a single discrete delay, with distributed delay, or with a variable delay is systematically analyzed. We show that a wave instability can appear from an equilibrium of single-species reaction-diffusion systems with fluctuating or distributed delay, which is not possible in similar systems with constant discrete delay or without delay. More precisely, we show by basic analytic arguments and by numerical simulations that fast asymmetric delay fluctuations or asymmetrically distributed delays can lead to wave instabilities in these systems. Examples, for the resulting traveling waves are shown for a Fisher-KPP equation with distributed delay in the reaction term. In addition, we have studied diffusion-induced instabilities from homogeneous periodic orbits in the same systems with variable delay, where the homogeneous periodic orbits are attracting resonant periodic solutions of the system without diffusion, i.e., periodic orbits of the Hutchinson equation with time-varying delay. If diffusion is introduced, standing waves can emerge whose temporal period is equal to the period of the variable delay.

Instability of turing patterns in reaction-diffusion-ODE systems.

PubMed

Marciniak-Czochra, Anna; Karch, Grzegorz; Suzuki, Kanako

2017-02-01

The aim of this paper is to contribute to the understanding of the pattern formation phenomenon in reaction-diffusion equations coupled with ordinary differential equations. Such systems of equations arise, for example, from modeling of interactions between cellular processes such as cell growth, differentiation or transformation and diffusing signaling factors. We focus on stability analysis of solutions of a prototype model consisting of a single reaction-diffusion equation coupled to an ordinary differential equation. We show that such systems are very different from classical reaction-diffusion models. They exhibit diffusion-driven instability (turing instability) under a condition of autocatalysis of non-diffusing component. However, the same mechanism which destabilizes constant solutions of such models, destabilizes also all continuous spatially heterogeneous stationary solutions, and consequently, there exist no stable Turing patterns in such reaction-diffusion-ODE systems. We provide a rigorous result on the nonlinear instability, which involves the analysis of a continuous spectrum of a linear operator induced by the lack of diffusion in the destabilizing equation. These results are extended to discontinuous patterns for a class of nonlinearities.

Interplay between inhibited transport and reaction in nanoporous materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ackerman, David Michael

2013-01-01

This work presents a detailed formulation of reaction and diffusion dynamics of molecules in confined pores such as mesoporous silica and zeolites. A general reaction-diffusion model and discrete Monte Carlo simulations are presented. Both transient and steady state behavior is covered. Failure of previous mean-field models for these systems is explained and discussed. A coarse-grained, generalized hydrodynamic model is developed that accurately captures the interplay between reaction and restricted transport in these systems. This method incorporates the non-uniform chemical diffusion behavior present in finite pores with multi-component diffusion. Two methods of calculating these diffusion values are developed: a random walkmore » based approach and a driven diffusion model based on an extension of Fick's law. The effects of reaction, diffusion, pore length, and catalytic site distribution are investigated. In addition to strictly single file motion, quasi-single file diffusion is incorporated into the model to match a range of experimental systems. The connection between these experimental systems and model parameters is made through Langevin dynamics modeling of particles in confined pores.« less

Preservation of glutamic acid-iron chelate into montmorillonite to efficiently degrade Reactive Blue 19 in a Fenton system under sunlight irradiation at neutral pH

NASA Astrophysics Data System (ADS)

Huang, Zhujian; Wu, Pingxiao; Gong, Beini; Yang, Shanshan; Li, Hailing; Zhu, Ziao; Cui, Lihua

2016-05-01

To further enhance the visible light responsive property and the chemical stability of Fe/clay mineral catalysts, glutamic acid-iron chelate intercalated montmorillonite (G-Fe-Mt) was developed. The physiochemical properties of G-Fe-Mt were investigated by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), UV-vis diffuse reflectance spectroscopy (DRS), etc. The results showed that glutamic acid-iron chelates were successfully intercalated into the gallery of montmorillonite and the intercalated glutamic acid-iron chelate molecules were well preserved. The product G-Fe-Mt displayed excellent catalytic performance in heterogeneous photo-Fenton reaction under sunlight irradiation at acidic and neutral pH values. The chelation and the visible light responsiveness of glutamic acid produce a synergistic effect leading to greatly enhanced sunlight-Fenton reaction catalyzed by the heterogeneous G-Fe-Mt under neutral pH. G-Fe-Mt is a promising catalyst for advanced oxidation processes.

Femtosecond dynamics in hydrogen-bonded solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castner, E.W. Jr.; Chang, Y.J.

1993-09-01

We present results on the ultrafast dynamics of pure hydrogen-bonding solvents, obtained using femtosecond Fourier-transform optical-heterodyne-detected, Raman-induced Kerr effect spectroscopy. Solvent systems we have studied include the formamides, water, ethylene glycol, and acetic acid. Inertial and diffusive motions are clearly resolved. We comment on the effect that such ultrafast solvent motions have on chemical reactions in solution.

Kinetic multi-layer model of aerosol surface and bulk chemistry (KM-SUB): the influence of interfacial transport and bulk diffusion on the oxidation of oleic acid by ozone

NASA Astrophysics Data System (ADS)

Shiraiwa, Manabu; Pfrang, Christian; Pöschl, Ulrich

2010-05-01

Aerosols are ubiquitous in the atmosphere and have strong effects on climate and public health. Gas-particle interactions can significantly change the physical and chemical properties of aerosols such as toxicity, reactivity, hygroscopicity and radiative properties. Chemical reactions and mass transport lead to continuous transformation and changes in the composition of atmospheric aerosols ("chemical aging"). Resistor model formulations are widely used to describe and investigate heterogeneous reactions and multiphase processes in laboratory, field and model studies of atmospheric chemistry. The traditional resistor models, however, are usually based on simplifying assumptions such as steady state conditions, homogeneous mixing, and limited numbers of non-interacting species and processes. In order to overcome these limitations, Pöschl, Rudich and Ammann have developed a kinetic model framework (PRA framework) with a double-layer surface concept and universally applicable rate equations and parameters for mass transport and chemical reactions at the gas-particle interface of aerosols and clouds [1]. Based on the PRA framework, we present a novel kinetic multi-layer model that explicitly resolves mass transport and chemical reaction at the surface and in the bulk of aerosol particles (KM-SUB) [2]. The model includes reversible adsorption, surface reactions and surface-bulk exchange as well as bulk diffusion and reaction. Unlike earlier models, KM-SUB does not require simplifying assumptions about steady-state conditions and radial mixing. The temporal evolution and concentration profiles of volatile and non-volatile species at the gas-particle interface and in the particle bulk can be modeled along with surface concentrations and gas uptake coefficients. In this study we explore and exemplify the effects of bulk diffusion on the rate of reactive gas uptake for a simple reference system, the ozonolysis of oleic acid particles, in comparison to experimental data and earlier model studies. We demonstrate how KM-SUB can be used to interpret and analyze experimental data from laboratory studies, and how the results can be extrapolated to atmospheric conditions. In particular, we show how interfacial transport and bulk transport, i.e., surface accommodation, bulk accommodation and bulk diffusion, influence the kinetics of the chemical reaction. Sensitivity studies suggest that in fine air particulate matter oleic acid and compounds with similar reactivity against ozone (C=C double bonds) can reach chemical life-times of multiple hours only if they are embedded in a (semi-)solid matrix with very low diffusion coefficients (~10-10 cm2 s-1). Depending on the complexity of the investigated system, unlimited numbers of volatile and non-volatile species and chemical reactions can be flexibly added and treated with KM-SUB. We propose and intend to pursue the application of KM-SUB as a basis for the development of a detailed master mechanism of aerosol chemistry as well as for the derivation of simplified but realistic parameterizations for large-scale atmospheric and climate models. References [1] Pöschl et al., Atmos. Chem. and Phys., 7, 5989-6023 (2007). [2] Shiraiwa et al., Atmos. Chem. Phys. Discuss., 10, 281-326 (2010).

A hybrid continuous-discrete method for stochastic reaction-diffusion processes.

PubMed

Lo, Wing-Cheong; Zheng, Likun; Nie, Qing

2016-09-01

Stochastic fluctuations in reaction-diffusion processes often have substantial effect on spatial and temporal dynamics of signal transductions in complex biological systems. One popular approach for simulating these processes is to divide the system into small spatial compartments assuming that molecules react only within the same compartment and jump between adjacent compartments driven by the diffusion. While the approach is convenient in terms of its implementation, its computational cost may become prohibitive when diffusive jumps occur significantly more frequently than reactions, as in the case of rapid diffusion. Here, we present a hybrid continuous-discrete method in which diffusion is simulated using continuous approximation while reactions are based on the Gillespie algorithm. Specifically, the diffusive jumps are approximated as continuous Gaussian random vectors with time-dependent means and covariances, allowing use of a large time step, even for rapid diffusion. By considering the correlation among diffusive jumps, the approximation is accurate for the second moment of the diffusion process. In addition, a criterion is obtained for identifying the region in which such diffusion approximation is required to enable adaptive calculations for better accuracy. Applications to a linear diffusion system and two nonlinear systems of morphogens demonstrate the effectiveness and benefits of the new hybrid method.

Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics.

PubMed

Chen, Minghan; Li, Fei; Wang, Shuo; Cao, Young

2017-03-14

Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion systems is reaction diffusion master equation (RDME). Previous studies have discovered that for the RDME, when discretization size approaches zero, reaction time for bimolecular reactions in high dimensional domains tends to infinity. In this paper, we demonstrate that in the 1D domain, highly nonlinear reaction dynamics given by Hill function may also have dramatic change when discretization size is smaller than a critical value. Moreover, we discuss methods to avoid this problem: smoothing over space, fixed length smoothing over space and a hybrid method. Our analysis reveals that the switch-like Hill dynamics reduces to a linear function of discretization size when the discretization size is small enough. The three proposed methods could correctly (under certain precision) simulate Hill function dynamics in the microscopic RDME system.

Theoretical modeling of PEB procedure on EUV resist using FDM formulation

NASA Astrophysics Data System (ADS)

Kim, Muyoung; Moon, Junghwan; Choi, Joonmyung; Lee, Byunghoon; Jeong, Changyoung; Kim, Heebom; Cho, Maenghyo

2018-03-01

Semiconductor manufacturing industry has reduced the size of wafer for enhanced productivity and performance, and Extreme Ultraviolet (EUV) light source is considered as a promising solution for downsizing. A series of EUV lithography procedures contain complex photo-chemical reaction on photoresist, and it causes technical difficulties on constructing theoretical framework which facilitates rigorous investigation of underlying mechanism. Thus, we formulated finite difference method (FDM) model of post exposure bake (PEB) process on positive chemically amplified resist (CAR), and it involved acid diffusion coupled-deprotection reaction. The model is based on Fick's second law and first-order chemical reaction rate law for diffusion and deprotection, respectively. Two kinetic parameters, diffusion coefficient of acid and rate constant of deprotection, which were obtained by experiment and atomic scale simulation were applied to the model. As a result, we obtained time evolutional protecting ratio of each functional group in resist monomer which can be used to predict resulting polymer morphology after overall chemical reactions. This achievement will be the cornerstone of multiscale modeling which provides fundamental understanding on important factors for EUV performance and rational design of the next-generation photoresist.

Turing instability in reaction-diffusion systems with nonlinear diffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zemskov, E. P., E-mail: zemskov@ccas.ru

2013-10-15

The Turing instability is studied in two-component reaction-diffusion systems with nonlinear diffusion terms, and the regions in parametric space where Turing patterns can form are determined. The boundaries between super- and subcritical bifurcations are found. Calculations are performed for one-dimensional brusselator and oregonator models.

Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics

NASA Astrophysics Data System (ADS)

Naruemon, Rueangkham; Charin, Modchang

2016-04-01

Most biochemical processes in cells are usually modeled by reaction-diffusion (RD) equations. In these RD models, the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement (MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times. The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations. Project supported by the Thailand Research Fund and Mahidol University (Grant No. TRG5880157), the Thailand Center of Excellence in Physics (ThEP), CHE, Thailand, and the Development Promotion of Science and Technology.

Stochastic Analysis of Reaction–Diffusion Processes

PubMed Central

Hu, Jifeng; Kang, Hye-Won

2013-01-01

Reaction and diffusion processes are used to model chemical and biological processes over a wide range of spatial and temporal scales. Several routes to the diffusion process at various levels of description in time and space are discussed and the master equation for spatially discretized systems involving reaction and diffusion is developed. We discuss an estimator for the appropriate compartment size for simulating reaction–diffusion systems and introduce a measure of fluctuations in a discretized system. We then describe a new computational algorithm for implementing a modified Gillespie method for compartmental systems in which reactions are aggregated into equivalence classes and computational cells are searched via an optimized tree structure. Finally, we discuss several examples that illustrate the issues that have to be addressed in general systems. PMID:23719732

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

NASA Astrophysics Data System (ADS)

Kim, Changho; Nonaka, Andy; Bell, John B.; Garcia, Alejandro L.; Donev, Aleksandar

2017-03-01

We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. By comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

DOE PAGES

Kim, Changho; Nonaka, Andy; Bell, John B.; ...

2017-03-24

Here, we develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules,more » to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. Furthermore, by comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.« less

Combined Excitatory and Inhibitory Coupling in a 1-D Array of Belousov-Zhabotinsky Droplets

DTIC Science & Technology

2014-01-01

with numerical chemical models of the BZ reaction in which components that participate in the excitatory (bromine dioxide and bromous acid) and...verify the transport through the fluorinated oil of chlorine dioxide and several weak acids, including malonic acid. 1. Introduction Recent studies1...finite element model (COMSOLs) of the reaction - diffusion equation in 1-D, 2-D and 3-D, where each drop is modeled as a point, disk or sphere

The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems.

PubMed

Lampoudi, Sotiria; Gillespie, Dan T; Petzold, Linda R

2009-03-07

The Inhomogeneous Stochastic Simulation Algorithm (ISSA) is a variant of the stochastic simulation algorithm in which the spatially inhomogeneous volume of the system is divided into homogeneous subvolumes, and the chemical reactions in those subvolumes are augmented by diffusive transfers of molecules between adjacent subvolumes. The ISSA can be prohibitively slow when the system is such that diffusive transfers occur much more frequently than chemical reactions. In this paper we present the Multinomial Simulation Algorithm (MSA), which is designed to, on the one hand, outperform the ISSA when diffusive transfer events outnumber reaction events, and on the other, to handle small reactant populations with greater accuracy than deterministic-stochastic hybrid algorithms. The MSA treats reactions in the usual ISSA fashion, but uses appropriately conditioned binomial random variables for representing the net numbers of molecules diffusing from any given subvolume to a neighbor within a prescribed distance. Simulation results illustrate the benefits of the algorithm.

A theoretical study of concentration of profiles of primary cytochemical-enzyme reaction products in membrane-bound cell organelles and its application to lysosomal acid phosphatase.

PubMed

Cornelisse, C J; Hermens, W T; Joe, M T; Duijndam, W A; van Duijn, P

1976-11-01

A numerical method was developed for computing the steady-state concentration gradient of a diffusible enzyme reaction product in a membrane-limited compartment of a simplified theoretical cell model. In cytochemical enzyme reactions proceeding according to the metal-capture principle, the local concentration of the primary reaction product is an important factor in the onset of the precipitation process and in the distribution of the final reaction product. The following variables were incorporated into the model: enzyme activity, substrate concentration, Km, diffusion coefficient of substrate and product, particle radius and cell radius. The method was applied to lysosomal acid phosphatase. Numerical values for the variables were estimated from experimental data in the literature. The results show that the calculated phosphate concentrations inside lysosomes are several orders of magnitude lower than the critical concentrations for efficient phosphate capture found in a previous experimental model study. Reasons for this apparent discrepancy are discussed.

Textbook Errors and Misconceptions in Biology: Cell Physiology.

ERIC Educational Resources Information Center

Storey, Richard D.

1992-01-01

Considers topics about cell function often misunderstood, misrepresented, or omitted from biology textbooks: enzyme catalyzed reactions; RNA as a catalyst; protein levels in cells; amino acids; organic acids; glucose and fructose; gluconeogenesis; fatty acids and ketone bodies; diffusion; and transport across membranes. (Contains 25 references.)…

A Simple Demonstration of Convective Effects on Reaction-Diffusion Systems: A Burning Cigarette.

ERIC Educational Resources Information Center

Pojman, John A.

1990-01-01

Described is a demonstration that provides an introduction to nonequilibrium reaction-diffusion systems and the coupling of hydrodynamics to chemical reactions. Experiments that demonstrate autocatalytic behavior that are effected by gravity and convection are included. (KR)

Cross-Diffusion Driven Instability for a Lotka-Volterra Competitive Reaction-Diffusion System

NASA Astrophysics Data System (ADS)

Gambino, G.; Lombardo, M. C.; Sammartino, M.

2008-04-01

In this work we investigate the possibility of the pattern formation for a reaction-diffusion system with nonlinear diffusion terms. Through a linear stability analysis we find the conditions which allow a homogeneous steady state (stable for the kinetics) to become unstable through a Turing mechanism. In particular, we show how cross-diffusion effects are responsible for the initiation of spatial patterns. Finally, we find a Fisher amplitude equation which describes the weakly nonlinear dynamics of the system near the marginal stability.

Influence of physical state on the ozonolysis of shikimic acid

NASA Astrophysics Data System (ADS)

Steimer, Sarah; Krieger, Ulrich; Lampimäki, Markus; Peter, Thomas; Ammann, Markus

2014-05-01

Atmospheric aerosols are an important focus of environmental research due to their effect on climate, air quality and human health. They undergo continuous transformation, changing their physical and chemical properties. Recent findings show that secondary organic aerosol (SOA) particles can form amorphous solids and semi-solids under atmospheric conditions [1]. Since such physical states are highly viscous, diffusivity within the bulk decreases. The decrease in mass transport could slow down chemical reactions, thereby increasing the lifetime of the organic compounds involved. First indications of such behavior were recently shown for reaction of thin protein films with ozone [2], formation of organonitrogen from ammonia uptake to α-pinene secondary organic material [3] and reaction of SOA-coated benzo[a]pyrene with ozone [4]. In this study, we investigated the influence of physical state on the ozonolysis of shikimic acid. Said carboxylic acid is a constituent of biomass burning aerosols and used here as a proxy for oxygenated organic material. Its viscosity was adjusted by varying the humidity of the system between 0% and 92% RH, assuming correlation between the two parameters since water acts as a plasticizer. The system was probed with three complementary techniques: an electrodynamic balance (EDB), measuring the response of single particles to changes in humidity, coated wall flow tube measurements, where uptake of ozone is measured via loss from the gas phase and in situ X-ray microspectroscopy on single particles, where oxidation of the bulk can be observed. Additionally, a kinetic model was used to facilitate data analysis. EDB measurements showed clear evidence of humidity dependent glass formation and correlation of water content and water diffusivity. The dependence of the ozonolysis on relative humidity was observed with both flow tube and microspectroscopy measurements. The coated wall flow tube experiments showed a long term, gradually changing ozone uptake over more than 15 hours, the magnitude of which varied over nearly two orders between lowest and highest humidity. It was possible to separate the uptake into two distinct kinetic regimes, the first of which displayed a Langmuir-Hinshelwood type behavior regarding the ozone gas phase concentration. Microspectroscopy showed that the speed at which the characteristic double bond peak of shikimic acid disappeared was humidity dependent. The measured dependence of the reaction kinetics on humidity supports the hypothesis that the uptake coefficient is highly dependent on the diffusion coefficients of ozone and/or shikimic acid in the organic film. [1] Virtanen, A., et al., An amorphous solid state of biogenic secondary organic aerosol particles. Nature, 2010. 467(7317): p. 824-827. [2] Shiraiwa, M., et al., Gas uptake and chemical aging of semisolid organic aerosol particles. Proceedings of the National Academy of Sciences of the United States of America, 2011. 108(27): p. 11003-11008. [3] Kuwata, M. and Martin, S. T., Phase of atmospheric secondary organic material affects its reactivity. Proceedings of the National Academy of Sciences of the United States of America, 109(43): p. 17354-17359. [4] Zhou, S., et al., Kinetic limitations in gas-particle reactions arising from slow diffusion in secondary organic aerosol. Faraday Discussions, 2013. 165: p. 391-406.

A reaction-diffusion model of CO2 influx into an oocyte

PubMed Central

Somersalo, Erkki; Occhipinti, Rossana; Boron, Walter F.; Calvetti, Daniela

2012-01-01

We have developed and implemented a novel mathematical model for simulating transients in surface pH (pHS) and intracellular pH (pHi) caused by the influx of carbon dioxide (CO2) into a Xenopus oocyte. These transients are important tools for studying gas channels. We assume that the oocyte is a sphere surrounded by a thin layer of unstirred fluid, the extracellular unconvected fluid (EUF), which is in turn surrounded by the well-stirred bulk extracellular fluid (BECF) that represents an infinite reservoir for all solutes. Here, we assume that the oocyte plasma membrane is permeable only to CO2. In both the EUF and intracellular space, solute concentrations can change because of diffusion and reactions. The reactions are the slow equilibration of the CO2 hydration-dehydration reactions and competing equilibria among carbonic acid (H2CO3)/bicarbonate ( HCO3-) and a multitude of non-CO2/HCO3- buffers. Mathematically, the model is described by a coupled system of reaction-diffusion equations that—assuming spherical radial symmetry—we solved using the method of lines with appropriate stiff solvers. In agreement with experimental data (Musa-Aziz et al, PNAS 2009, 106:5406–5411), the model predicts that exposing the cell to extracellular 1.5% CO2/10 mM HCO3- (pH 7.50) causes pHi to fall and pHS to rise rapidly to a peak and then decay. Moreover, the model provides insights into the competition between diffusion and reaction processes when we change the width of the EUF, membrane permeability to CO2, native extra-and intracellular carbonic anhydrase-like activities, the non-CO2/HCO3- (intrinsic) intracellular buffering power, or mobility of intrinsic intracellular buffers. PMID:22728674

An incomplete assembly with thresholding algorithm for systems of reaction-diffusion equations in three space dimensions IAT for reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Moore, Peter K.

2003-07-01

Solving systems of reaction-diffusion equations in three space dimensions can be prohibitively expensive both in terms of storage and CPU time. Herein, I present a new incomplete assembly procedure that is designed to reduce storage requirements. Incomplete assembly is analogous to incomplete factorization in that only a fixed number of nonzero entries are stored per row and a drop tolerance is used to discard small values. The algorithm is incorporated in a finite element method-of-lines code and tested on a set of reaction-diffusion systems. The effect of incomplete assembly on CPU time and storage and on the performance of the temporal integrator DASPK, algebraic solver GMRES and preconditioner ILUT is studied.

Clustering and optimal arrangement of enzymes in reaction-diffusion systems.

PubMed

Buchner, Alexander; Tostevin, Filipe; Gerland, Ulrich

2013-05-17

Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion model. The optimal arrangement transitions from a cluster to a distributed profile as a single parameter, which controls the probability of reaction versus diffusive loss of pathway intermediates, is varied. We introduce the concept of enzyme exposure to explain how this transition arises from the stochastic nature of molecular reactions and diffusion.

Spontaneous Symmetry Breaking Turing-Type Pattern Formation in a Confined Dictyostelium Cell Mass

NASA Astrophysics Data System (ADS)

Sawai, Satoshi; Maeda, Yasuo; Sawada, Yasuji

2000-09-01

We have discovered a new type of patterning which occurs in a two-dimensionally confined cell mass of the cellular slime mold Dictyostelium discoideum. Besides the longitudinal structure reported earlier, we observed a spontaneous symmetry breaking spot pattern whose wavelength shows similar strain dependency to that of the longitudinal pattern. We propose that these structures are due to a reaction-diffusion Turing instability similar to the one which has been exemplified by CIMA (chlorite-iodide-malonic acid) reaction. The present finding may exhibit the first biochemical Turing structure in a developmental system with a controllable boundary condition.

Linking actin networks and cell membrane via a reaction-diffusion-elastic description of nonlinear filopodia initiation.

PubMed

Ben Isaac, Eyal; Manor, Uri; Kachar, Bechara; Yochelis, Arik; Gov, Nir S

2013-08-01

Reaction-diffusion models have been used to describe pattern formation on the cellular scale, and traditionally do not include feedback between cellular shape changes and biochemical reactions. We introduce here a distinct reaction-diffusion-elasticity approach: The reaction-diffusion part describes bistability between two actin orientations, coupled to the elastic energy of the cell membrane deformations. This coupling supports spatially localized patterns, even when such solutions do not exist in the uncoupled self-inhibited reaction-diffusion system. We apply this concept to describe the nonlinear (threshold driven) initiation mechanism of actin-based cellular protrusions and provide support by several experimental observations.

Primal-mixed formulations for reaction-diffusion systems on deforming domains

NASA Astrophysics Data System (ADS)

Ruiz-Baier, Ricardo

2015-10-01

We propose a finite element formulation for a coupled elasticity-reaction-diffusion system written in a fully Lagrangian form and governing the spatio-temporal interaction of species inside an elastic, or hyper-elastic body. A primal weak formulation is the baseline model for the reaction-diffusion system written in the deformed domain, and a finite element method with piecewise linear approximations is employed for its spatial discretization. On the other hand, the strain is introduced as mixed variable in the equations of elastodynamics, which in turn acts as coupling field needed to update the diffusion tensor of the modified reaction-diffusion system written in a deformed domain. The discrete mechanical problem yields a mixed finite element scheme based on row-wise Raviart-Thomas elements for stresses, Brezzi-Douglas-Marini elements for displacements, and piecewise constant pressure approximations. The application of the present framework in the study of several coupled biological systems on deforming geometries in two and three spatial dimensions is discussed, and some illustrative examples are provided and extensively analyzed.

Theory of ion transport with fast acid-base equilibrations in bioelectrochemical systems.

PubMed

Dykstra, J E; Biesheuvel, P M; Bruning, H; Ter Heijne, A

2014-07-01

Bioelectrochemical systems recover valuable components and energy in the form of hydrogen or electricity from aqueous organic streams. We derive a one-dimensional steady-state model for ion transport in a bioelectrochemical system, with the ions subject to diffusional and electrical forces. Since most of the ionic species can undergo acid-base reactions, ion transport is combined in our model with infinitely fast ion acid-base equilibrations. The model describes the current-induced ammonia evaporation and recovery at the cathode side of a bioelectrochemical system that runs on an organic stream containing ammonium ions. We identify that the rate of ammonia evaporation depends not only on the current but also on the flow rate of gas in the cathode chamber, the diffusion of ammonia from the cathode back into the anode chamber, through the ion exchange membrane placed in between, and the membrane charge density.

Efficient reactive Brownian dynamics

DOE PAGES

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

2018-01-21

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently processmore » reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.« less

Efficient reactive Brownian dynamics

NASA Astrophysics Data System (ADS)

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

2018-01-01

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.

Efficient reactive Brownian dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently processmore » reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.« less

Modeling Morphogenesis with Reaction-Diffusion Equations Using Galerkin Spectral Methods

DTIC Science & Technology

2002-05-06

reaction- diffusion equation is a difficult problem in analysis that will not be addressed here. Errors will also arise from numerically approx solutions to...the ODEs. When comparing the approximate solution to actual reaction- diffusion systems found in nature, we must also take into account errors that...

A multipumping flow system for in vitro screening of peroxynitrite scavengers.

PubMed

Ribeiro, Marta F T; Dias, Ana C B; Santos, João L M; Fernandes, Eduarda; Lima, José L F C; Zagatto, Elias A G

2007-09-01

Peroxynitrite anion is a reactive nitrogen species formed in vivo by the rapid, controlled diffusion reaction between nitric oxide and superoxide radicals. By reacting with several biological molecules, peroxynitrite may cause important cellular and tissue deleterious effects, which have been associated with many diseases. In this work, an automated flow-based procedure for the in vitro generation of peroxynitrite and subsequent screening of the scavenging activity of selected compounds is developed. This procedure involves a multipumping flow system (MPFS) and exploits the ability of compounds such as lipoic acid, dihydrolipoic acid, cysteine, reduced glutathione, oxidized glutathione, sulindac, and sulindac sulfone to inhibit the chemiluminescent reaction of luminol with peroxynitrite under physiological simulated conditions. Peroxynitrite was generated in the MPFS by the online reaction of acidified hydrogen peroxide with nitrite, followed by a subsequent stabilization by merging with a sodium hydroxide solution to rapidly quench the developing reaction. The pulsed flow and the timed synchronized insertion of sample and reagent solutions provided by the MPFS ensure the establishment of the reaction zone only inside the flow cell, thus allowing maximum chemiluminescence emission detection. The results obtained for the assayed compounds show that, with the exception of oxidized glutathione, all are highly potent scavengers of peroxynitrite at the studied concentrations.

Modelling and simulating reaction-diffusion systems using coloured Petri nets.

PubMed

Liu, Fei; Blätke, Mary-Ann; Heiner, Monika; Yang, Ming

2014-10-01

Reaction-diffusion systems often play an important role in systems biology when developmental processes are involved. Traditional methods of modelling and simulating such systems require substantial prior knowledge of mathematics and/or simulation algorithms. Such skills may impose a challenge for biologists, when they are not equally well-trained in mathematics and computer science. Coloured Petri nets as a high-level and graphical language offer an attractive alternative, which is easily approachable. In this paper, we investigate a coloured Petri net framework integrating deterministic, stochastic and hybrid modelling formalisms and corresponding simulation algorithms for the modelling and simulation of reaction-diffusion processes that may be closely coupled with signalling pathways, metabolic reactions and/or gene expression. Such systems often manifest multiscaleness in time, space and/or concentration. We introduce our approach by means of some basic diffusion scenarios, and test it against an established case study, the Brusselator model. Copyright © 2014 Elsevier Ltd. All rights reserved.

Diffusion in the Formation of Photopolymer Holograms

DTIC Science & Technology

1992-04-01

based on the reactions of acrylic acid and related compounds that can be dye-sensitized to polymerize under the influence of visible light. 1. Acrylic...rates in what is known as the sector method [36]. The photopolymerizable system is exposed to light of intensity I through a 50% duty cycle rotating...such as methylene blue, with a sulfinic compound [53]. Methylene blue exists as a positive ion in solution; its narrow absorption band peaks in the

Multilevel Preconditioners for Reaction-Diffusion Problems with Discontinuous Coefficients

DOE PAGES

Kolev, Tzanio V.; Xu, Jinchao; Zhu, Yunrong

2015-08-23

In this study, we extend some of the multilevel convergence results obtained by Xu and Zhu, to the case of second order linear reaction-diffusion equations. Specifically, we consider the multilevel preconditioners for solving the linear systems arising from the linear finite element approximation of the problem, where both diffusion and reaction coefficients are piecewise-constant functions. We discuss in detail the influence of both the discontinuous reaction and diffusion coefficients to the performance of the classical BPX and multigrid V-cycle preconditioner.

Nonequilibrium Self-Assembly of π-Conjugated Oligopeptides in Solution.

PubMed

Li, Bo; Li, Songsong; Zhou, Yuecheng; Ardoña, Herdeline Ann M; Valverde, Lawrence R; Wilson, William L; Tovar, John D; Schroeder, Charles M

2017-02-01

Supramolecular assembly is a powerful method that can be used to generate materials with well-defined structures across multiple length scales. Supramolecular assemblies consisting of biopolymer-synthetic polymer subunits are specifically known to exhibit exceptional structural and functional diversity as well as programmable control of noncovalent interactions through hydrogen bonding in biopolymer subunits. Despite recent progress, there is a need to control and quantitatively understand assembly under nonequilibrium conditions. In this work, we study the nonequilibrium self-assembly of π-conjugated synthetic oligopeptides using a combination of experiments and analytical modeling. By isolating an aqueous peptide solution droplet within an immiscible organic layer, the rate of peptide assembly in the aqueous solution can be controlled by tuning the transport rate of acid that is used to trigger assembly. Using this approach, peptides are guided to assemble under reaction-dominated and diffusion-dominated conditions, with results showing a transition from a diffusion-limited reaction front to spatially homogeneous assembly as the transport rate of acid decreases. Interestingly, our results show that the morphology of self-assembled peptide fibers is controlled by the assembly kinetics such that increasingly homogeneous structures of self-assembled synthetic oligopeptides were generally obtained using slower rates of assembly. We further developed an analytical reaction-diffusion model to describe oligopeptide assembly, and experimental results are compared to the reaction-diffusion model across a range of parameters. Overall, this work highlights the importance of molecular self-assembly under nonequilibrium conditions, specifically showing that oligopeptide assembly is governed by a delicate balance between reaction kinetics and transport processes.

Physarum machines: encapsulating reaction-diffusion to compute spanning tree

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2007-12-01

The Physarum machine is a biological computing device, which employs plasmodium of Physarum polycephalum as an unconventional computing substrate. A reaction-diffusion computer is a chemical computing device that computes by propagating diffusive or excitation wave fronts. Reaction-diffusion computers, despite being computationally universal machines, are unable to construct certain classes of proximity graphs without the assistance of an external computing device. I demonstrate that the problem can be solved if the reaction-diffusion system is enclosed in a membrane with few ‘growth points’, sites guiding the pattern propagation. Experimental approximation of spanning trees by P. polycephalum slime mold demonstrates the feasibility of the approach. Findings provided advance theory of reaction-diffusion computation by enriching it with ideas of slime mold computation.

Interface Reactions and Synthetic Reaction of Composite Systems

PubMed Central

Park, Joon Sik; Kim, Jeong Min

2010-01-01

Interface reactions in composite systems often determine their overall properties, since product phases usually formed at interfaces during composite fabrication processing make up a large portion of the composites. Since most composite materials represent a ternary or higher order materials system, many studies have focused on analyses of diffusion phenomena and kinetics in multicomponent systems. However, the understanding of the kinetic behavior increases the complexity, since the kinetics of each component during interdiffusion reactions need to be defined for interpreting composite behaviors. From this standpoint, it is important to clarify the interface reactions for producing compatible interfaces with desired product phases. A thermodynamic evaluation such as a chemical potential of involving components can provide an understanding of the diffusion reactions, which govern diffusion pathways and product phase formation. A strategic approach for designing compatible interfaces is discussed in terms of chemical potential diagrams and interface morphology, with some material examples.

An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping.

PubMed

Koh, Wonryull; Blackwell, Kim T

2011-04-21

Stochastic simulation of reaction-diffusion systems enables the investigation of stochastic events arising from the small numbers and heterogeneous distribution of molecular species in biological cells. Stochastic variations in intracellular microdomains and in diffusional gradients play a significant part in the spatiotemporal activity and behavior of cells. Although an exact stochastic simulation that simulates every individual reaction and diffusion event gives a most accurate trajectory of the system's state over time, it can be too slow for many practical applications. We present an accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems designed to improve the speed of simulation by reducing the number of time-steps required to complete a simulation run. This method is unique in that it employs two strategies that have not been incorporated in existing spatial stochastic simulation algorithms. First, diffusive transfers between neighboring subvolumes are based on concentration gradients. This treatment necessitates sampling of only the net or observed diffusion events from higher to lower concentration gradients rather than sampling all diffusion events regardless of local concentration gradients. Second, we extend the non-negative Poisson tau-leaping method that was originally developed for speeding up nonspatial or homogeneous stochastic simulation algorithms. This method calculates each leap time in a unified step for both reaction and diffusion processes while satisfying the leap condition that the propensities do not change appreciably during the leap and ensuring that leaping does not cause molecular populations to become negative. Numerical results are presented that illustrate the improvement in simulation speed achieved by incorporating these two new strategies.

Electro-fenton and photoelectro-fenton degradation of sulfanilic acid using a boron-doped diamond anode and an air diffusion cathode.

PubMed

El-Ghenymy, Abdellatif; Garrido, José Antonio; Centellas, Francesc; Arias, Conchita; Cabot, Pere Lluís; Rodríguez, Rosa María; Brillas, Enric

2012-04-05

The mineralization of sulfanilic acid has been studied by electro-Fenton (EF) and photoelectro-Fenton (PEF) reaction with UVA light using an undivided electrochemical cell with a boron-doped diamond (BDD) anode and an air diffusion cathode able to generate H(2)O(2). Organics were then oxidized by hydroxyl radicals formed at the anode surface from water oxidation and in the bulk from Fenton's reaction between generated H(2)O(2) and added Fe(2+). The UVA irradiation in PEF enhanced the production of hydroxyl radicals in the bulk, accelerating the removal of organics and photodecomposed intermediates like Fe(III)-carboxylate complexes. Partial decontamination of 1.39 mM sulfanilic acid solutions was achieved by EF until 100 mA cm(-2) at optimum conditions of 0.4 mM Fe(2+) and pH 3.0. The increase in current density and substrate content led to an almost total mineralization. In contrast, the PEF process was more powerful, yielding almost complete mineralization in less electrolysis time under comparable conditions. The kinetics for sulfanilic acid decay always followed a pseudo-first-order reaction. Hydroquinone and p-benzoquinone were detected as aromatic intermediates, whereas acetic, maleic, formic, oxalic, and oxamic acids were identified as generated carboxylic acids. NH(4)(+) ion was preferentially released in both treatments, along with NO(3)(-) ion in smaller proportion.

An efficient hybrid method for stochastic reaction-diffusion biochemical systems with delay

NASA Astrophysics Data System (ADS)

Sayyidmousavi, Alireza; Ilie, Silvana

2017-12-01

Many chemical reactions, such as gene transcription and translation in living cells, need a certain time to finish once they are initiated. Simulating stochastic models of reaction-diffusion systems with delay can be computationally expensive. In the present paper, a novel hybrid algorithm is proposed to accelerate the stochastic simulation of delayed reaction-diffusion systems. The delayed reactions may be of consuming or non-consuming delay type. The algorithm is designed for moderately stiff systems in which the events can be partitioned into slow and fast subsets according to their propensities. The proposed algorithm is applied to three benchmark problems and the results are compared with those of the delayed Inhomogeneous Stochastic Simulation Algorithm. The numerical results show that the new hybrid algorithm achieves considerable speed-up in the run time and very good accuracy.

Reaction-diffusion systems coupled at the boundary and the Morse-Smale property

NASA Astrophysics Data System (ADS)

Broche, Rita de Cássia D. S.; de Oliveira, Luiz Augusto F.

We study an one-dimensional nonlinear reaction-diffusion system coupled on the boundary. Such system comes from modeling problems of temperature distribution on two bars of same length, jointed together, with different diffusion coefficients. We prove the transversality property of unstable and stable manifolds assuming all equilibrium points are hyperbolic. To this end, we write the system as an equation with noncontinuous diffusion coefficient. We then study the nonincreasing property of the number of zeros of a linearized nonautonomous equation as well as the Sturm-Liouville properties of the solutions of a linear elliptic problem.

Recovery of lithium and cobalt from spent lithium-ion batteries using organic acids: Process optimization and kinetic aspects.

PubMed

Golmohammadzadeh, Rabeeh; Rashchi, Fereshteh; Vahidi, Ehsan

2017-06-01

An environmentally-friendly route based on hydrometallurgy was investigated for the recovery of cobalt and lithium from spent lithium ion batteries (LIBs) using different organic acids (citric acid, Dl-malic acid, oxalic acid and acetic acid). In this investigation, response surface methodology (RSM) was utilized to optimize leaching parameters including solid to liquid ratio (S/L), temperature, acid concentration, type of organic acid and hydrogen peroxide concentration. Based on the results obtained from optimizing procedure, temperature was recognized as the most influential parameter. In addition, while 81% of cobalt was recovered, the maximum lithium recovery of 92% was achieved at the optimum leaching condition of 60°C, S/L: 30gL -1 , citric acid concentration: 2M, hydrogen peroxide concentration: 1.25Vol.% and leaching time: 2h. Furthermore, results displayed that ultrasonic agitation will enhance the recovery of lithium and cobalt. It was found that the kinetics of cobalt leaching is controlled by surface chemical reaction at temperatures lower than 45°C. However, diffusion through the product layer at temperatures higher than 45°C controls the rate of cobalt leaching. Rate of lithium reaction is controlled by diffusion through the product layer at all the temperatures studied. Copyright © 2017 Elsevier Ltd. All rights reserved.

Similarity solutions of reaction–diffusion equation with space- and time-dependent diffusion and reaction terms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, C.-L.; Lee, C.-C., E-mail: chieh.no27@gmail.com

2016-01-15

We consider solvability of the generalized reaction–diffusion equation with both space- and time-dependent diffusion and reaction terms by means of the similarity method. By introducing the similarity variable, the reaction–diffusion equation is reduced to an ordinary differential equation. Matching the resulting ordinary differential equation with known exactly solvable equations, one can obtain corresponding exactly solvable reaction–diffusion systems. Several representative examples of exactly solvable reaction–diffusion equations are presented.

Cox process representation and inference for stochastic reaction-diffusion processes

NASA Astrophysics Data System (ADS)

Schnoerr, David; Grima, Ramon; Sanguinetti, Guido

2016-05-01

Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to the social sciences, yet they are notoriously difficult to simulate and calibrate to observational data. Here we use ideas from statistical physics and machine learning to provide a solution to the inverse problem of learning a stochastic reaction-diffusion process from data. Our solution relies on a non-trivial connection between stochastic reaction-diffusion processes and spatio-temporal Cox processes, a well-studied class of models from computational statistics. This connection leads to an efficient and flexible algorithm for parameter inference and model selection. Our approach shows excellent accuracy on numeric and real data examples from systems biology and epidemiology. Our work provides both insights into spatio-temporal stochastic systems, and a practical solution to a long-standing problem in computational modelling.

Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning.

PubMed

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2017-12-21

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.

Simulation tools for particle-based reaction-diffusion dynamics in continuous space

PubMed Central

2014-01-01

Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Certain systems however, require these investments to be modeled adequately. Here we present a review on the current field of particle-based reaction-diffusion software packages operating on continuous space. Four nested levels of modeling detail are identified that capture incrementing amount of detail. Their applicability to different biological questions is discussed, arching from straight diffusion simulations to sophisticated and expensive models that bridge towards coarse grained molecular dynamics. PMID:25737778

Analytical Solution for Transport with Bimolecular Reactions in Fracture-Matrix Systems with Application to In-Situ Chemical Oxidation

NASA Astrophysics Data System (ADS)

Rajaram, H.; Arshadi, M.

2016-12-01

In-situ chemical oxidation (ISCO) is an effective strategy for remediation of DNAPL contamination in fractured rock. During ISCO, an oxidant (e.g. permanganate) is typically injected through fractures and is consumed by bimolecular reactions with DNAPLs such as TCE and natural organic matter in the fracture and the adjacent rock matrix. Under these conditions, moving reaction fronts form and propagate along the fracture and into the rock matrix. The propagation of these reaction fronts is strongly influenced by the heterogeneity/discontinuity across the fracture-matrix interface (advective transport dominates in the fractures, while diffusive transport dominates in the rock matrix). We present analytical solutions for the concentrations of the oxidant, TCE and natural organic matter; and the propagation of the reaction fronts in a fracture-matrix system. Our approximate analytical solutions assume advection and reaction dominate over diffusion/dispersion in the fracture and neglect the latter. Diffusion and reaction with both TCE and immobile natural organic matter in the rock matrix are considered. The behavior of the reaction-diffusion equations in the rock matrix is posed as a Stefan problem where the diffusing oxidant reacts with both diffusing (TCE) and immobile (natural organic matter) reductants. Our analytical solutions establish that the reaction fronts propagate diffusively (i.e. as the square root of time) in both the matrix and the fracture. Our analytical solutions agree very well with numerical simulations for the case of uniform advection in the fracture. We also present extensions of our analytical solutions to non-uniform flows in the fracture by invoking a travel-time transformation. The non-uniform flow solutions are relevant to field applications of ISCO. The approximate analytical solutions are relevant to a broad class of reactive transport problems in fracture-matrix systems where moving reaction fronts occur.

Investigating the air oxidation of V(II) ions in a vanadium redox flow battery

NASA Astrophysics Data System (ADS)

Ngamsai, Kittima; Arpornwichanop, Amornchai

2015-11-01

The air oxidation of vanadium (V(II)) ions in a negative electrolyte reservoir is a major side reaction in a vanadium redox flow battery (VRB), which leads to electrolyte imbalance and self-discharge of the system during long-term operation. In this study, an 80% charged negative electrolyte solution is employed to investigate the mechanism and influential factors of the reaction in a negative-electrolyte reservoir. The results show that the air oxidation of V(II) ions occurs at the air-electrolyte solution interface area and leads to a concentration gradient of vanadium ions in the electrolyte solution and to the diffusion of V(II) and V(III) ions. The effect of the ratio of the electrolyte volume to the air-electrolyte solution interface area and the concentrations of vanadium and sulfuric acid in an electrolyte solution is investigated. A higher ratio of electrolyte volume to the air-electrolyte solution interface area results in a slower oxidation reaction rate. The high concentrations of vanadium and sulfuric acid solution also retard the air oxidation of V(II) ions. This information can be utilized to design an appropriate electrolyte reservoir for the VRB system and to prepare suitable ingredients for the electrolyte solution.

Pattern formation in the iodate-sulfite-thiosulfate reaction-diffusion system.

PubMed

Liu, Haimiao; Pojman, John A; Zhao, Yuemin; Pan, Changwei; Zheng, Juhua; Yuan, Ling; Horváth, Attila K; Gao, Qingyu

2012-01-07

Sodium polyacrylate-induced pH pattern formation and starch-induced iodine pattern formation were investigated in the iodate-sulfite-thiosulfate (IST) reaction in a one-side fed disc gel reactor (OSFR). As binding agents of the autocatalyst of hydrogen ions or iodide ions, different content of sodium polyacrylate or starch has induced various types of pattern formation. We observed pH pulses, striped patterns, mixed spots and stripes, and hexagonal spots upon increasing the content of sodium polyacrylate and observed iodine pulses, branched patterns, and labyrinthine patterns upon increasing the starch content in the system. Coexistence of a pH front and an iodine front was also studied in a batch IST reaction-diffusion system. Both pH and iodine front instabilities were observed in the presence of sodium polyacrylate, i.e., cellular fronts and transient Turing structures resulting from the decrease in diffusion coefficients of activators. The mechanism of multiple feedback may explain the different patterns in the IST reaction-diffusion system.

Link between alginate reaction front propagation and general reaction diffusion theory.

PubMed

Braschler, Thomas; Valero, Ana; Colella, Ludovica; Pataky, Kristopher; Brugger, Jürgen; Renaud, Philippe

2011-03-15

We provide a common theoretical framework reuniting specific models for the Ca(2+)-alginate system and general reaction diffusion theory along with experimental validation on a microfluidic chip. As a starting point, we use a set of nonlinear, partial differential equations that are traditionally solved numerically: the Mikkelsen-Elgsaeter model. Applying the traveling-wave hypothesis as a major simplification, we obtain an analytical solution. The solution indicates that the fundamental properties of the alginate reaction front are governed by a single dimensionless parameter λ. For small λ values, a large depletion zone accompanies the reaction front. For large λ values, the alginate reacts before having the time to diffuse significantly. We show that the λ parameter is of general importance beyond the alginate model system, as it can be used to classify known solutions for second-order reaction diffusion schemes, along with the novel solution presented here. For experimental validation, we develop a microchip model system, in which the alginate gel formation can be carried out in a highly controlled, essentially 1D environment. The use of a filter barrier enables us to rapidly renew the CaCl(2) solution, while maintaining flow speeds lower than 1 μm/s for the alginate compartment. This allows one to impose an exactly known bulk CaCl(2) concentration and diffusion resistance. This experimental model system, taken together with the theoretical development, enables the determination of the entire set of physicochemical parameters governing the alginate reaction front in a single experiment.

A study on ?-dissipative synchronisation of coupled reaction-diffusion neural networks with time-varying delays

NASA Astrophysics Data System (ADS)

Ali, M. Syed; Zhu, Quanxin; Pavithra, S.; Gunasekaran, N.

2018-03-01

This study examines the problem of dissipative synchronisation of coupled reaction-diffusion neural networks with time-varying delays. This paper proposes a complex dynamical network consisting of N linearly and diffusively coupled identical reaction-diffusion neural networks. By constructing a suitable Lyapunov-Krasovskii functional (LKF), utilisation of Jensen's inequality and reciprocally convex combination (RCC) approach, strictly ?-dissipative conditions of the addressed systems are derived. Finally, a numerical example is given to show the effectiveness of the theoretical results.

Generalized Hydrodynamic Treatment of the Interplay between Restricted Transport and Catalytic Reactions in Nanoporous Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ackerman, David M.; Wang, Jing; Evans, James W.

2012-05-30

Behavior of catalytic reactions in narrow pores is controlled by a delicate interplay between fluctuations in adsorption-desorption at pore openings, restricted diffusion, and reaction. This behavior is captured by a generalized hydrodynamic formulation of appropriate reaction-diffusion equations (RDE). These RDE incorporate an unconventional description of chemical diffusion in mixed-component quasi-single-file systems based on a refined picture of tracer diffusion for finite-length pores. The RDE elucidate the nonexponential decay of the steady-state reactant concentration into the pore and the non-mean-field scaling of the reactant penetration depth.

Generalized hydrodynamic treatment of the interplay between restricted transport and catalytic reactions in nanoporous materials.

PubMed

Ackerman, David M; Wang, Jing; Evans, James W

2012-06-01

Behavior of catalytic reactions in narrow pores is controlled by a delicate interplay between fluctuations in adsorption-desorption at pore openings, restricted diffusion, and reaction. This behavior is captured by a generalized hydrodynamic formulation of appropriate reaction-diffusion equations (RDE). These RDE incorporate an unconventional description of chemical diffusion in mixed-component quasi-single-file systems based on a refined picture of tracer diffusion for finite-length pores. The RDE elucidate the nonexponential decay of the steady-state reactant concentration into the pore and the non-mean-field scaling of the reactant penetration depth.

STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies.

PubMed

Hepburn, Iain; Chen, Weiliang; Wils, Stefan; De Schutter, Erik

2012-05-10

Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. We describe STEPS, a stochastic reaction-diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction-diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. STEPS simulates models of cellular reaction-diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/

Science Notes.

ERIC Educational Resources Information Center

Thurman, Shirley; And Others

1988-01-01

Describes 36 science activities. Topics include: osmosis, fermentation, anhydrobiotic organisms, breathing monitors, trypsin, weeds, amyloplasts, electrolysis, polarimeters, ethene ripening of fruit, colorimetry, diffusion, redox reactions, equilibria, acid-base relationships, electricity, power, resonance, measurement, parallax, amplifiers,…

Feynman-Kac equations for reaction and diffusion processes

NASA Astrophysics Data System (ADS)

Hou, Ru; Deng, Weihua

2018-04-01

This paper provides a theoretical framework for deriving the forward and backward Feynman-Kac equations for the distribution of functionals of the path of a particle undergoing both diffusion and reaction processes. Once given the diffusion type and reaction rate, a specific forward or backward Feynman-Kac equation can be obtained. The results in this paper include those for normal/anomalous diffusions and reactions with linear/nonlinear rates. Using the derived equations, we apply our findings to compute some physical (experimentally measurable) statistics, including the occupation time in half-space, the first passage time, and the occupation time in half-interval with an absorbing or reflecting boundary, for the physical system with anomalous diffusion and spontaneous evanescence.

The mechanism of proton conduction in phosphoric acid

NASA Astrophysics Data System (ADS)

Vilčiauskas, Linas; Tuckerman, Mark E.; Bester, Gabriel; Paddison, Stephen J.; Kreuer, Klaus-Dieter

2012-06-01

Neat liquid phosphoric acid (H3PO4) has the highest intrinsic proton conductivity of any known substance and is a useful model for understanding proton transport in other phosphate-based systems in biology and clean energy technologies. Here, we present an ab initio molecular dynamics study that reveals, for the first time, the microscopic mechanism of this high proton conductivity. Anomalously fast proton transport in hydrogen-bonded systems involves a structural diffusion mechanism in which intramolecular proton transfer is driven by specific hydrogen bond rearrangements in the surrounding environment. Aqueous media transport excess charge defects through local hydrogen bond rearrangements that drive individual proton transfer reactions. In contrast, strong, polarizable hydrogen bonds in phosphoric acid produce coupled proton motion and a pronounced protic dielectric response of the medium, leading to the formation of extended, polarized hydrogen-bonded chains. The interplay between these chains and a frustrated hydrogen-bond network gives rise to the high proton conductivity.

Class of self-limiting growth models in the presence of nonlinear diffusion

NASA Astrophysics Data System (ADS)

Kar, Sandip; Banik, Suman Kumar; Ray, Deb Shankar

2002-06-01

The source term in a reaction-diffusion system, in general, does not involve explicit time dependence. A class of self-limiting growth models dealing with animal and tumor growth and bacterial population in a culture, on the other hand, are described by kinetics with explicit functions of time. We analyze a reaction-diffusion system to study the propagation of spatial front for these models.

Multiscale Modeling of Diffusion in a Crowded Environment.

PubMed

Meinecke, Lina

2017-11-01

We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid. We then extract a macroscopic description from the resulting jump rates, where the excluded volume effect is modeled by a diffusion equation with space-dependent diffusion coefficient. The crowding molecules can be of arbitrary shape and size, and numerical experiments demonstrate that those factors together with the size of the diffusing molecule play a crucial role on the magnitude of the decrease in diffusive motion. When correcting the reaction rates for the altered diffusion we can show that molecular crowding either enhances or inhibits chemical reactions depending on local fluctuations of the obstacle density.

Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes.

PubMed

Chevalier, Michael W; El-Samad, Hana

2012-08-28

Diffusion of biological molecules on 2D biological membranes can play an important role in the behavior of stochastic biochemical reaction systems. Yet, we still lack a fundamental understanding of circumstances where explicit accounting of the diffusion and spatial coordinates of molecules is necessary. In this work, we illustrate how time-dependent, non-exponential reaction probabilities naturally arise when explicitly accounting for the diffusion of molecules. We use the analytical expression of these probabilities to derive a novel algorithm which, while ignoring the exact position of the molecules, can still accurately capture diffusion effects. We investigate the regions of validity of the algorithm and show that for most parameter regimes, it constitutes an accurate framework for studying these systems. We also document scenarios where large spatial fluctuation effects mandate explicit consideration of all the molecules and their positions. Taken together, our results derive a fundamental understanding of the role of diffusion and spatial fluctuations in these systems. Simultaneously, they provide a general computational methodology for analyzing a broad class of biological networks whose behavior is influenced by diffusion on membranes.

Lipoic acid and dihydrolipoic acid. A comprehensive theoretical study of their antioxidant activity supported by available experimental kinetic data.

PubMed

Castañeda-Arriaga, Romina; Alvarez-Idaboy, J Raul

2014-06-23

The free radical scavenging activity of lipoic acid (LA) and dihydrolipoic acid (DHLA) has been studied in nonpolar and aqueous solutions, using the density functional theory and several oxygen centered radicals. It was found that lipoic acid is capable of scavenging only very reactive radicals, while the dehydrogenated form is an excellent scavenger via a hydrogen transfer mechanism. The environment plays an important role in the free radical scavenging activity of DHLA because in water it is deprotonated, and this enhances its activity. In particular, the reaction rate constant of DHLA in water with an HOO(•) radical is close to the diffusion limit. This has been explained on the basis of the strong H-bonding interactions found in the transition state, which involve the carboxylate moiety, and it might have implications for other biological systems in which this group is present.

Breakdown of the reaction-diffusion master equation with nonelementary rates

NASA Astrophysics Data System (ADS)

Smith, Stephen; Grima, Ramon

2016-05-01

The chemical master equation (CME) is the exact mathematical formulation of chemical reactions occurring in a dilute and well-mixed volume. The reaction-diffusion master equation (RDME) is a stochastic description of reaction-diffusion processes on a spatial lattice, assuming well mixing only on the length scale of the lattice. It is clear that, for the sake of consistency, the solution of the RDME of a chemical system should converge to the solution of the CME of the same system in the limit of fast diffusion: Indeed, this has been tacitly assumed in most literature concerning the RDME. We show that, in the limit of fast diffusion, the RDME indeed converges to a master equation but not necessarily the CME. We introduce a class of propensity functions, such that if the RDME has propensities exclusively of this class, then the RDME converges to the CME of the same system, whereas if the RDME has propensities not in this class, then convergence is not guaranteed. These are revealed to be elementary and nonelementary propensities, respectively. We also show that independent of the type of propensity, the RDME converges to the CME in the simultaneous limit of fast diffusion and large volumes. We illustrate our results with some simple example systems and argue that the RDME cannot generally be an accurate description of systems with nonelementary rates.

Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Virk, Amninder; Stait-Gardner, Timothy; Willis, Scott; Torres, Allan; Price, William

2015-02-01

Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

Evaluation of shrinking core model in leaching process of Pomalaa nickel laterite using citric acid as leachant at atmospheric conditions

NASA Astrophysics Data System (ADS)

Wanta, K. C.; Perdana, I.; Petrus, H. T. B. M.

2016-11-01

Most of kinetics studies related to leaching process used shrinking core model to describe physical phenomena of the process. Generally, the model was developed in connection with transport and/or reaction of reactant components. In this study, commonly used internal diffusion controlled shrinking core model was evaluated for leaching process of Pomalaa nickel laterite using citric acid as leachant. Particle size was varied at 60-70, 100-120, -200 meshes, while the operating temperature was kept constant at 358 K, citric acid concentration at 0.1 M, pulp density at 20% w/v and the leaching time was for 120 minutes. Simulation results showed that the shrinking core model was inadequate to closely approach the experimental data. Meanwhile, the experimental data indicated that the leaching process was determined by the mobility of product molecules in the ash layer pores. In case of leaching resulting large product molecules, a mathematical model involving steps of reaction and product diffusion might be appropriate to develop.

Nonequilibrium transition and pattern formation in a linear reaction-diffusion system with self-regulated kinetics

NASA Astrophysics Data System (ADS)

Paul, Shibashis; Ghosh, Shyamolina; Ray, Deb Shankar

2018-02-01

We consider a reaction-diffusion system with linear, stochastic activator-inhibitor kinetics where the time evolution of concentration of a species at any spatial location depends on the relative average concentration of its neighbors. This self-regulating nature of kinetics brings in spatial correlation between the activator and the inhibitor. An interplay of this correlation in kinetics and disparity of diffusivities of the two species leads to symmetry breaking non-equilibrium transition resulting in stationary pattern formation. The role of initial noise strength and the linear reaction terms has been analyzed for pattern selection.

Kinetic and Mechanism Study of Vanadium Acid Leaching from Black Shale Using Microwave Heating Method

NASA Astrophysics Data System (ADS)

Wang, Jing-peng; Zhang, Yi-min; Huang, Jing; Liu, Tao

2018-04-01

The leaching kinetics of the vanadium leaching process were investigated by the comparison of microwave heating and conventional heating methods. Microwave heating with CaF2 had a synergistic effect and improved the vanadium leaching efficiency. In contrast to conventional heating leaching, microwave heating accelerated the vanadium leaching rate by approximately 1-3% and by approximately 15% when CaF2 was also used. The kinetics analysis showed that the calculated activation energy decreased in the microwave heating method in the presence and absence of CaF2. The control procedure of leaching also changed from a chemical reaction control step to a mixed chemical diffusion control step upon the addition of CaF2. Microwave heating was shown to be suitable for leaching systems with diffusion or mixed chemical diffusion control steps when the target mineral does not have a microwave absorbing ability.

Kinetic and Mechanism Study of Vanadium Acid Leaching from Black Shale Using Microwave Heating Method

NASA Astrophysics Data System (ADS)

Wang, Jing-peng; Zhang, Yi-min; Huang, Jing; Liu, Tao

2018-06-01

The leaching kinetics of the vanadium leaching process were investigated by the comparison of microwave heating and conventional heating methods. Microwave heating with CaF2 had a synergistic effect and improved the vanadium leaching efficiency. In contrast to conventional heating leaching, microwave heating accelerated the vanadium leaching rate by approximately 1-3% and by approximately 15% when CaF2 was also used. The kinetics analysis showed that the calculated activation energy decreased in the microwave heating method in the presence and absence of CaF2. The control procedure of leaching also changed from a chemical reaction control step to a mixed chemical diffusion control step upon the addition of CaF2. Microwave heating was shown to be suitable for leaching systems with diffusion or mixed chemical diffusion control steps when the target mineral does not have a microwave absorbing ability.

Fluorescence correlation spectroscopy experiments to quantify free diffusion coefficients in reaction-diffusion systems: The case of Ca2 + and its dyes

NASA Astrophysics Data System (ADS)

Sigaut, Lorena; Villarruel, Cecilia; Ponce, María Laura; Ponce Dawson, Silvina

2017-06-01

Many cell signaling pathways involve the diffusion of messengers that bind and unbind to and from intracellular components. Quantifying their net transport rate under different conditions then requires having separate estimates of their free diffusion coefficient and binding or unbinding rates. In this paper, we show how performing sets of fluorescence correlation spectroscopy (FCS) experiments under different conditions, it is possible to quantify free diffusion coefficients and on and off rates of reaction-diffusion systems. We develop the theory and present a practical implementation for the case of the universal second messenger, calcium (Ca2 +) and single-wavelength dyes that increase their fluorescence upon Ca2 + binding. We validate the approach with experiments performed in aqueous solutions containing Ca2 + and Fluo4 dextran (both in its high and low affinity versions). Performing FCS experiments with tetramethylrhodamine-dextran in Xenopus laevis oocytes, we infer the corresponding free diffusion coefficients in the cytosol of these cells. Our approach can be extended to other physiologically relevant reaction-diffusion systems to quantify biophysical parameters that determine the dynamics of various variables of interest.

Computational methods for diffusion-influenced biochemical reactions.

PubMed

Dobrzynski, Maciej; Rodríguez, Jordi Vidal; Kaandorp, Jaap A; Blom, Joke G

2007-08-01

We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli. In the regime where the number of molecules is small and reactions are diffusion-limited predicted fluctuations in the product number vary between the methods, while the average is the same. Computational approaches at the level of the reaction-diffusion master equation compute the same fluctuations as the reference result obtained from the particle-based method if the size of the sub-volumes is comparable to the diameter of reactants. Using numerical simulations of reversible binding of a pair of molecules we argue that the disagreement in predicted fluctuations is due to different modeling of inter-arrival times between reaction events. Simulations for a more complex biological study show that the different approaches lead to different results due to modeling issues. Finally, we present the physical assumptions behind the mesoscopic models for the reaction-diffusion systems. Input files for the simulations and the source code of GMP can be found under the following address: http://www.cwi.nl/projects/sic/bioinformatics2007/

Backstepping-based boundary control design for a fractional reaction diffusion system with a space-dependent diffusion coefficient.

PubMed

Chen, Juan; Cui, Baotong; Chen, YangQuan

2018-06-11

This paper presents a boundary feedback control design for a fractional reaction diffusion (FRD) system with a space-dependent (non-constant) diffusion coefficient via the backstepping method. The contribution of this paper is to generalize the results of backstepping-based boundary feedback control for a FRD system with a space-independent (constant) diffusion coefficient to the case of space-dependent diffusivity. For the boundary stabilization problem of this case, a designed integral transformation treats it as a problem of solving a hyperbolic partial differential equation (PDE) of transformation's kernel, then the well posedness of the kernel PDE is solved for the plant with non-constant diffusivity. Furthermore, by the fractional Lyapunov stability (Mittag-Leffler stability) theory and the backstepping-based boundary feedback controller, the Mittag-Leffler stability of the closed-loop FRD system with non-constant diffusivity is proved. Finally, an extensive numerical example for this closed-loop FRD system with non-constant diffusivity is presented to verify the effectiveness of our proposed controller. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

A fully coupled 3D transport model in SPH for multi-species reaction-diffusion systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adami, Stefan; Hu, X. Y.; Adams, N. A.

2011-08-23

Abstract—In this paper we present a fully generalized transport model for multiple species in complex two and threedimensional geometries. Based on previous work [1] we have extended our interfacial reaction-diffusion model to handle arbitrary numbers of species allowing for coupled reaction models. Each species is tracked independently and we consider different physics of a species with respect to the bulk phases in contact. We use our SPH model to simulate the reaction-diffusion problem on a pore-scale level of a solid oxide fuel cell (SOFC) with special emphasize on the effect of surface diffusion.

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics.

PubMed

Strehl, Robert; Ilie, Silvana

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

Atomistic modeling of water diffusion in hydrolytic biomaterials.

PubMed

Gautieri, Alfonso; Mezzanzanica, Andrea; Motta, Alberto; Redealli, Alberto; Vesentini, Simone

2012-04-01

One of the most promising applications of hydrolytically degrading biomaterials is their use as drug release carriers. These uses, however, require that the degradation and diffusion of drug are reliably predicted, which is complex to achieve through present experimental methods. Atomistic modeling can help in the knowledge-based design of degrading biomaterials with tuned drug delivery properties, giving insights on the small molecules diffusivity at intermediate states of the degradation process. We present here an atomistic-based approach to investigate the diffusion of water (through which hydrolytic degradation occurs) in degrading bulk models of poly(lactic acid) or PLA. We determine the water diffusion coefficient for different swelling states of the polymeric matrix (from almost dry to pure water) and for different degrees of degradation. We show that water diffusivity is highly influenced by the swelling degree, while little or not influenced by the degradation state. This approach, giving water diffusivity for different states of the matrix, can be combined with diffusion-reaction analytical methods in order to predict the degradation path on longer time scales. Furthermore, atomistic approach can be used to investigate diffusion of other relevant small molecules, eventually leading to the a priori knowledge of degradable biomaterials transport properties, helping the design of the drug delivery systems.

Mathematical Description Development of Reactions of Metallic Gallium Using Kinetic Block Diagram

NASA Astrophysics Data System (ADS)

Yakovleva, A. A.; Soboleva, V. G.; Filatova, E. G.

2018-05-01

A kinetic block diagram based on a logical sequence of actions in the mathematical processing of a kinetic data is used. A type of reactions of metallic gallium in hydrochloric acid solutions is determined. It has been established that the reactions of the formation of gallium oxide and its salts proceed independently and in the absence of the diffusion resistance. Kinetic models connecting the constants of the reaction rate with the activation energy and describing the evolution of the process are obtained.

Nonlinear stability in reaction-diffusion systems via optimal Lyapunov functions

NASA Astrophysics Data System (ADS)

Lombardo, S.; Mulone, G.; Trovato, M.

2008-06-01

We define optimal Lyapunov functions to study nonlinear stability of constant solutions to reaction-diffusion systems. A computable and finite radius of attraction for the initial data is obtained. Applications are given to the well-known Brusselator model and a three-species model for the spatial spread of rabies among foxes.

The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.

PubMed

Drawert, Brian; Lawson, Michael J; Petzold, Linda; Khammash, Mustafa

2010-02-21

We have developed a computational framework for accurate and efficient simulation of stochastic spatially inhomogeneous biochemical systems. The new computational method employs a fractional step hybrid strategy. A novel formulation of the finite state projection (FSP) method, called the diffusive FSP method, is introduced for the efficient and accurate simulation of diffusive transport. Reactions are handled by the stochastic simulation algorithm.

The dissolution mechanisms of silicate and glass-ionomer dental cements.

PubMed

Kuhn, A T; Wilson, A D

1985-11-01

The mechanism of dissolution of two dental cements of the acid-base setting types (silicate and glass-ionomer) is considered. Dissolution is incongruent, probably because most of the leached species can derive both from the matrix (polysalt gel) and the partly reacted glass particles. The release occurs by means of three discrete mechanisms, surface wash-off, diffusion through pores and cracks or diffusion through the bulk. Such behaviour is shown to be capable of being modelled with extremely high goodness-of-fit values, using equations such as y = const + at1/2 + bt. Analogies with research from the fields of geochemistry and nuclear fuel storage are made and these systems obey similar relationships. The dental cement systems differ, however, in that their dissolution is to some extent reversible. This is explained in terms of formation of insoluble complexes, either by reaction of the constituent ions, or by replacement of OH-, for example, with F-.

Experimental and theoretical study on chemical reactions and species diffusion by a nano-pulse discharged bubble for water treatment

NASA Astrophysics Data System (ADS)

He, Yuchen; Uehara, Satoshi; Takana, Hidemasa; Nishiyama, Hideya

2018-01-01

Advanced oxidation processes using hydroxyl radicals (ṡOH) generated inside bubbles in water has drawn widely interest for the high oxidation potential of OH radical to decompose persistent organic pollutants such as dioxins and humic acid for water purification. In this study, a two-dimensional diffusion model for a nano-pulse discharged bubble in water is established. Based on the experimental results of streamer propagation inside a bubble, the diffusion processes around the bubble interface and reactions of chemical species in liquids are simulated. The simulation results show that OH radicals can diffuse only several micrometers away from the bubble interface in water. Furthermore, the optimal operating voltage and frequency conditions for OH generation is obtained by comparing the OH concentration in water obtained from numerical simulation with that measured by spectroscopy in experiment.

Phenomena during thermal removal of binders

NASA Astrophysics Data System (ADS)

Hrdina, Kenneth Edward

The research presented herein has focused on debinding of an ethylene copolymer from a SiC based molded ceramic green body. Examination of the binder burnout process was carried out by breaking down the process into two distinct regions: those events which occur before any weight loss begins, and those events occurring during binder removal. Below the temperature of observed binder loss (175sp°C), both reversible and irreversible displacement was observed to occur. The displacement was accounted for by relaxation of molding stresses, thermal expansion of the system, and melting of the semicrystalline copolymer occurring during heating. Upon further heating the binder undergoes a two stage thermal degradation process. In the first stage, acetic acid is the only degradation product formed, as determined by GC/MS analysis. In this stage, component shrinkage persisted and it was found that one unit volume of shrinkage corresponded with one unit volume of binder removed, indicating that no porosity developed. The escaping acetic acid effluents must diffuse through liquid polymer filled porous regions to escape. The gas pressure of the acetic acid species produced in the first stage of the thermal degradation may exceed the ambient pressure promoting bubble formation. Controlling the heating rate of the specimen maintains the gas pressure below the bubbling threshold and minimizes the degradation time. Experiments have determined the kinetics of the reaction in the presence of the high surface area (10-15msp2/g) ceramic powder and then verified that acetic acid was diffusing through the polymer phase to the specimen surface where evaporation is taking place. The sorption method measured the diffusivity and activity of acetic acid within the filled ceramic system within a TGA. These data were incorporated into a Fickian type model which included the rate of generation of the diffusing species. The modeling process involved prediction of the bloating temperature as a function of the sample size for a given heating rate. The predicted results and experimental results show good correlation. The model was used to optimize the heating schedule which minimized the binder removal time.

Multi-Algorithm Particle Simulations with Spatiocyte.

PubMed

Arjunan, Satya N V; Takahashi, Koichi

2017-01-01

As quantitative biologists get more measurements of spatially regulated systems such as cell division and polarization, simulation of reaction and diffusion of proteins using the data is becoming increasingly relevant to uncover the mechanisms underlying the systems. Spatiocyte is a lattice-based stochastic particle simulator for biochemical reaction and diffusion processes. Simulations can be performed at single molecule and compartment spatial scales simultaneously. Molecules can diffuse and react in 1D (filament), 2D (membrane), and 3D (cytosol) compartments. The implications of crowded regions in the cell can be investigated because each diffusing molecule has spatial dimensions. Spatiocyte adopts multi-algorithm and multi-timescale frameworks to simulate models that simultaneously employ deterministic, stochastic, and particle reaction-diffusion algorithms. Comparison of light microscopy images to simulation snapshots is supported by Spatiocyte microscopy visualization and molecule tagging features. Spatiocyte is open-source software and is freely available at http://spatiocyte.org .

Multispecies reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Aghamohammadi, A.; Fatollahi, A. H.; Khorrami, M.; Shariati, A.

2000-10-01

Multispecies reaction-diffusion systems, for which the time evolution equations of correlation functions become a closed set, are considered. A formal solution for the average densities is found. Some special interactions and the exact time dependence of the average densities in these cases are also studied. For the general case, the large-time behavior of the average densities has also been obtained.

Science Notes.

ERIC Educational Resources Information Center

Murray, A. J. S.; And Others

1988-01-01

Presents 31 science activities for use with high school or college science classes. Topics included are: chromatography, ecology, invertebrates, enzymes, genetics, botany, creep, crystals, diffusion, computer interfaces, acid rain, teaching techniques, chemical reactions, waves, electric fields, rainbows, electricity, magnetic fields, and a Pitot…

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strehl, Robert; Ilie, Silvana, E-mail: silvana@ryerson.ca

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated onmore » three benchmarking systems, with special focus on approximation accuracy and efficiency.« less

Determination of the diffusion coefficient of hydrogen ion in hydrogels.

PubMed

Schuszter, Gábor; Gehér-Herczegh, Tünde; Szűcs, Árpád; Tóth, Ágota; Horváth, Dezső

2017-05-17

The role of diffusion in chemical pattern formation has been widely studied due to the great diversity of patterns emerging in reaction-diffusion systems, particularly in H + -autocatalytic reactions where hydrogels are applied to avoid convection. A custom-made conductometric cell is designed to measure the effective diffusion coefficient of a pair of strong electrolytes containing sodium ions or hydrogen ions with a common anion. This together with the individual diffusion coefficient for sodium ions, obtained from PFGSE-NMR spectroscopy, allows the determination of the diffusion coefficient of hydrogen ions in hydrogels. Numerical calculations are also performed to study the behavior of a diffusion-migration model describing ionic diffusion in our system. The method we present for one particular case may be extended for various hydrogels and diffusing ions (such as hydroxide) which are relevant e.g. for the development of pH-regulated self-healing mechanisms and hydrogels used for drug delivery.

Use of Both Anode and Cathode Reactions in Wastewater Treatment

NASA Astrophysics Data System (ADS)

Brillas, Enric; Sirés, Ignasi; Cabot, Pere LluíS.

Here, we describe the fundamentals, laboratory experiments, and environmental applications of indirect electrooxidation methods based on H2O2 electrogeneration such as electro-Fenton, photoelectro-Fenton and peroxicoagulation for the treatment of acidic wastewaters containing toxic and recalcitrant organics. These methods are electrochemical advanced oxidation processes that can be used in divided and undivided electrolytic cells in which pollutants are oxidized by hydroxyl radical (•OH) produced from anode and/or cathode reactions. H2O2 is generated from the two-electron reduction of O2 at reticulated vitreous carbon, graphite, carbon-felt, and O2-diffusion cathodes. The most usual method is electro-Fenton where Fe2 + added to the wastewater reacts with electrogenerated H2O2 to yield •OH and Fe3 + from Fenton's reaction. An advantage of this technique is that Fe2 + is continuously regenerated from cathodic reduction of Fe3 +. The characteristics of different electro-Fenton systems where pollutants are simultaneously destroyed by •OH formed in the medium from Fenton's reaction and at the anode surface from water oxidation are explained. The effect of the anode [Pt or boron-doped diamond (BDD)] and cathode (carbon-felt or O2-diffusion) on the degradation rate of persistent industrial by-products, herbicides, pharmaceuticals, dyes, etc. is examined. Initial pollutants react much more rapidly with •OH formed in the medium and their degradation sequences are discussed from aromatic intermediates and finally short aliphatic acids are detected. The synergetic positive catalytic effect of Cu2 + on the electro-Fenton process is evidenced. The photoelectro-Fenton method involves the irradiation of the wastewater with UVA light that rapidly photodecomposes complexes of Fe3 + with final carboxylic acids enhancing total decontamination. The peroxicoagulation method uses a sacrificial Fe anode that is continuously oxidized to Fe2 + and organics are either mineralized with •OH formed from both electrogenerated Fe2 + and H2O2 or removed by parallel coagulation with the FeOH3 precipitate formed from the excess of Fe3 + generated from Fenton's reaction.

Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

PubMed Central

Hummer, Gerhard

2015-01-01

We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green's function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions. PMID:26005592

Pattern formation in mass conserving reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Brauns, Fridtjof; Halatek, Jacob; Frey, Erwin

We present a rigorous theoretical framework able to generalize and unify pattern formation for quantitative mass conserving reaction-diffusion models. Mass redistribution controls chemical equilibria locally. Separation of diffusive mass redistribution on the level of conserved species provides a general mathematical procedure to decompose complex reaction-diffusion systems into effectively independent functional units, and to reveal the general underlying bifurcation scenarios. We apply this framework to Min protein pattern formation and identify the mechanistic roles of both involved protein species. MinD generates polarity through phase separation, whereas MinE takes the role of a control variable regulating the existence of MinD phases. Hence, polarization and not oscillations is the generic core dynamics of Min proteins in vivo. This establishes an intrinsic mechanistic link between the Min system and a broad class of intracellular pattern forming systems based on bistability and phase separation (wave-pinning). Oscillations are facilitated by MinE redistribution and can be understood mechanistically as relaxation oscillations of the polarization direction.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia, Andres

Transport and reaction in zeolites and other porous materials, such as mesoporous silica particles, has been a focus of interest in recent years. This is in part due to the possibility of anomalous transport effects (e.g. single-file diffusion) and its impact in the reaction yield in catalytic processes. Computational simulations are often used to study these complex nonequilibrium systems. Computer simulations using Molecular Dynamics (MD) techniques are prohibitive, so instead coarse grained one-dimensional models with the aid of Kinetic Monte Carlo (KMC) simulations are used. Both techniques can be computationally expensive, both time and resource wise. These coarse-grained systems canmore » be exactly described by a set of coupled stochastic master equations, that describe the reaction-diffusion kinetics of the system. The equations can be written exactly, however, coupling between the equations and terms within the equations make it impossible to solve them exactly; approximations must be made. One of the most common methods to obtain approximate solutions is to use Mean Field (MF) theory. MF treatments yield reasonable results at high ratios of reaction rate k to hop rate h of the particles, but fail completely at low k=h due to the over-estimation of fluxes of particles within the pore. We develop a method to estimate fluxes and intrapore diffusivity in simple one- dimensional reaction-diffusion models at high and low k=h, where the pores are coupled to an equilibrated three-dimensional fluid. We thus successfully describe analytically these simple reaction-diffusion one-dimensional systems. Extensions to models considering behavior with long range steric interactions and wider pores require determination of multiple boundary conditions. We give a prescription to estimate the required parameters for these simulations. For one dimensional systems, if single-file diffusion is relaxed, additional parameters to describe particle exchange have to be introduced. We use Langevin Molecular Dynamics (MD) simulations to assess these parameters.« less

Domainal cleavage as an Anisotropic Reaction-diffusion Process

NASA Astrophysics Data System (ADS)

Mulchrone, Kieran; Meere, Patrick

2017-04-01

Domainal cleavage comprises zones dominated by quartz and feldspar (QF-domains) and zones dominated by Mica (M-domains) which form at low metamorphic grades. The protolith is typically fairly homogeneous mudstone, siltstone, sandstone or limestone. Wet diffusion or pressure solution along grain boundaries is a key mechanism in the development of domanial cleavage. However, this does not explain why M-domains become sub-regularly spaced, visually evident in coarser-grained rocks, and take on an anastomising morphology. The ratio of M to QF-domains by volume can range from 1 to 0.1 and lower i.e. in extreme cases M-domains are intermittent but regularly spaced. It is suggested here that an anisotropic reaction-diffusion process model can explain these features. The imposed stress field instantaneously leads to anisotropy of diffusion by narrowing intergranular channels perpendicular to the principal stress. This leads to a preferred diffusion of chemicals parallel to the principal stress direction and lower diffusion rates in the normal direction. Combining this with the chemical reaction of pressure solution produces an anisotropic reaction-diffusion system. Both isotropic and anistropic reaction diffusion systems lead to pattern formation as discovered by Alan Turing on the 1950's as an explanation for patterns found in animal skins such as spots and stripes. Thus domanial cleavage is a striped pattern induced by diffusion anisotropy combined with a chemical reaction. Furthermore, rates of chemical reaction in intergranular fluids is likely to be many orders of magnitude greater that rates of deformation. Therefore we expect domanial cleavage to form relatively rapidly. As deformation progresses the M-domains behave less competently and may be the site of enhanced shearing. An example from Co. Cork, Ireland demonstrates shear folding in low-grade metasedimentary rocks with reverse shear along M-domains at a high angle to the maximum compressive stress.

Reaction-diffusion systems and external morphogen gradients: the two-dimensional case, with an application to skeletal pattern formation.

PubMed

Glimm, Tilmann; Zhang, Jianying; Shen, Yun-Qiu; Newman, Stuart A

2012-03-01

We investigate a reaction-diffusion system consisting of an activator and an inhibitor in a two-dimensional domain. There is a morphogen gradient in the domain. The production of the activator depends on the concentration of the morphogen. Mathematically, this leads to reaction-diffusion equations with explicitly space-dependent terms. It is well known that in the absence of an external morphogen, the system can produce either spots or stripes via the Turing bifurcation. We derive first-order expansions for the possible patterns in the presence of an external morphogen and show how both stripes and spots are affected. This work generalizes previous one-dimensional results to two dimensions. Specifically, we consider the quasi-one-dimensional case of a thin rectangular domain and the case of a square domain. We apply the results to a model of skeletal pattern formation in vertebrate limbs. In the framework of reaction-diffusion models, our results suggest a simple explanation for some recent experimental findings in the mouse limb which are much harder to explain in positional-information-type models.

Diffusivity of dicarboxylic acids molecules to secondary organic material governed by particle phase state

NASA Astrophysics Data System (ADS)

Han, Y.; Gong, Z.; Liu, P.; de Sá, S. S.; McKinney, K. A.; Martin, S. T.

2017-12-01

Atmospheric secondary organic material (SOM) from oxidation of volatile organic compounds can exist in amorphous solid, semisolid, and liquid states depending on a range of factors such as relative humidity (RH), temperature, and reaction history. The phase state of SOM affects the dynamic exchange and reactivity between particles and gas-phase molecules. Dicarboxylic acids are ubiquitous in ambient atmosphere and the uptake of which may lead to substantial changes in hygroscopicity, absorption property, and light scattering of aerosol particles. This study investigates the diffusivity of dicarboxylic acids to the matrix of SOM particles. SOM was generated from dark ozonolysis of a-pinene in Harvard Environmental Chamber. The produced SOM particles were passed through an ozone scrubber to remove gas-phase chemistry before being led into a flask reactor, where gas-phase dicarboxylic acid was injected continuously and RH was varied from 5% to 85%. The probe dicarboxylic acids molecules including malonic acid and a-ketoglutaric acid have been investigated for the uptake to SOM particles. Organic composition in the outflow of the flask was measured with a high-resolution time-of-flight aerosol mass spectrometer. The mass fractions of tracer ions in total organic mass for both malonic acid and a-ketoglutaric acid increased substantially with the increase of RH values. The tracer ions of malonic acid were also more abundant in a-pinene SOM particles with increased gas-phase concentrations. These results suggest that the diffusion of the studied dicarboxylic acids molecules to a-pinene SOM particles was enhanced at increased RH values, which is possibly due to the phase transition of a-pinene SOM particles from non-liquid to liquid states. Therefore, particle phase state may be an important factor governing the diffusivity of dicarboxylic acids molecules to a-pinene SOM. Further dicarboxylic acids with various functional groups will be investigated to understand the effects of volatility and structure on their diffusivity.

A Transition in the Cumulative Reaction Rate of Two Species Diffusion with Bimolecular Reaction

NASA Astrophysics Data System (ADS)

Rajaram, Harihar; Arshadi, Masoud

2015-04-01

Diffusion and bimolecular reaction between two initially separated reacting species is a prototypical small-scale description of reaction induced by transverse mixing. It is also relevant to diffusion controlled transport regimes as encountered in low-permeability matrix blocks in fractured media. In previous work, the reaction-diffusion problem has been analyzed as a Stefan problem involving a distinct moving boundary (reaction front), which predicts that front motion scales as √t, and the cumulative reaction rate scales as 1/√t-. We present a general non-dimensionalization of the problem and a perturbation analysis to show that there is an early time regime where the cumulative reaction rate scales as √t- rather than 1/√t. The duration of this early time regime (where the cumulative rate is kinetically rather than diffusion controlled) depends on the rate parameter, in a manner that is consistently predicted by our non-dimensionalization. We also present results on the scaling of the reaction front width. We present numerical simulations in homogeneous and heterogeneous porous media to demonstrate the limited influence of heterogeneity on the behavior of the reaction-diffusion system. We illustrate applications to the practical problem of in-situ chemical oxidation of TCE and PCE by permanganate, which is employed to remediate contaminated sites where the DNAPLs are largely dissolved in the rock matrix.

Diffusion and Surface Reaction in Heterogeneous Catalysis

ERIC Educational Resources Information Center

Baiker, A.; Richarz, W.

1978-01-01

Ethylene hydrogenation on a platinum catalyst, electrolytically applied to a tube wall, is a good system for the study of the interactions between diffusion and surface reaction in heterogeneous catalysis. Theoretical background, apparatus, procedure, and student performance of this experiment are discussed. (BB)

Nuclemeter: A Reaction-Diffusion Column for Quantifying Nucleic Acids Undergoing Enzymatic Amplification

NASA Astrophysics Data System (ADS)

Bau, Haim; Liu, Changchun; Killawala, Chitvan; Sadik, Mohamed; Mauk, Michael

2014-11-01

Real-time amplification and quantification of specific nucleic acid sequences plays a major role in many medical and biotechnological applications. In the case of infectious diseases, quantification of the pathogen-load in patient specimens is critical to assessing disease progression, effectiveness of drug therapy, and emergence of drug-resistance. Typically, nucleic acid quantification requires sophisticated and expensive instruments, such as real-time PCR machines, which are not appropriate for on-site use and for low resource settings. We describe a simple, low-cost, reactiondiffusion based method for end-point quantification of target nucleic acids undergoing enzymatic amplification. The number of target molecules is inferred from the position of the reaction-diffusion front, analogous to reading temperature in a mercury thermometer. We model the process with the Fisher Kolmogoroff Petrovskii Piscounoff (FKPP) Equation and compare theoretical predictions with experimental observations. The proposed method is suitable for nucleic acid quantification at the point of care, compatible with multiplexing and high-throughput processing, and can function instrument-free. C.L. was supported by NIH/NIAID K25AI099160; M.S. was supported by the Pennsylvania Ben Franklin Technology Development Authority; C.K. and H.B. were funded, in part, by NIH/NIAID 1R41AI104418-01A1.

An experimental design method leading to chemical Turing patterns.

PubMed

Horváth, Judit; Szalai, István; De Kepper, Patrick

2009-05-08

Chemical reaction-diffusion patterns often serve as prototypes for pattern formation in living systems, but only two isothermal single-phase reaction systems have produced sustained stationary reaction-diffusion patterns so far. We designed an experimental method to search for additional systems on the basis of three steps: (i) generate spatial bistability by operating autoactivated reactions in open spatial reactors; (ii) use an independent negative-feedback species to produce spatiotemporal oscillations; and (iii) induce a space-scale separation of the activatory and inhibitory processes with a low-mobility complexing agent. We successfully applied this method to a hydrogen-ion autoactivated reaction, the thiourea-iodate-sulfite (TuIS) reaction, and noticeably produced stationary hexagonal arrays of spots and parallel stripes of pH patterns attributed to a Turing bifurcation. This method could be extended to biochemical reactions.

Incomplete Mixing and Reactions - A Lagrangian Approach in a Pure Shear Flow

NASA Astrophysics Data System (ADS)

Paster, A.; Aquino, T.; Bolster, D.

2014-12-01

Incomplete mixing of reactive solutes is well known to slow down reaction rates relative to what would be expected from assuming perfect mixing. As reactions progress in a system and deplete reactant concentrations, initial fluctuations in the concentrations of reactions can be amplified relative to mean background concentrations and lead to spatial segregation of reactants. As the system evolves, in the absence of sufficient mixing, this segregation will increase, leading to a persistence of incomplete mixing that fundamentally changes the effective rate at which overall reactions will progress. On the other hand, non-uniform fluid flows are known to affect mixing between interacting solutes. Thus a natural question arises: Can non-uniform flows sufficiently enhance mixing to suppress incomplete mixing effects, and if so, under what conditions? In this work we address this question by considering one of the simplest possible flows, a laminar pure shear flow, which is known to significantly enhance mixing relative to diffusion alone. To study this system we adapt a novel Lagrangian particle-based random walk method, originally designed to simulate reactions in purely diffusive systems, to the case of advection and diffusion in a shear flow. To interpret the results we develop a semi-analytical solution, by proposing a closure approximation that aims to capture the effect of incomplete mixing. The results obtained via the Lagrangian model and the semi-analytical solutions consistently highlight that if shear effects in the system are not sufficiently strong, incomplete mixing effects initially similar to purely diffusive systems will occur, slowing down the overall reaction rate. Then, at some later time, dependent on the strength of the shear, the system will return to behaving as if it were well-mixed, but represented by a reduced effective reaction rate. If shear effects are sufficiently strong, the incomplete mixing regime never emerges and the system can behave as well-mixed at all times.

Incomplete Mixing and Reactions - A Lagrangian Approach in a Pure Shear Flow

NASA Astrophysics Data System (ADS)

Paster, Amir; Bolster, Diogo; Aquino, Tomas

2015-04-01

Incomplete mixing of reactive solutes is well known to slow down reaction rates relative to what would be expected from assuming perfect mixing. As reactions progress in a system and deplete reactant concentrations, initial fluctuations in the concentrations of reactions can be amplified relative to mean background concentrations and lead to spatial segregation of reactants. As the system evolves, in the absence of sufficient mixing, this segregation will increase, leading to a persistence of incomplete mixing that fundamentally changes the effective rate at which overall reactions will progress. On the other hand, nonuniform fluid flows are known to affect mixing between interacting solutes. Thus a natural question arises: Can non-uniform flows sufficiently enhance mixing to suppress incomplete mixing effects, and if so, under what conditions? In this work we address this question by considering one of the simplest possible flows, a laminar pure shear flow, which is known to significantly enhance mixing relative to diffusion alone. To study this system we adapt a novel Lagrangian particle-based random walk method, originally designed to simulate reactions in purely diffusive systems, to the case of advection and diffusion in a shear flow. To interpret the results we develop a semi-analytical solution, by proposing a closure approximation that aims to capture the effect of incomplete mixing. The results obtained via the Lagrangian model and the semi-analytical solutions consistently highlight that if shear effects in the system are not sufficiently strong, incomplete mixing effects initially similar to purely diffusive systems will occur, slowing down the overall reaction rate. Then, at some later time, dependent on the strength of the shear, the system will return to behaving as if it were well-mixed, but represented by a reduced effective reaction rate. If shear effects are sufficiently strong, the incomplete mixing regime never emerges and the system can behave as well-mixed at all times.

Long-time behavior and Turing instability induced by cross-diffusion in a three species food chain model with a Holling type-II functional response.

PubMed

Haile, Dawit; Xie, Zhifu

2015-09-01

In this paper, we study a strongly coupled reaction-diffusion system describing three interacting species in a food chain model, where the third species preys on the second one and simultaneously the second species preys on the first one. An intra-species competition b2 among the second predator is introduced to the food chain model. This parameter produces some very interesting result in linear stability and Turing instability. We first show that the unique positive equilibrium solution is locally asymptotically stable for the corresponding ODE system when the intra-species competition exists among the second predator. The positive equilibrium solution remains linearly stable for the reaction diffusion system without cross diffusion, hence it does not belong to the classical Turing instability scheme. But it becomes linearly unstable only when cross-diffusion also plays a role in the reaction-diffusion system, hence the instability is driven solely from the effect of cross diffusion. Our results also exhibit some interesting combining effects of cross-diffusion, intra-species competitions and inter-species interactions. Numerically, we conduct a one parameter analysis which illustrate how the interactions change the existence of stable equilibrium, limit cycle, and chaos. Some interesting dynamical phenomena occur when we perform analysis of interactions in terms of self-production of prey and intra-species competition of the middle predator. By numerical simulations, it illustrates the existence of nonuniform steady solutions and new patterns such as spot patterns, strip patterns and fluctuations due to the diffusion and cross diffusion in two-dimension. Published by Elsevier Inc.

A hybrid continuous-discrete method for stochastic reaction–diffusion processes

PubMed Central

Zheng, Likun; Nie, Qing

2016-01-01

Stochastic fluctuations in reaction–diffusion processes often have substantial effect on spatial and temporal dynamics of signal transductions in complex biological systems. One popular approach for simulating these processes is to divide the system into small spatial compartments assuming that molecules react only within the same compartment and jump between adjacent compartments driven by the diffusion. While the approach is convenient in terms of its implementation, its computational cost may become prohibitive when diffusive jumps occur significantly more frequently than reactions, as in the case of rapid diffusion. Here, we present a hybrid continuous-discrete method in which diffusion is simulated using continuous approximation while reactions are based on the Gillespie algorithm. Specifically, the diffusive jumps are approximated as continuous Gaussian random vectors with time-dependent means and covariances, allowing use of a large time step, even for rapid diffusion. By considering the correlation among diffusive jumps, the approximation is accurate for the second moment of the diffusion process. In addition, a criterion is obtained for identifying the region in which such diffusion approximation is required to enable adaptive calculations for better accuracy. Applications to a linear diffusion system and two nonlinear systems of morphogens demonstrate the effectiveness and benefits of the new hybrid method. PMID:27703710

On the Green's function of the partially diffusion-controlled reversible ABCD reaction for radiation chemistry codes

NASA Astrophysics Data System (ADS)

Plante, Ianik; Devroye, Luc

2015-09-01

Several computer codes simulating chemical reactions in particles systems are based on the Green's functions of the diffusion equation (GFDE). Indeed, many types of chemical systems have been simulated using the exact GFDE, which has also become the gold standard for validating other theoretical models. In this work, a simulation algorithm is presented to sample the interparticle distance for partially diffusion-controlled reversible ABCD reaction. This algorithm is considered exact for 2-particles systems, is faster than conventional look-up tables and uses only a few kilobytes of memory. The simulation results obtained with this method are compared with those obtained with the independent reaction times (IRT) method. This work is part of our effort in developing models to understand the role of chemical reactions in the radiation effects on cells and tissues and may eventually be included in event-based models of space radiation risks. However, as many reactions are of this type in biological systems, this algorithm might play a pivotal role in future simulation programs not only in radiation chemistry, but also in the simulation of biochemical networks in time and space as well.

Partitioned coupling of advection-diffusion-reaction systems and Brinkman flows

NASA Astrophysics Data System (ADS)

Lenarda, Pietro; Paggi, Marco; Ruiz Baier, Ricardo

2017-09-01

We present a partitioned algorithm aimed at extending the capabilities of existing solvers for the simulation of coupled advection-diffusion-reaction systems and incompressible, viscous flow. The space discretisation of the governing equations is based on mixed finite element methods defined on unstructured meshes, whereas the time integration hinges on an operator splitting strategy that exploits the differences in scales between the reaction, advection, and diffusion processes, considering the global system as a number of sequentially linked sets of partial differential, and algebraic equations. The flow solver presents the advantage that all unknowns in the system (here vorticity, velocity, and pressure) can be fully decoupled and thus turn the overall scheme very attractive from the computational perspective. The robustness of the proposed method is illustrated with a series of numerical tests in 2D and 3D, relevant in the modelling of bacterial bioconvection and Boussinesq systems.

Multiphase chemical kinetics of OH radical uptake by molecular organic markers of biomass burning aerosols: humidity and temperature dependence, surface reaction, and bulk diffusion.

PubMed

Arangio, Andrea M; Slade, Jonathan H; Berkemeier, Thomas; Pöschl, Ulrich; Knopf, Daniel A; Shiraiwa, Manabu

2015-05-14

Multiphase reactions of OH radicals are among the most important pathways of chemical aging of organic aerosols in the atmosphere. Reactive uptake of OH by organic compounds has been observed in a number of studies, but the kinetics of mass transport and chemical reaction are still not fully understood. Here we apply the kinetic multilayer model of gas-particle interactions (KM-GAP) to experimental data from OH exposure studies of levoglucosan and abietic acid, which serve as surrogates and molecular markers of biomass burning aerosol (BBA). The model accounts for gas-phase diffusion within a cylindrical coated-wall flow tube, reversible adsorption of OH, surface-bulk exchange, bulk diffusion, and chemical reactions at the surface and in the bulk of the condensed phase. The nonlinear dependence of OH uptake coefficients on reactant concentrations and time can be reproduced by KM-GAP. We find that the bulk diffusion coefficient of the organic molecules is approximately 10(-16) cm(2) s(-1), reflecting an amorphous semisolid state of the organic substrates. The OH uptake is governed by reaction at or near the surface and can be kinetically limited by surface-bulk exchange or bulk diffusion of the organic reactants. Estimates of the chemical half-life of levoglucosan in 200 nm particles in a biomass burning plume increase from 1 day at high relative humidity to 1 week under dry conditions. In BBA particles transported to the free troposphere, the chemical half-life of levoglucosan can exceed 1 month due to slow bulk diffusion in a glassy matrix at low temperature.

Efficient Green's Function Reaction Dynamics (GFRD) simulations for diffusion-limited, reversible reactions

NASA Astrophysics Data System (ADS)

Bashardanesh, Zahedeh; Lötstedt, Per

2018-03-01

In diffusion controlled reversible bimolecular reactions in three dimensions, a dissociation step is typically followed by multiple, rapid re-association steps slowing down the simulations of such systems. In order to improve the efficiency, we first derive an exact Green's function describing the rate at which an isolated pair of particles undergoing reversible bimolecular reactions and unimolecular decay separates beyond an arbitrarily chosen distance. Then the Green's function is used in an algorithm for particle-based stochastic reaction-diffusion simulations for prediction of the dynamics of biochemical networks. The accuracy and efficiency of the algorithm are evaluated using a reversible reaction and a push-pull chemical network. The computational work is independent of the rates of the re-associations.

Turing patterns and a stochastic individual-based model for predator-prey systems

NASA Astrophysics Data System (ADS)

Nagano, Seido

2012-02-01

Reaction-diffusion theory has played a very important role in the study of pattern formations in biology. However, a group of individuals is described by a single state variable representing population density in reaction-diffusion models and interaction between individuals can be included only phenomenologically. Recently, we have seamlessly combined individual-based models with elements of reaction-diffusion theory. To include animal migration in the scheme, we have adopted a relationship between the diffusion and the random numbers generated according to a two-dimensional bivariate normal distribution. Thus, we have observed the transition of population patterns from an extinction mode, a stable mode, or an oscillatory mode to the chaotic mode as the population growth rate increases. We show our phase diagram of predator-prey systems and discuss the microscopic mechanism for the stable lattice formation in detail.

Multi-Dimensional, Mesoscopic Monte Carlo Simulations of Inhomogeneous Reaction-Drift-Diffusion Systems on Graphics-Processing Units

PubMed Central

Vigelius, Matthias; Meyer, Bernd

2012-01-01

For many biological applications, a macroscopic (deterministic) treatment of reaction-drift-diffusion systems is insufficient. Instead, one has to properly handle the stochastic nature of the problem and generate true sample paths of the underlying probability distribution. Unfortunately, stochastic algorithms are computationally expensive and, in most cases, the large number of participating particles renders the relevant parameter regimes inaccessible. In an attempt to address this problem we present a genuine stochastic, multi-dimensional algorithm that solves the inhomogeneous, non-linear, drift-diffusion problem on a mesoscopic level. Our method improves on existing implementations in being multi-dimensional and handling inhomogeneous drift and diffusion. The algorithm is well suited for an implementation on data-parallel hardware architectures such as general-purpose graphics processing units (GPUs). We integrate the method into an operator-splitting approach that decouples chemical reactions from the spatial evolution. We demonstrate the validity and applicability of our algorithm with a comprehensive suite of standard test problems that also serve to quantify the numerical accuracy of the method. We provide a freely available, fully functional GPU implementation. Integration into Inchman, a user-friendly web service, that allows researchers to perform parallel simulations of reaction-drift-diffusion systems on GPU clusters is underway. PMID:22506001

Chemical and Isotopic Characterization of Waters in Rio Tinto, Spain, Shows Possible Origin of the Blueberry Haematite Nodules in Meridiani Planum, Mars

NASA Astrophysics Data System (ADS)

Coleman, M. L.; Hubbard, C. G.; Mielke, R. E.; Black, S.

2005-12-01

Meridiani Planum sediments formed in an acid environment and include jarosite and other evaporitic sulfate minerals. Nodular spheroidal concretions appear to have grown in situ and are predominantly hematite. The source of the Rio Tinto, S. Spain, drains an area of extensive sulfide mineralization and is dominated by acid mine drainage processes. The system is not a Mars analog but potentially similar processes of sulfide oxidation produce sulfate rich waters which feed into the river and precipitate a large range of evaporitic sulfates including jarosite. Iron oxide minerals associated with the evaporites are either dispersed or bedded but not nodular. The water compositions appear to be mixtures of a few discreet end-members: the two most significant occur in undiluted form as inputs to the river and are relevant to many such systems. They both have all sulfur totally oxidized as sulfate. The first is a bright red water, pH ~1.5, Fe/S 0.5 and 23 g/L iron which is greater than 95% Fe3+. Its sulfate oxygen isotope composition is +2‰SMOW and about +7‰, relative to the water O isotope composition. These data indicate pyrite oxidation by Fe3+ with O in sulfate coming mainly from water. The second end-member is a pale green water, pH ~0.7, Fe/S 0.7, 50 g/L iron present mainly as Fe2+ and O isotope composition of sulfate about +6‰SMOW , about +12.5‰ relative to the water O value. Oxygen in sulfate comes mainly from atmospheric oxygen resulting from pyrite oxidation by molecular oxygen dissolved in water. Although the Rio Tinto system reactions probably are microbiologically mediated (relevant genera have been identified there) similar processes could occur abiotically but more slowly. Meridiani Planum sediments and nodules can be described by a plausible set of similar end-member processes. The primary source of sulfate is oxidation of sulfides present in basalt (pyrite, FeS2 or pyrrhotite, FeS) and weathering would have produced oxidized sulfate rich solutions at low pH. Ground water migration could produce evaporitic ponds where various bedded sulfate mineral sediments could form. The intergranular pore-spaces would be water filled. Most terrestrial spheroidal nodular concretions form by radial diffusion in pore-water of a chemical component of a very different oxidation state from that of the surrounding water. A nodular concretion is most usually formed by the reaction of the diffusive component with others in the pore-water. There are two main possible reaction sets for formation of the Blueberries that are consistent with all current data. 1. Local concentrations of organic matter (pre-biotic or biotic) formed reduction spots in which a small amount of Fe3+ either in solution or from evaporite mineral salts, was reduced to Fe2+ and then diffused radially to form an iron oxide nodule by reaction with inwardly diffusing dissolved oxygen. 2. Similar local concentrations of organic matter could also have engendered sulfate reduction and consequent outward diffusion of dissolved sulfide reacted with iron in solution to produce an iron sulfide nodule, subsequently oxidized in situ to hematite (maybe via goethite). Our current work is successfully identifying chemical and stable isotopic characteristics for both microbial and abiotic modes of all relevant reactions.

A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems

PubMed Central

Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing

2012-01-01

An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton’s method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton’s method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton’s method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space. PMID:22773849

Catalytic conversion reactions mediated by single-file diffusion in linear nanopores: hydrodynamic versus stochastic behavior.

PubMed

Ackerman, David M; Wang, Jing; Wendel, Joseph H; Liu, Da-Jiang; Pruski, Marek; Evans, James W

2011-03-21

We analyze the spatiotemporal behavior of species concentrations in a diffusion-mediated conversion reaction which occurs at catalytic sites within linear pores of nanometer diameter. Diffusion within the pores is subject to a strict single-file (no passing) constraint. Both transient and steady-state behavior is precisely characterized by kinetic Monte Carlo simulations of a spatially discrete lattice-gas model for this reaction-diffusion process considering various distributions of catalytic sites. Exact hierarchical master equations can also be developed for this model. Their analysis, after application of mean-field type truncation approximations, produces discrete reaction-diffusion type equations (mf-RDE). For slowly varying concentrations, we further develop coarse-grained continuum hydrodynamic reaction-diffusion equations (h-RDE) incorporating a precise treatment of single-file diffusion in this multispecies system. The h-RDE successfully describe nontrivial aspects of transient behavior, in contrast to the mf-RDE, and also correctly capture unreactive steady-state behavior in the pore interior. However, steady-state reactivity, which is localized near the pore ends when those regions are catalytic, is controlled by fluctuations not incorporated into the hydrodynamic treatment. The mf-RDE partly capture these fluctuation effects, but cannot describe scaling behavior of the reactivity.

Catalytic conversion reactions in nanoporous systems with concentration-dependent selectivity: Statistical mechanical modeling

DOE PAGES

Garcia, Andres; Wang, Jing; Windus, Theresa L.; ...

2016-05-20

Statistical mechanical modeling is developed to describe a catalytic conversion reaction A → B c or B t with concentration-dependent selectivity of the products, B c or B t, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Hence, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, A.

Sub-millitesla magnetic field effects on the recombination reaction of flavin and ascorbic acid radicals

NASA Astrophysics Data System (ADS)

Evans, Emrys W.; Kattnig, Daniel R.; Henbest, Kevin B.; Hore, P. J.; Mackenzie, Stuart R.; Timmel, Christiane R.

2016-08-01

Even though the interaction of a <1 mT magnetic field with an electron spin is less than a millionth of the thermal energy at room temperature (kBT), it still can have a profound effect on the quantum yields of radical pair reactions. We present a study of the effects of sub-millitesla magnetic fields on the photoreaction of flavin mononucleotide with ascorbic acid. Direct control of the reaction pathway is achieved by varying the rate of electron transfer from ascorbic acid to the photo-excited flavin. At pH 7.0, we verify the theoretical prediction that, apart from a sign change, the form of the magnetic field effect is independent of the initial spin configuration of the radical pair. The data agree well with model calculations based on a Green's function approach that allows multinuclear spin systems to be treated including the diffusive motion of the radicals, their spin-selective recombination reactions, and the effects of the inter-radical exchange interaction. The protonation states of the radicals are uniquely determined from the form of the magnetic field-dependence. At pH 3.0, the effects of two chemically distinct radical pair complexes combine to produce a pronounced response to ˜500 μT magnetic fields. These findings are relevant to the magnetic responses of cryptochromes (flavin-containing proteins proposed as magnetoreceptors in birds) and may aid the evaluation of effects of weak magnetic fields on other biologically relevant electron transfer processes.

The Effect of Limited Diffusion and Wet-Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids.

PubMed

Higgs, Paul G

2016-06-08

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction.

The Effect of Limited Diffusion and Wet–Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids

PubMed Central

Higgs, Paul G.

2016-01-01

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction. PMID:27338479

Evaluation of intratympanic formulations for inner ear delivery: methodology and sustained release formulation testing

PubMed Central

Liu, Hongzhuo; Feng, Liang; Tolia, Gaurav; Liddell, Mark R.; Hao, Jinsong; Li, S. Kevin

2013-01-01

A convenient and efficient in vitro diffusion cell method to evaluate formulations for inner ear delivery via the intratympanic route is currently not available. The existing in vitro diffusion cell systems commonly used to evaluate drug formulations do not resemble the physical dimensions of the middle ear and round window membrane. The objectives of this study were to examine a modified in vitro diffusion cell system of a small diffusion area for studying sustained release formulations in inner ear drug delivery and to identify a formulation for sustained drug delivery to the inner ear. Four formulations and a control were examined in this study using cidofovir as the model drug. Drug release from the formulations in the modified diffusion cell system was slower than that in the conventional diffusion cell system due to the decrease in the diffusion surface area of the modified diffusion cell system. The modified diffusion cell system was able to show different drug release behaviors among the formulations and allowed formulation evaluation better than the conventional diffusion cell system. Among the formulations investigated, poly(lactic-co-glycolic acid)–poly(ethylene glycol)–poly(lactic-co-glycolic acid) triblock copolymer systems provided the longest sustained drug delivery, probably due to their rigid gel structures and/or polymer-to-cidofovir interactions. PMID:23631539

Polymerase chain reaction system using magnetic beads for analyzing a sample that includes nucleic acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nasarabadi, Shanavaz

2011-01-11

A polymerase chain reaction system for analyzing a sample containing nucleic acid includes providing magnetic beads; providing a flow channel having a polymerase chain reaction chamber, a pre polymerase chain reaction magnet position adjacent the polymerase chain reaction chamber, and a post pre polymerase magnet position adjacent the polymerase chain reaction chamber. The nucleic acid is bound to the magnetic beads. The magnetic beads with the nucleic acid flow to the pre polymerase chain reaction magnet position in the flow channel. The magnetic beads and the nucleic acid are washed with ethanol. The nucleic acid in the polymerase chain reactionmore » chamber is amplified. The magnetic beads and the nucleic acid are separated into a waste stream containing the magnetic beads and a post polymerase chain reaction mix containing the nucleic acid. The reaction mix containing the nucleic acid flows to an analysis unit in the channel for analysis.« less

Unimodal dynamical systems: Comparison principles, spreading speeds and travelling waves

NASA Astrophysics Data System (ADS)

Yi, Taishan; Chen, Yuming; Wu, Jianhong

Reaction diffusion equations with delayed nonlinear reaction terms are used as prototypes to motivate an appropriate abstract formulation of dynamical systems with unimodal nonlinearity. For such non-monotone dynamical systems, we develop a general comparison principle and show how this general comparison principle, coupled with some existing results for monotone dynamical systems, can be used to establish results on the asymptotic speeds of spread and travelling waves. We illustrate our main results by an integral equation which includes a nonlocal delayed reaction diffusion equation and a nonlocal delayed lattice differential system in an unbounded domain, with the non-monotone nonlinearities including the Ricker birth function and the Mackey-Glass hematopoiesis feedback.

Transport of Organic Compounds Through Porous Systems Containing Humic Acids.

PubMed

Smilek, Jiri; Sedlacek, Petr; Lastuvkova, Marcela; Kalina, Michal; Klucakova, Martina

2017-03-01

Soil pollution by the presence of different contaminants (e.g. heavy metal ions or pesticides) is one of the biggest problems worldwide. The positive affinity of natural humic acids towards these contaminants might contribute to the soil and ground water protection; therefore it is necessary to study the reactivity and barrier properties of humic acids. An original reactivity-mapping tool based on diffusion techniques designed to study the reactivity and barrier properties of polyelectrolytes was developed and tested on humic acids. The results of diffusion experiments demonstrate that the electrostatic interactions between humic acids functioning as a polyelectrolyte interpenetrated in a supporting hydrogel matrix (agarose) and cationic dye (methylene blue) as a model solute have a crucial impact on the rate of diffusion processes and on the barrier properties of hydrogels. The intensity of interactions was evaluated by fundamental diffusion parameters (effective diffusion coefficients and breakthrough time). The impact of modification of humic acids was also studied by means of diffusion experiments conducted on two types of standard humic acids (Leonardite 1S104H) and humic acids with selectively methylated carboxylic groups.

Emergent structures in reaction-advection-diffusion systems on a sphere.

PubMed

Krause, Andrew L; Burton, Abigail M; Fadai, Nabil T; Van Gorder, Robert A

2018-04-01

We demonstrate unusual effects due to the addition of advection into a two-species reaction-diffusion system on the sphere. We find that advection introduces emergent behavior due to an interplay of the traditional Turing patterning mechanisms with the compact geometry of the sphere. Unidirectional advection within the Turing space of the reaction-diffusion system causes patterns to be generated at one point of the sphere, and transported to the antipodal point where they are destroyed. We illustrate these effects numerically and deduce conditions for Turing instabilities on local projections to understand the mechanisms behind these behaviors. We compare this behavior to planar advection which is shown to only transport patterns across the domain. Analogous transport results seem to hold for the sphere under azimuthal transport or away from the antipodal points in unidirectional flow regimes.

Emergent structures in reaction-advection-diffusion systems on a sphere

NASA Astrophysics Data System (ADS)

Krause, Andrew L.; Burton, Abigail M.; Fadai, Nabil T.; Van Gorder, Robert A.

2018-04-01

We demonstrate unusual effects due to the addition of advection into a two-species reaction-diffusion system on the sphere. We find that advection introduces emergent behavior due to an interplay of the traditional Turing patterning mechanisms with the compact geometry of the sphere. Unidirectional advection within the Turing space of the reaction-diffusion system causes patterns to be generated at one point of the sphere, and transported to the antipodal point where they are destroyed. We illustrate these effects numerically and deduce conditions for Turing instabilities on local projections to understand the mechanisms behind these behaviors. We compare this behavior to planar advection which is shown to only transport patterns across the domain. Analogous transport results seem to hold for the sphere under azimuthal transport or away from the antipodal points in unidirectional flow regimes.

Control of transversal instabilities in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Totz, Sonja; Löber, Jakob; Totz, Jan Frederik; Engel, Harald

2018-05-01

In two-dimensional reaction-diffusion systems, local curvature perturbations on traveling waves are typically damped out and vanish. However, if the inhibitor diffuses much faster than the activator, transversal instabilities can arise, leading from flat to folded, spatio-temporally modulated waves and to spreading spiral turbulence. Here, we propose a scheme to induce or inhibit these instabilities via a spatio-temporal feedback loop. In a piecewise-linear version of the FitzHugh–Nagumo model, transversal instabilities and spiral turbulence in the uncontrolled system are shown to be suppressed in the presence of control, thereby stabilizing plane wave propagation. Conversely, in numerical simulations with the modified Oregonator model for the photosensitive Belousov–Zhabotinsky reaction, which does not exhibit transversal instabilities on its own, we demonstrate the feasibility of inducing transversal instabilities and study the emerging wave patterns in a well-controlled manner.

Mathematical approach to nonlocal interactions using a reaction-diffusion system.

PubMed

Tanaka, Yoshitaro; Yamamoto, Hiroko; Ninomiya, Hirokazu

2017-06-01

In recent years, spatial long range interactions during developmental processes have been introduced as a result of the integration of microscopic information, such as molecular events and signaling networks. They are often called nonlocal interactions. If the profile of a nonlocal interaction is determined by experiments, we can easily investigate how patterns generate by numerical simulations without detailed microscopic events. Thus, nonlocal interactions are useful tools to understand complex biosystems. However, nonlocal interactions are often inconvenient for observing specific mechanisms because of the integration of information. Accordingly, we proposed a new method that could convert nonlocal interactions into a reaction-diffusion system with auxiliary unknown variables. In this review, by introducing biological and mathematical studies related to nonlocal interactions, we will present the heuristic understanding of nonlocal interactions using a reaction-diffusion system. © 2017 Japanese Society of Developmental Biologists.

Anomalous dimension in a two-species reaction-diffusion system

NASA Astrophysics Data System (ADS)

Vollmayr-Lee, Benjamin; Hanson, Jack; McIsaac, R. Scott; Hellerick, Joshua D.

2018-01-01

We study a two-species reaction-diffusion system with the reactions A+A\\to (0, A) and A+B\\to A , with general diffusion constants D A and D B . Previous studies showed that for dimensions d≤slant 2 the B particle density decays with a nontrivial, universal exponent that includes an anomalous dimension resulting from field renormalization. We demonstrate via renormalization group methods that the scaled B particle correlation function has a distinct anomalous dimension resulting in the asymptotic scaling \\tilde CBB(r, t) ˜ tφf(r/\\sqrt{t}) , where the exponent ϕ results from the renormalization of the square of the field associated with the B particles. We compute this exponent to first order in \

Why do proton conducting polybenzimidazole phosphoric acid membranes perform well in high-temperature PEM fuel cells?

PubMed

Melchior, Jan-Patrick; Majer, Günter; Kreuer, Klaus-Dieter

2016-12-21

Transport properties and hydration behavior of phosphoric acid/(benz)imidazole mixtures are investigated by diverse NMR techniques, thermogravimetric analysis (TGA) and conductivity measurements. The monomeric systems can serve as models for phosphoric acid/poly-benzimidazole membranes which are known for their exceptional performance in high temperature PEM fuel cells. 1 H- and 31 P-NMR data show benzimidazole acting as a strong Brønsted base with respect to neat phosphoric acid. Since benzimidazole's nitrogens are fully protonated with a low rate for proton exchange with phosphate species, proton diffusion and conduction processes must take place within the hydrogen bond network of phosphoric acid only. The proton exchange dynamics between phosphate and benzimidazole species pass through the intermediate exchange regime (with respect to NMR line separations) with exchange times being close to typical diffusion times chosen in PFG-NMR diffusion measurements (ms regime). The resulting effects, as described by the Kärger equation, are included into the evaluation of PFG-NMR data for obtaining precise proton diffusion coefficients. The highly reduced proton diffusion coefficient within the phosphoric acid part of the model systems compared to neat phosphoric acid is suggested to be the immediate consequence of proton subtraction from phosphoric acid. This reduces hydrogen bond network frustration (imbalance of the number of proton donors and acceptors) and therefore also the rate of structural proton diffusion, phosphoric acid's acidity and hygroscopicity. Reduced water uptake, shown by TGA, goes along with reduced electroosmotic water drag which is suggested to be the reason for PBI-phosphoric acid membranes performing better in fuel cells than other phosphoric-acid-containing electrolytes with higher protonic conductivity.

Convective instability and boundary driven oscillations in a reaction-diffusion-advection model

NASA Astrophysics Data System (ADS)

Vidal-Henriquez, Estefania; Zykov, Vladimir; Bodenschatz, Eberhard; Gholami, Azam

2017-10-01

In a reaction-diffusion-advection system, with a convectively unstable regime, a perturbation creates a wave train that is advected downstream and eventually leaves the system. We show that the convective instability coexists with a local absolute instability when a fixed boundary condition upstream is imposed. This boundary induced instability acts as a continuous wave source, creating a local periodic excitation near the boundary, which initiates waves travelling both up and downstream. To confirm this, we performed analytical analysis and numerical simulations of a modified Martiel-Goldbeter reaction-diffusion model with the addition of an advection term. We provide a quantitative description of the wave packet appearing in the convectively unstable regime, which we found to be in excellent agreement with the numerical simulations. We characterize this new instability and show that in the limit of high advection speed, it is suppressed. This type of instability can be expected for reaction-diffusion systems that present both a convective instability and an excitable regime. In particular, it can be relevant to understand the signaling mechanism of the social amoeba Dictyostelium discoideum that may experience fluid flows in its natural habitat.

Stabilization of a spatially uniform steady state in two systems exhibiting Turing patterns

NASA Astrophysics Data System (ADS)

Konishi, Keiji; Hara, Naoyuki

2018-05-01

This paper deals with the stabilization of a spatially uniform steady state in two coupled one-dimensional reaction-diffusion systems with Turing instability. This stabilization corresponds to amplitude death that occurs in a coupled system with Turing instability. Stability analysis of the steady state shows that stabilization does not occur if the two reaction-diffusion systems are identical. We derive a sufficient condition for the steady state to be stable for any length of system and any boundary conditions. Our analytical results are supported with numerical examples.

The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems

PubMed Central

Wu, Sheng; Li, Hong; Petzold, Linda R.

2015-01-01

The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy. PMID:26609185

Exact Solutions of Coupled Multispecies Linear Reaction-Diffusion Equations on a Uniformly Growing Domain.

PubMed

Simpson, Matthew J; Sharp, Jesse A; Morrow, Liam C; Baker, Ruth E

2015-01-01

Embryonic development involves diffusion and proliferation of cells, as well as diffusion and reaction of molecules, within growing tissues. Mathematical models of these processes often involve reaction-diffusion equations on growing domains that have been primarily studied using approximate numerical solutions. Recently, we have shown how to obtain an exact solution to a single, uncoupled, linear reaction-diffusion equation on a growing domain, 0 < x < L(t), where L(t) is the domain length. The present work is an extension of our previous study, and we illustrate how to solve a system of coupled reaction-diffusion equations on a growing domain. This system of equations can be used to study the spatial and temporal distributions of different generations of cells within a population that diffuses and proliferates within a growing tissue. The exact solution is obtained by applying an uncoupling transformation, and the uncoupled equations are solved separately before applying the inverse uncoupling transformation to give the coupled solution. We present several example calculations to illustrate different types of behaviour. The first example calculation corresponds to a situation where the initially-confined population diffuses sufficiently slowly that it is unable to reach the moving boundary at x = L(t). In contrast, the second example calculation corresponds to a situation where the initially-confined population is able to overcome the domain growth and reach the moving boundary at x = L(t). In its basic format, the uncoupling transformation at first appears to be restricted to deal only with the case where each generation of cells has a distinct proliferation rate. However, we also demonstrate how the uncoupling transformation can be used when each generation has the same proliferation rate by evaluating the exact solutions as an appropriate limit.

Event-triggered synchronization for reaction-diffusion complex networks via random sampling

NASA Astrophysics Data System (ADS)

Dong, Tao; Wang, Aijuan; Zhu, Huiyun; Liao, Xiaofeng

2018-04-01

In this paper, the synchronization problem of the reaction-diffusion complex networks (RDCNs) with Dirichlet boundary conditions is considered, where the data is sampled randomly. An event-triggered controller based on the sampled data is proposed, which can reduce the number of controller and the communication load. Under this strategy, the synchronization problem of the diffusion complex network is equivalently converted to the stability of a of reaction-diffusion complex dynamical systems with time delay. By using the matrix inequality technique and Lyapunov method, the synchronization conditions of the RDCNs are derived, which are dependent on the diffusion term. Moreover, it is found the proposed control strategy can get rid of the Zeno behavior naturally. Finally, a numerical example is given to verify the obtained results.

Ultrasound augmented leaching of nickel sulfate in sulfuric acid and hydrogen peroxide media.

PubMed

Li, Haoyu; Li, Shiwei; Peng, Jinhui; Srinivasakannan, Chandrasekar; Zhang, Libo; Yin, Shaohua

2018-01-01

A new method of preparation high purity nickel sulfate assisted by ultrasonic was studied. The process mechanism was analyzed by Inductively Coupled Plasma (ICP), X-ray diffraction (XRD), Scanning electron microscopy (SEM), and Energy dispersive X-ray spectrometry (EDS).The reaction mechanisms of oxidizing leaching and ultrasonic leaching were explored, respectively. Results showed that ultrasonic treatment peel off the oxide film on the surface of nickel. The leachate under strongly agitated, the yield rate of nickel sulfate was accelerate. And the reaction area was increased by the cavitation effect, the liquid-solid reaction was promoted, and the activation energy was reduced. The leaching rate of nickel reached 46.29% by conventional leaching, which takes about 5h. Under the same conditions, the ultrasonic leaching rate reached 40%, only half of the conventional leaching time. Concentration of leaching agent, reaction temperature, ultrasonic power, leaching time had significant effect on the enhancement of the leaching reaction with ultrasonic radiation. The leaching rate of 60.41% under the optimum experiment conditions as follows: sulfuric acid concentration 30%, hydrogen peroxide 10%, leaching temperature 333K, ultrasonic power 200W and leaching time 4h. The kinetic study of the system was investigated, and the reaction rates of conventional leaching and ultrasonic leaching were controlled by diffusion, and the apparent activation energies were 16.2kJ/mol and 11.83kJ/mol. Copyright © 2017. Published by Elsevier B.V.

A model for the compositions of non-stoichiometric intermediate phases formed by diffusion reactions, and its application to Nb 3Sn superconductors

DOE PAGES

Xu, X.; Sumption, M. D.

2016-01-12

In this work we explore the compositions of non-stoichiometric intermediate phases formed by diffusion reactions: a mathematical framework is developed and tested against the specific case of Nb 3Sn superconductors. In the first part, the governing equations for the bulk diffusion and interphase interface reactions during the growth of a compound are derived, numerical solutions to which give both the composition profile and growth rate of the compound layer. The analytic solutions are obtained with certain approximations made. In the second part, we explain an effect that the composition characteristics of compounds can be quite different depending on whether itmore » is the bulk diffusion or grain boundary diffusion that dominates in the compounds, and that “frozen” bulk diffusion leads to unique composition characteristics that the bulk composition of a compound layer remains unchanged after its initial formation instead of varying with the diffusion reaction system; here the model is modified for the case of grain boundary diffusion. Lastly, we apply this model to the Nb 3Sn superconductors and propose approaches to control their compositions.« less

Infrared Emission from Gas-Aerosol Reactions

DTIC Science & Technology

1982-09-01

Gaseous Amonia Infrared (IR) "Gas-aerosol Reactions Sulfuric Acid- amonia IR Luminescence Exothermic Reactions Octanoic Acid- amonia IR Laser Acid-base...of radiation observed from the reactions of chloro- sulfuric acid aerosol with gaseous amonia and water. Other systems which were screened including

A coupled theory for chemically active and deformable solids with mass diffusion and heat conduction

NASA Astrophysics Data System (ADS)

Zhang, Xiaolong; Zhong, Zheng

2017-10-01

To analyse the frequently encountered thermo-chemo-mechanical problems in chemically active material applications, we develop a thermodynamically-consistent continuum theory of coupled deformation, mass diffusion, heat conduction and chemical reaction. Basic balance equations of force, mass and energy are presented at first, and then fully coupled constitutive laws interpreting multi-field interactions and evolving equations governing irreversible fluxes are constructed according to the energy dissipation inequality and the chemical kinetics. To consider the essential distinction between mass diffusion and chemical reactions in affecting free energy and dissipations of a highly coupled system, we regard both the concentrations of diffusive species and the extent of reaction as independent state variables. This new formulation then distinguishes between the energy contribution from the diffusive species entering the solid and that from the subsequent chemical reactions occurring among these species and the host solid, which not only interact with stresses or strains in different manners and on different time scales, but also induce different variations of solid microstructures and material properties. Taking advantage of this new description, we further establish a specialized isothermal model to predict precisely the transient chemo-mechanical response of a swelling solid with a proposed volumetric constraint that accounts for material incompressibility. Coupled kinetics is incorporated to capture the volumetric swelling of the solid caused by imbibition of external species and the simultaneous dilation arised from chemical reactions between the diffusing species and the solid. The model is then exemplified with two numerical examples of transient swelling accompanied by chemical reaction. Various ratios of characteristic times of diffusion and chemical reaction are taken into account to shed light on the dependency on kinetic time scales of evolution patterns for a diffusion-reaction controlled deformable solid.

Remodelling of cellular excitation (reaction) and intercellular coupling (diffusion) by chronic atrial fibrillation represented by a reaction-diffusion system

NASA Astrophysics Data System (ADS)

Zhang, Henggui; Garratt, Clifford J.; Kharche, Sanjay; Holden, Arun V.

2009-06-01

Human atrial tissue is an excitable system, in which myocytes are excitable elements, and cell-to-cell electrotonic interactions are via diffusive interactions of cell membrane potentials. We developed a family of excitable system models for human atrium at cellular, tissue and anatomical levels for both normal and chronic atrial fibrillation (AF) conditions. The effects of AF-induced remodelling of cell membrane ionic channels (reaction kinetics) and intercellular gap junctional coupling (diffusion) on atrial excitability, conduction of excitation waves and dynamics of re-entrant excitation waves are quantified. Both ionic channel and gap junctional coupling remodelling have rate dependent effects on atrial propagation. Membrane channel conductance remodelling allows the propagation of activity at higher rates than those sustained in normal tissue or in tissue with gap junctional remodelling alone. Membrane channel conductance remodelling is essential for the propagation of activity at rates higher than 300/min as seen in AF. Spatially heterogeneous gap junction coupling remodelling increased the risk of conduction block, an essential factor for the genesis of re-entry. In 2D and 3D anatomical models, the dynamical behaviours of re-entrant excitation waves are also altered by membrane channel modelling. This study provides insights to understand the pro-arrhythmic effects of AF-induced reaction and diffusion remodelling in atrial tissue.

Convergence to equilibrium of renormalised solutions to nonlinear chemical reaction–diffusion systems

NASA Astrophysics Data System (ADS)

Fellner, Klemens; Tang, Bao Quoc

2018-06-01

The convergence to equilibrium for renormalised solutions to nonlinear reaction-diffusion systems is studied. The considered reaction-diffusion systems arise from chemical reaction networks with mass action kinetics and satisfy the complex balanced condition. By applying the so-called entropy method, we show that if the system does not have boundary equilibria, i.e. equilibrium states lying on the boundary of R_+^N, then any renormalised solution converges exponentially to the complex balanced equilibrium with a rate, which can be computed explicitly up to a finite-dimensional inequality. This inequality is proven via a contradiction argument and thus not explicitly. An explicit method of proof, however, is provided for a specific application modelling a reversible enzyme reaction by exploiting the specific structure of the conservation laws. Our approach is also useful to study the trend to equilibrium for systems possessing boundary equilibria. More precisely, to show the convergence to equilibrium for systems with boundary equilibria, we establish a sufficient condition in terms of a modified finite-dimensional inequality along trajectories of the system. By assuming this condition, which roughly means that the system produces too much entropy to stay close to a boundary equilibrium for infinite time, the entropy method shows exponential convergence to equilibrium for renormalised solutions to complex balanced systems with boundary equilibria.

A programmable soft chemo-mechanical actuator exploiting a catalyzed photochemical water-oxidation reaction.

PubMed

Yuan, P; McCracken, J M; Gross, D E; Braun, P V; Moore, J S; Nuzzo, R G

2017-10-18

We describe a composite hydrogel containing an embedding coupled chemistry for light-sensitized catalytic reactions that enables chemo-mechanical actuation of poly(acrylic acid)-based gels. In these materials, a photosensitizer and catalyst-ruthenium trisbipyridine and iridium dioxide nanoparticles, respectively-are incorporated into the hydrogel where together, with visible light irradiation, they undergo a catalytic water-oxidation reaction that lowers the pH and induces a dissipative/chemically-driven strain change in the gel. To demonstrate the capacity for 3D chemo-mechanical actuation, a layer of non-pH responsive poly(2-hydroxyethyl methacrylate) is added to the photo-active composite gel to create a model bimorph actuator. Triggering and terminating the water-oxidation reaction leads to a programmatic expansion and contraction of the active layer, which induces different modes of biomimetic curling motions in the bimorph actuator in light and dark environments. The efficiency of this system is fundamentally limited by the system-level design, which provides no capacity to sustain a local pH gradient against diffusive mixing. Even so, if the initial pH of the background solution is reestablished either actively or passively between each reaction cycle, it is possible to realize multiple cycles of reversible actuation. We describe a thermodynamic analysis of this system which identifies specific features mediating efficiency losses and conceptual requirements for mesoscopic design rules for optimization of this system and for advancing soft actuation systems in general.

Noise-induced symmetry breaking far from equilibrium and the emergence of biological homochirality

NASA Astrophysics Data System (ADS)

Jafarpour, Farshid; Biancalani, Tommaso; Goldenfeld, Nigel

2017-03-01

The origin of homochirality, the observed single-handedness of biological amino acids and sugars, has long been attributed to autocatalysis, a frequently assumed precursor for early life self-replication. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross-inhibition of the two chiral states, an unlikely scenario for early life self-replicators. Here we present a theory for a stochastic individual-level model of autocatalytic prebiotic self-replicators that are maintained out of thermal equilibrium. Without chiral inhibition, the racemic state is the global attractor of the deterministic dynamics, but intrinsic multiplicative noise stabilizes the homochiral states. Moreover, we show that this noise-induced bistability is robust with respect to diffusion of molecules of opposite chirality, and systems of diffusively coupled autocatalytic chemical reactions synchronize their final homochiral states when the self-replication is the dominant production mechanism for the chiral molecules. We conclude that nonequilibrium autocatalysis is a viable mechanism for homochirality, without imposing additional nonlinearities such as chiral inhibition.

Modeling and simulation of enzymatic gluconic acid production using immobilized enzyme and CSTR-PFTR circulation reaction system.

PubMed

Li, Can; Lin, Jianqun; Gao, Ling; Lin, Huibin; Lin, Jianqiang

2018-04-01

Production of gluconic acid by using immobilized enzyme and continuous stirred tank reactor-plug flow tubular reactor (CSTR-PFTR) circulation reaction system. A production system is constructed for gluconic acid production, which consists of a continuous stirred tank reactor (CSTR) for pH control and liquid storage and a plug flow tubular reactor (PFTR) filled with immobilized glucose oxidase (GOD) for gluconic acid production. Mathematical model is developed for this production system and simulation is made for the enzymatic reaction process. The pH inhibition effect on GOD is modeled by using a bell-type curve. Gluconic acid can be efficiently produced by using the reaction system and the mathematical model developed for this system can simulate and predict the process well.

Pattern dynamics of the reaction-diffusion immune system.

PubMed

Zheng, Qianqian; Shen, Jianwei; Wang, Zhijie

2018-01-01

In this paper, we will investigate the effect of diffusion, which is ubiquitous in nature, on the immune system using a reaction-diffusion model in order to understand the dynamical behavior of complex patterns and control the dynamics of different patterns. Through control theory and linear stability analysis of local equilibrium, we obtain the optimal condition under which the system loses stability and a Turing pattern occurs. By combining mathematical analysis and numerical simulation, we show the possible patterns and how these patterns evolve. In addition, we establish a bridge between the complex patterns and the biological mechanism using the results from a previous study in Nature Cell Biology. The results in this paper can help us better understand the biological significance of the immune system.

A discrete model to study reaction-diffusion-mechanics systems.

PubMed

Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V

2011-01-01

This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

A Discrete Model to Study Reaction-Diffusion-Mechanics Systems

PubMed Central

Weise, Louis D.; Nash, Martyn P.; Panfilov, Alexander V.

2011-01-01

This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects. PMID:21804911

Versatile microanalytical system with porous polypropylene capillary membrane for calibration gas generation and trace gaseous pollutants sampling applied to the analysis of formaldehyde, formic acid, acetic acid and ammonia in outdoor air.

PubMed

Coelho, Lúcia H G; Melchert, Wanessa R; Rocha, Flavio R; Rocha, Fábio R P; Gutz, Ivano G R

2010-11-15

The analytical determination of atmospheric pollutants still presents challenges due to the low-level concentrations (frequently in the μg m(-3) range) and their variations with sampling site and time. In this work, a capillary membrane diffusion scrubber (CMDS) was scaled down to match with capillary electrophoresis (CE), a quick separation technique that requires nothing more than some nanoliters of sample and, when combined with capacitively coupled contactless conductometric detection (C(4)D), is particularly favorable for ionic species that do not absorb in the UV-vis region, like the target analytes formaldehyde, formic acid, acetic acid and ammonium. The CMDS was coaxially assembled inside a PTFE tube and fed with acceptor phase (deionized water for species with a high Henry's constant such as formaldehyde and carboxylic acids, or acidic solution for ammonia sampling with equilibrium displacement to the non-volatile ammonium ion) at a low flow rate (8.3 nL s(-1)), while the sample was aspirated through the annular gap of the concentric tubes at 2.5 mL s(-1). A second unit, in all similar to the CMDS, was operated as a capillary membrane diffusion emitter (CMDE), generating a gas flow with know concentrations of ammonia for the evaluation of the CMDS. The fluids of the system were driven with inexpensive aquarium air pumps, and the collected samples were stored in vials cooled by a Peltier element. Complete protocols were developed for the analysis, in air, of NH(3), CH(3)COOH, HCOOH and, with a derivatization setup, CH(2)O, by associating the CMDS collection with the determination by CE-C(4)D. The ammonia concentrations obtained by electrophoresis were checked against the reference spectrophotometric method based on Berthelot's reaction. Sensitivity enhancements of this reference method were achieved by using a modified Berthelot reaction, solenoid micro-pumps for liquid propulsion and a long optical path cell based on a liquid core waveguide (LCW). All techniques and methods of this work are in line with the green analytical chemistry trends. Copyright © 2010 Elsevier B.V. All rights reserved.

Ozonation of Canadian Athabasca asphaltene

NASA Astrophysics Data System (ADS)

Cha, Zhixiong

Application of ozonation in the petrochemical industry for heavy hydrocarbon upgrading has not been sufficiently explored. Among heavy hydrocarbons, asphaltenes are the heaviest and the most difficult fractions for analysis and treatment. Therefore, ozonation of asphaltenes presents an interesting application in the petrochemical industry. Commercial application of ozonation in the petrochemical industry has three obstacles: availability of an ozone-resistant and environmentally friendly solvent, the precipitation of ozonation intermediates during reaction, and recovery of the solvent and separation of the ozonation products. Preliminary ozonation of Athabasca oil sands asphaltene in nonparticipating solvents encountered serious precipitation of the ozonation intermediates. The precipitated intermediates could be polymeric ozonides and intermolecular ozonides or polymeric peroxides. Because the inhomogeneous reaction medium caused low ozone efficiency, various participating solvents such as methanol and acetic acid were added to form more soluble hydroperoxides. The mass balance results showed that on average, one asphaltene molecule reacted with 12 ozone molecules through the electrophilic reaction and the subsequent decomposition of ozonation intermediates generated acetone extractable products. GC/MS analysis of these compounds indicated that the free radical reactions could be important for generation of volatile products. The extensively ozonated asphaltene in the presence of participating solvents were refluxed with methanol to generate more volatile products. GC/MS analysis of the methanol-esterified ozonation products indicated that most volatile products were aliphatic carboxylic acid esters generated through cleavage of substituents. Reaction kinetics study showed that asphaltene ozonation was initially a diffusion rate-controlled reaction and later developed to a chemical reaction rate-controlled reaction after depletion of the reactive aromatic sites. Two new solvent systems, a self-sustaining ozonation system and a cyclohexane/acetone/water or a cyclohexane/acetone/methanol system, were studied to overcome the drawback of using halogenated solvents. The self-sustaining ozonation process employed the final ozonation products as the reaction solvent. Compared to the self-sustaining ozonation, the cyclohexane solvent system showed higher ozone efficiency; however, it required dynamic adjustment of the solvent system during ozonation. An extensively ozonated asphaltene's weight would be doubled. Distillation of the products separated about 45% volatile products having biodiesel-style chemical structures. Compared to distillation, more than 90% of the ozonation products were extractable by acetone. The remaining acetone-insoluble part was further classified by dichloromethane and other solvents of different polarities. The separated ozonation products were good fuel additives or materials for other products.

A new necessary condition for Turing instabilities.

PubMed

Elragig, Aiman; Townley, Stuart

2012-09-01

Reactivity (a.k.a initial growth) is necessary for diffusion driven instability (Turing instability). Using a notion of common Lyapunov function we show that this necessary condition is a special case of a more powerful (i.e. tighter) necessary condition. Specifically, we show that if the linearised reaction matrix and the diffusion matrix share a common Lyapunov function, then Turing instability is not possible. The existence of common Lyapunov functions is readily checked using semi-definite programming. We apply this result to the Gierer-Meinhardt system modelling regenerative properties of Hydra, the Oregonator, to a host-parasite-hyperparasite system with diffusion and to a reaction-diffusion-chemotaxis model for a multi-species host-parasitoid community. Copyright © 2012 Elsevier Inc. All rights reserved.

A Role of the Reaction Kernel in Propagation and Stabilization of Edge Diffusion Flames of C1-C3 Hydrocarbons

NASA Technical Reports Server (NTRS)

Takahashi, Fumiaki; Katta, Viswanath R.

2003-01-01

Diffusion flame stabilization is of essential importance in both Earth-bound combustion systems and spacecraft fire safety. Local extinction, re-ignition, and propagation processes may occur as a result of interactions between the flame zone and vortices or fire-extinguishing agents. By using a computational fluid dynamics code with a detailed chemistry model for methane combustion, the authors have revealed the chemical kinetic structure of the stabilizing region of both jet and flat-plate diffusion flames, predicted the flame stability limit, and proposed diffusion flame attachment and detachment mechanisms in normal and microgravity. Because of the unique geometry of the edge of diffusion flames, radical back-diffusion against the oxygen-rich entrainment dramatically enhanced chain reactions, thus forming a peak reactivity spot, i.e., reaction kernel, responsible for flame holding. The new results have been obtained for the edge diffusion flame propagation and attached flame structure using various C1-C3 hydrocarbons.

Nucleation and growth of crystals under cirrus and polar stratospheric cloud conditions

NASA Technical Reports Server (NTRS)

Hallett, John; Queen, Brian; Teets, Edward; Fahey, James

1995-01-01

Laboratory studies examine phase changes of hygroscopic substances which occur as aerosol in stratosphere and troposphere (sodium chloride, ammonium sulfate, ammonium bisulfate, nitric acid, sulfuric acid), under controlled conditions, in samples volume 1 to 10(exp -4) ml. Crystallization of salts from supersaturated solutions is examined by slowly evaporating a solution drop on a substrate, under controlled relative humidity, until self nucleation occurs; controlled nucleation of ice in a mm capillary U-tube gives a measured ice crystallization velocity at known supercooling. Two states of crystallization occur for regions where hydrates exist. It is inferred that all of the materials readily exist as supersaturated/supercooled solutions; the degree of metastability appears to be slightly enhanced by inclusion of aircraft produced soot. The crystallization velocity is taken as a measure of viscosity. Results suggest an approach to a glass transition at high molality, supersaturation and/or supercooling within the range of atmospheric interest. It is hypothesized that surface reactions occur more readily on solidified particles - either crystalline or glass, whereas volume reactions are more important on droplets with sufficiently low viscosity and volume diffusivity. Implications are examined for optical properties of such particles in the atmosphere. In a separate experiment, crystal growth was examined in a modified thermal vapor diffusion chamber over the range of cirrus temperature (-30 to -70 C) and under controlled supersaturation and air pressure. The crystals grew at a velocity of 1-2 microns/s, thickness 60-70 micron, in the form of thin column crystals. Design criteria are given for a system to investigate particle growth down to -100 C, (PSC temperatures) where nitric acid particles can be grown under similar control and in the form of hydrate crystals.

Sub-millitesla magnetic field effects on the recombination reaction of flavin and ascorbic acid radicals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evans, Emrys W.; Henbest, Kevin B.; Timmel, Christiane R., E-mail: christiane.timmel@chem.ox.ac.uk, E-mail: stuart.mackenzie@chem.ox.ac.uk

Even though the interaction of a <1 mT magnetic field with an electron spin is less than a millionth of the thermal energy at room temperature (k{sub B}T), it still can have a profound effect on the quantum yields of radical pair reactions. We present a study of the effects of sub-millitesla magnetic fields on the photoreaction of flavin mononucleotide with ascorbic acid. Direct control of the reaction pathway is achieved by varying the rate of electron transfer from ascorbic acid to the photo-excited flavin. At pH 7.0, we verify the theoretical prediction that, apart from a sign change, themore » form of the magnetic field effect is independent of the initial spin configuration of the radical pair. The data agree well with model calculations based on a Green’s function approach that allows multinuclear spin systems to be treated including the diffusive motion of the radicals, their spin-selective recombination reactions, and the effects of the inter-radical exchange interaction. The protonation states of the radicals are uniquely determined from the form of the magnetic field-dependence. At pH 3.0, the effects of two chemically distinct radical pair complexes combine to produce a pronounced response to ∼500 μT magnetic fields. These findings are relevant to the magnetic responses of cryptochromes (flavin-containing proteins proposed as magnetoreceptors in birds) and may aid the evaluation of effects of weak magnetic fields on other biologically relevant electron transfer processes.« less

Mittag-Leffler synchronization of fractional neural networks with time-varying delays and reaction-diffusion terms using impulsive and linear controllers.

PubMed

Stamova, Ivanka; Stamov, Gani

2017-12-01

In this paper, we propose a fractional-order neural network system with time-varying delays and reaction-diffusion terms. We first develop a new Mittag-Leffler synchronization strategy for the controlled nodes via impulsive controllers. Using the fractional Lyapunov method sufficient conditions are given. We also study the global Mittag-Leffler synchronization of two identical fractional impulsive reaction-diffusion neural networks using linear controllers, which was an open problem even for integer-order models. Since the Mittag-Leffler stability notion is a generalization of the exponential stability concept for fractional-order systems, our results extend and improve the exponential impulsive control theory of neural network system with time-varying delays and reaction-diffusion terms to the fractional-order case. The fractional-order derivatives allow us to model the long-term memory in the neural networks, and thus the present research provides with a conceptually straightforward mathematical representation of rather complex processes. Illustrative examples are presented to show the validity of the obtained results. We show that by means of appropriate impulsive controllers we can realize the stability goal and to control the qualitative behavior of the states. An image encryption scheme is extended using fractional derivatives. Copyright © 2017 Elsevier Ltd. All rights reserved.

A hollow-fiber membrane extraction process for recovery and separation of lactic acid from aqueous solution.

PubMed

Huang, Hanjing; Yang, Shang-Tian; Ramey, David E

2004-01-01

An energy-efficient hollow-fiber membrane extraction process was successfully developed to separate and recover lactic acid produced in fermentation. Although many fermentation processes have been developed for lactic acid production, an economical method for lactic acid recovery from the fermentation broth is still needed. Continuous extraction of lactic acid from a simulated aqueous stream was achieved by using Alamine 336 in 2-octanol contained in a hollow-fiber membrane extractor. In this process, the extractant was simultaneously regenerated by stripping with NaOH in a second membrane extractor, and the final product is a concentrated lactate salt solution. The extraction rate increased linearly with an increase in the Alamine 336 content in the solvent (from 5 to 40%). Increasing the concentration of the undissociated lactic acid in the feed solution by either increasing the lactate concentration (from 5 to 40 g/L) or decreasing the solution pH (from 5.0 to 4.0) also increased the extraction rate. Based on these observations, a reactive extraction model with a first-order reaction mechanism for both lactic acid and amine concentrations was proposed. The extraction rate also increased with an increase in the feed flow rate, but not the flow rates of solvent and the stripping solution, suggesting that the process was not limited by diffusion in the liquid films or membrane pores. A mathematical model considering both diffusion and chemical reaction in the extractor and back extractor was developed to simulate the process. The model fits the experimental data well and can be used in scale up design of the process.

Time-Dependent ATR-FTIR Spectroscopic Studies on Fatty Acid Diffusion and the Formation of Metal Soaps in Oil Paint Model Systems.

PubMed

Baij, Lambert; Hermans, Joen J; Keune, Katrien; Iedema, Piet

2018-06-18

The formation of metal soaps (metal complexes of saturated fatty acids) is a serious problem affecting the appearance and structural integrity of many oil paintings. Tailored model systems for aged oil paint and time-dependent attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy were used to study the diffusion of palmitic acid and subsequent metal soap crystallization. The simultaneous presence of free saturated fatty acids and polymer-bound metal carboxylates leads to rapid metal soap crystallization, following a complex mechanism that involves both acid and metal diffusion. Solvent flow, water, and pigments all enhance metal soap crystallization in the model systems. These results contribute to the development of paint cleaning strategies, a better understanding of oil paint degradation, and highlight the potential of time-dependent ATR-FTIR spectroscopy for studying dynamic processes in polymer films. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Permeation across hydrated DPPC lipid bilayers: simulation of the titrable amphiphilic drug valproic acid.

PubMed

Ulander, Johan; Haymet, A D J

2003-12-01

Valproic acid is a short branched fatty acid used as an anticonvulsant drug whose therapeutic action has been proposed to arise from membrane-disordering properties. Static and kinetic properties of valproic acid interacting with fully hydrated dipalmitoyl phosphatidylcholine lipid bilayers are studied using molecular-dynamics simulations. We calculate spatially resolved free energy profiles and local diffusion coefficients using the distance between the bilayer and valproic acid respective centers-of-mass along the bilayer normal as reaction coordinate. To investigate the pH dependence, we calculate profiles for the neutral valproic acid as well as its water-soluble anionic conjugate base valproate. The local diffusion constants for valproate/valproic acid along the bilayer normal are found to be approximately 10(-6) to 10(-5) cm2 s(-1). Assuming protonation of valproic acid upon association with--or insertion into--the lipid bilayer, we calculate the permeation coefficient to be approximately 2.0 10(-3) cm s(-1), consistent with recent experimental estimates of fast fatty acid transport. The ability of the lipid bilayer to sustain local defects such as water intrusions stresses the importance of going beyond mean field and taking into account correlation effects in theoretical descriptions of bilayer translocation processes.

Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions.

PubMed

Bauler, Patricia; Huber, Gary A; McCammon, J Andrew

2012-04-28

Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetric diffusion systems.

Rethinking pattern formation in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Halatek, J.; Frey, E.

2018-05-01

The present theoretical framework for the analysis of pattern formation in complex systems is mostly limited to the vicinity of fixed (global) equilibria. Here we present a new theoretical approach to characterize dynamical states arbitrarily far from (global) equilibrium. We show that reaction-diffusion systems that are driven by locally mass-conserving interactions can be understood in terms of local equilibria of diffusively coupled compartments. Diffusive coupling generically induces lateral redistribution of the globally conserved quantities, and the variable local amounts of these quantities determine the local equilibria in each compartment. We find that, even far from global equilibrium, the system is well characterized by its moving local equilibria. We apply this framework to in vitro Min protein pattern formation, a paradigmatic model for biological pattern formation. Within our framework we can predict and explain transitions between chemical turbulence and order arbitrarily far from global equilibrium. Our results reveal conceptually new principles of self-organized pattern formation that may well govern diverse dynamical systems.

Interchange reaction of disulfides and denaturation of oxytocin by copper(II)/ascorbic acid/O2 system.

PubMed

Inoue, H; Hirobe, M

1987-05-29

The interchange reaction of disulfides was caused by the copper(II)/ascorbic acid/O2 system. The incubation of two symmetric disulfides, L-cystinyl-bis-L-phenylalanine (PP) and L-cystinyl-bis-L-tyrosine (TT), with L-ascorbic acid and CuSO4 in potassium phosphate buffer (pH 7.2, 50 mM) resulted in the formation of an asymmetric disulfide, L-cystinyl-L-phenylalanine-L-tyrosine (PT), and the final ratio of PP:PT:TT was 1:2:1. As the reaction was inhibited by catalase and DMSO only at the initial time, hydroxyl radical generated by the copper(II)/ascorbic acid/O2 system seemed to be responsible for the initiation of the reaction. Oxytocin and insulin were denatured by this system, and catalase and DMSO similarly inhibited these denaturations. As the composition of amino acids was unchanged after the reaction, hydroxyl radical was thought to cause the cleavage and/or interchange reaction of disulfides to denature the peptides.

Up-Scaling Geochemical Reaction Rates for Carbon Dioxide (CO2) in Deep Saline Aquifers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, Catherine A

2013-02-28

Geochemical reactions in deep subsurface environments are complicated by the consolidated nature and mineralogical complexity of sedimentary rocks. Understanding the kinetics of these reactions is critical to our ability to make long-term predictions about subsurface processes such as pH buffering, alteration in rock structure, permeability changes, and formation of secondary precipitates. In this project, we used a combination of experiments and numerical simulation to bridge the gap between our knowledge of these reactions at the lab scale and rates that are meaningful for modeling reactive transport at core scales. The focus is on acid-driven mineral dissolution, which is specifically relevantmore » in the context of CO2-water-rock interactions in geological sequestration of carbon dioxide. The project led to major findings in three areas. First, we modeled reactive transport in pore-network systems to investigate scaling effects in geochemical reaction rates. We found significant scaling effects when CO2 concentrations are high and reaction rates are fast. These findings indicate that the increased acidity associated with geological sequestration can generate conditions for which proper scaling tools are yet to be developed. Second, we used mathematical modeling to investigate the extent to which SO2, if co-injected with CO2, would acidify formation brines. We found that there exist realistic conditions in which the impact on brine acidity will be limited due to diffusion rate-limited SO2 dissolution from the CO2 phase, and the subsequent pH shift may also be limited by the lack of availability of oxidants to produce sulfuric acid. Third, for three Viking sandstones (Alberta sedimentary basin, Canada), we employed backscattered electron microscopy and energy dispersive X-ray spectroscopy to statistically characterize mineral contact with pore space. We determined that for reactive minerals in sedimentary consolidated rocks, abundance alone is not a good predictor of mineral accessible surface area, and should not be used in reactive transport modeling. Our work showed that reaction rates would be overestimated by three to five times.« less

Modeling transport kinetics in clinoptilolite-phosphate rock systems

NASA Technical Reports Server (NTRS)

Allen, E. R.; Ming, D. W.; Hossner, L. R.; Henninger, D. L.

1995-01-01

Nutrient release in clinoptilolite-phosphate rock (Cp-PR) systems occurs through dissolution and cation-exchange reactions. Investigating the kinetics of these reactions expands our understanding of nutrient release processes. Research was conducted to model transport kinetics of nutrient release in Cp-PR systems. The objectives were to identify empirical models that best describe NH4, K, and P release and define diffusion-controlling processes. Materials included a Texas clinoptilolite (Cp) and North Carolina phosphate rock (PR). A continuous-flow thin-disk technique was used. Models evaluated included zero order, first order, second order, parabolic diffusion, simplified Elovich, Elovich, and power function. The power-function, Elovich, and parabolic-diffusion models adequately described NH4, K, and P release. The power-function model was preferred because of its simplicity. Models indicated nutrient release was diffusion controlled. Primary transport processes controlling nutrient release for the time span observed were probably the result of a combination of several interacting transport mechanisms.

Interactions of the "piano-stool" [ruthenium(II)(η(6) -arene)(quinolone)Cl](+) complexes with water; DFT computational study.

PubMed

Zábojníková, Tereza; Cajzl, Radim; Kljun, Jakob; Chval, Zdeněk; Turel, Iztok; Burda, Jaroslav V

2016-07-15

Full optimizations of stationary points along the reaction coordinate for the hydration of several quinolone Ru(II) half-sandwich complexes were performed in water environment using the B3PW91/6-31+G(d)/PCM/UAKS method. The role of diffuse functions (especially on oxygen) was found crucial for correct geometries along the reaction coordinate. Single-point (SP) calculations were performed at the B3LYP/6-311++G(2df,2pd)/DPCM/saled-UAKS level. In the first part, two possible reaction mechanisms-associative and dissociative were compared. It was found that the dissociative mechanism of the hydration process is kinetically slightly preferred. Another important conclusion concerns the reaction channels. It was found that substitution of chloride ligand (abbreviated in the text as dechlorination reaction) represents energetically and kinetically the most feasible pathway. In the second part the same hydration reaction was explored for reactivity comparison of the Ru(II)-complexes with several derivatives of nalidixic acid: cinoxacin, ofloxacin, and (thio)nalidixic acid. The hydration process is about four orders of magnitude faster in a basic solution compared to neutral/acidic environment with cinoxacin and nalidixic acid as the most reactive complexes in the former and latter environments, respectively. The explored hydration reaction is in all cases endergonic; nevertheless the endergonicity is substantially lower (by ∼6 kcal/mol) in basic environment. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Eco-friendly methodology for efficient synthesis and scale-up of 2-ethylhexyl-p-methoxycinnamate using Rhizopus oryzae lipase and its biological evaluation.

PubMed

Kumar, Vinod; Jahan, Firdaus; Kameswaran, Karthikeya; Mahajan, Richi V; Saxena, Rajendra Kumar

2014-06-01

Lipase-mediated synthesis of phenolic acid esters is a green and economical alternative to current chemical methods. Octyl methoxycinnamate, an important UVB-absorbing compound, was synthesized by the esterification of p-methoxycinnamic acid with 2-ethyl hexanol using Rhizopus oryzae lipase. A molar ratio of 1:2 of p-methoxycinnamic acid and 2-ethyl hexanol was found to give an optimum yield using cyclo-octane (50 ml) as reaction solvent, at a temperature of 45 °C, and 750 U of lipase, resulting in a yield of 91.3 % in 96 h. This reaction was successfully scaled up to 400-ml reaction size where 88.6 %bioconversion was achieved. The synthesized compound was found to have superior antioxidant activity as compared to ascorbic acid. The synthesized compound also exhibited good antimicrobial activity against Escherichia coli, Klebsiella pneumonia, Salmonella typhi, Staphylococcus aures, Candida albicans (yeast), Aspergillus niger, Alternaria solani, and Fussarium oxysporum by well diffusion method in terms of zone of inhibitions (in mm).

Reaction rates for a generalized reaction-diffusion master equation

DOE PAGES

Hellander, Stefan; Petzold, Linda

2016-01-19

It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is refined further. In this paper we extend the standard reaction-diffusion master equation to allow molecules occupying neighboring voxels to react, in contrast to the traditional approach in which molecules react only when occupying the same voxel. We derive reaction rates, in two dimensions as well as three dimensions, to obtain an optimal match to the more fine-grained Smoluchowski model, and show inmore » two numerical examples that the extended algorithm is accurate for a wide range of mesh sizes, allowing us to simulate systems that are intractable with the standard reaction-diffusion master equation. In addition, we show that for mesh sizes above the fundamental lower limit of the standard algorithm, the generalized algorithm reduces to the standard algorithm. We derive a lower limit for the generalized algorithm which, in both two dimensions and three dimensions, is on the order of the reaction radius of a reacting pair of molecules.« less

Reaction rates for a generalized reaction-diffusion master equation

PubMed Central

Hellander, Stefan; Petzold, Linda

2016-01-01

It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is refined further. In this paper we extend the standard reaction-diffusion master equation to allow molecules occupying neighboring voxels to react, in contrast to the traditional approach in which molecules react only when occupying the same voxel. We derive reaction rates, in two dimensions as well as three dimensions, to obtain an optimal match to the more fine-grained Smoluchowski model, and show in two numerical examples that the extended algorithm is accurate for a wide range of mesh sizes, allowing us to simulate systems that are intractable with the standard reaction-diffusion master equation. In addition, we show that for mesh sizes above the fundamental lower limit of the standard algorithm, the generalized algorithm reduces to the standard algorithm. We derive a lower limit for the generalized algorithm which, in both two dimensions and three dimensions, is on the order of the reaction radius of a reacting pair of molecules. PMID:26871190

Hybrid stochastic simulations of intracellular reaction-diffusion systems.

PubMed

Kalantzis, Georgios

2009-06-01

With the observation that stochasticity is important in biological systems, chemical kinetics have begun to receive wider interest. While the use of Monte Carlo discrete event simulations most accurately capture the variability of molecular species, they become computationally costly for complex reaction-diffusion systems with large populations of molecules. On the other hand, continuous time models are computationally efficient but they fail to capture any variability in the molecular species. In this study a hybrid stochastic approach is introduced for simulating reaction-diffusion systems. We developed an adaptive partitioning strategy in which processes with high frequency are simulated with deterministic rate-based equations, and those with low frequency using the exact stochastic algorithm of Gillespie. Therefore the stochastic behavior of cellular pathways is preserved while being able to apply it to large populations of molecules. We describe our method and demonstrate its accuracy and efficiency compared with the Gillespie algorithm for two different systems. First, a model of intracellular viral kinetics with two steady states and second, a compartmental model of the postsynaptic spine head for studying the dynamics of Ca+2 and NMDA receptors.

Koch–Haaf reaction of adamantanols in an acid-tolerant hastelloy-made microreactor

PubMed Central

Mukai, Yu

2011-01-01

Summary The Koch–Haaf reaction of adamantanols was successfully carried out in a microflow system at room temperature. By combining an acid-tolerant hastelloy-made micromixer, a PTFE tube, and a hastelloy-made microextraction unit, a packaged reaction-to-workup system was developed. By means of the present system, the multigram scale synthesis of 1-adamantanecarboxylic acid was achieved in ca. one hour operation. PMID:21977213

DSC and EPR investigations on effects of cholesterol component on molecular interactions between paclitaxel and phospholipid within lipid bilayer membrane.

PubMed

Zhao, Lingyun; Feng, Si-Shen; Kocherginsky, Nikolai; Kostetski, Iouri

2007-06-29

Differential scanning calorimetry (DSC) and electron paramagnetic resonance spectroscopy (EPR) were applied to investigate effects of cholesterol component on molecular interactions between paclitaxel, which is one of the best antineoplastic agents found from nature, and dipalmitoylphosphatidylcholine (DPPC) within lipid bilayer vesicles (liposomes), which could also be used as a model cell membrane. DSC analysis showed that incorporation of paclitaxel into the DPPC bilayer causes a reduction in the cooperativity of bilayer phase transition, leading to a looser and more flexible bilayer structure. Including cholesterol component in the DPPC/paclitaxel mixed bilayer can facilitate the molecular interaction between paclitaxel and lipid and make the tertiary system more stable. EPR analysis demonstrated that both of paclitaxel and cholesterol have fluidization effect on the DPPC bilayer membranes although cholesterol has more significant effect than paclitaxel does. The reduction kinetics of nitroxides by ascorbic acid showed that paclitaxel can inhibit the reaction by blocking the diffusion of either the ascorbic acid or nitroxide molecules since the reaction is tested to be a first order one. Cholesterol can remarkably increase the reduction reaction speed. This research may provide useful information for optimizing liposomal formulation of the drug as well as for understanding the pharmacology of paclitaxel.

Reaction-diffusion processes at the nano- and microscales

NASA Astrophysics Data System (ADS)

Epstein, Irving R.; Xu, Bing

2016-04-01

The bottom-up fabrication of nano- and microscale structures from primary building blocks (molecules, colloidal particles) has made remarkable progress over the past two decades, but most research has focused on structural aspects, leaving our understanding of the dynamic and spatiotemporal aspects at a relatively primitive stage. In this Review, we draw inspiration from living cells to argue that it is now time to move beyond the generation of structures and explore dynamic processes at the nanoscale. We first introduce nanoscale self-assembly, self-organization and reaction-diffusion processes as essential features of cells. Then, we highlight recent progress towards designing and controlling these fundamental features of life in abiological systems. Specifically, we discuss examples of reaction-diffusion processes that lead to such outcomes as self-assembly, self-organization, unique nanostructures, chemical waves and dynamic order to illustrate their ubiquity within a unifying context of dynamic oscillations and energy dissipation. Finally, we suggest future directions for research on reaction-diffusion processes at the nano- and microscales that we find hold particular promise for a new understanding of science at the nanoscale and the development of new kinds of nanotechnologies for chemical transport, chemical communication and integration with living systems.

Synthesis, characterization and heterogeneous base catalysis of amino functionalized lanthanide metal-organic frameworks

NASA Astrophysics Data System (ADS)

Huang, Jinping; Li, Chunmei; Tao, Lingling; Zhu, Huilin; Hu, Gang

2017-10-01

Lanthanide metal-organic frameworks (Ln-MOFs) are featured by their tolerance to water and dense structure. In this work, an amine-functionalized Ln-MOF was facilely synthesized by coordination of terbium with 2-aminoterephthalic acid under the condition of microwave irradiation. The crystal structure was characterized by single crystal X-ray diffraction, FT-IR, Raman, TG-DTA and XPS analysis. The basic catalytic activity of the NH2-Tb-MOF was evaluated for Knoevenagel condensation and Henry reactions. Apart from the high activity and 100% selectivity to the condensation product, the NH2-Tb-MOF catalyst could be easily recycled and reused owing to the high stability of the MOF framework formed by coordination of Tb3+ with carboxylic groups. Remarkably, the NH2-Tb-MOF exhibited size-selective catalysis to substrates. For the small-sized reactants, it displayed comparable activity to the homogeneous catalyst of aniline owing to the high dispersion of NH2- active sites and the low diffusion limits. However, in the same reaction system, extremely poor activity in Knoevenagel condensation and Henry reaction for the bulky substrate 4-(tert-butyl) benzaldehyde was observed due to the both effects of substitute and inhibition of diffusion into the micropores. Crystal structure analysis provided a mechanistic evidence that the heterogeneous base catalysis arose from the amino groups densely distributed inside the micropores.

Genipin diffusion and reaction into a gelatin matrix for tissue engineering applications.

PubMed

Montemurro, Francesca; De Maria, Carmelo; Orsi, Gianni; Ghezzi, Lisa; Tinè, Maria Rosaria; Vozzi, Giovanni

2017-04-01

Genipin is a natural low-toxic cross-linker for molecules with primary amino groups, and its use with collagen and gelatin has shown a great potential in tissue engineering applications. The fabrication of scaffolds with a well-organized micro and macro topology using additive manufacturing systems requires an accurate control of working parameters, such as reaction rate, gelling time, and diffusion constant. A polymeric system of 5% w/v gelatin in PBS with 2 mg/mL collagen solutions in a 1:1 weight ratio was used as template to perform measurements varying genipin concentration in a range of 0.1-1.5% w/w with respect to gelatin. In the first part of this work, the reaction rate of the polymeric system was estimated using a new colorimetric analysis of the reaction. Then its workability time, closely related to the gelling time, was evaluated thanks to rheological analysis: finally, the quantification of static and dynamic diffusion constants of genipin across nonreacting and reacting membranes, made respectively by agarose and gelatin, was performed. It was shown that the colorimetric analysis is a good indicator of the reaction progress. The gelling time depends on the genipin concentration, but a workability window of 40 min guaranteed up to 0.5% w/w genipin. The dynamic diffusion constant of genipin in the proposed polymeric system is in the order of magnitude of 10 -7 . The obtained results indicated the possibility to use the genipin, gelatin, and collagen, in the proposed concentrations, to build well-defined hydrogel scaffolds with both extrusion-based and 3D ink-jet system. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 473-480, 2017. © 2015 Wiley Periodicals, Inc.

Wave reflection in a reaction-diffusion system: breathing patterns and attenuation of the echo.

PubMed

Tsyganov, M A; Ivanitsky, G R; Zemskov, E P

2014-05-01

Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).

Wave reflection in a reaction-diffusion system: Breathing patterns and attenuation of the echo

NASA Astrophysics Data System (ADS)

Tsyganov, M. A.; Ivanitsky, G. R.; Zemskov, E. P.

2014-05-01

Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).

Sulfate passivation in the lead-acid system as a capacity limiting process

NASA Astrophysics Data System (ADS)

Kappus, W.; Winsel, A.

1982-10-01

Calculations of the discharge capacity of Pb and PbO 2 electrodes as a function of various parameters are presented. They are based on the solution-precipitation mechanism for the discharge reaction and its formulation by Winsel et al. A logarithmic pore size distribution is used to fit experimental porosigrams of Pb and PbO 2 electrodes. Based on this pore size distribution the capacity is calculated as a function of current, BET surface, and porosity of the PbSO 4 diaphragm. The PbSO 4 supersaturation as the driving force of the diffusive transport is chosen as a free parameter.

Shikimic Acid Ozonolysis is Influenced by its Physical State

NASA Astrophysics Data System (ADS)

Steimer, S.; Krieger, U. K.; Lampimäki, M.; Peter, T.; Ammann, M.

2013-12-01

Atmospheric aerosols play an important role in climate, air quality and human health. They undergo continuous transformation, changing their physical and chemical properties. Recent findings show that secondary organic aerosol (SOA) particles can form amorphous solids and semi-solids under atmospheric conditions [1]. Such physical states are highly viscous, leading to a decreased diffusivity within the bulk of the material. Inhibited mass transport could slow down chemical reactions, thereby increasing the lifetime of the organic compounds involved. First indications of such behavior were recently shown for the reaction of thin protein films with ozone [2] and formation of organonitrogen from ammonia uptake to α-pinene secondary organic material [3]. In this study, we investigated the influence of physical state on the ozonolysis of shikimic acid. This carboxylic acid is a constituent of biomass burning aerosols and used here as a proxy for oxygenated organic aerosol. The viscosity of the organic material was adjusted by varying the humidity of the system between 0% and 92% RH, assuming a correlation between the two parameters since water acts as a plasticizer. The system was probed with two complementary techniques: coated wall flow tube measurements, where the uptake of ozone is measured via loss from the gas phase and in situ X-ray microspectroscopy on single particles, where oxidation of the bulk can be observed. Additionally, data from electrodynamic balance measurements and kinetic modeling were used to facilitate data analysis. The dependence of the ozonolysis on relative humidity was clearly observed with both techniques. The coated wall flow tube measurements showed a long term, gradually changing ozone uptake over more than 15 hours, the magnitude of which varied over nearly two orders between driest and wettest conditions. It was possible to separate the uptake into two distinct kinetic regimes, the first of which displayed a Langmuir-Hinshelwood type behavior regarding the ozone gas phase concentration. Microspectroscopy showed that the speed at which the characteristic double bond peak of shikimic acid disappeared was humidity dependent. The measured humidity dependence supports the hypothesis that the uptake coefficient is highly dependent on the diffusion coefficients of ozone and/or shikimic acid in the organic film. [1] Nature, 2010, 467, 824-827. [2] Proc. Natl. Acad. Sci. U. S. A., 2011, 108, 11003-11008. [3] Proc. Natl. Acad. Sci. U. S. A., 2012, 109, 17354-17359.

Reaction rates for mesoscopic reaction-diffusion kinetics

DOE PAGES

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2015-02-23

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In thismore » paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. Finally, we show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results.« less

Reaction rates for mesoscopic reaction-diffusion kinetics

PubMed Central

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2016-01-01

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. We show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results. PMID:25768640

Density profiles around A+B→C reaction-diffusion fronts in partially miscible systems: A general classification.

PubMed

Loodts, V; Trevelyan, P M J; Rongy, L; De Wit, A

2016-10-01

Various spatial density profiles can develop in partially miscible stratifications when a phase A dissolves with a finite solubility into a host phase containing a dissolved reactant B. We investigate theoretically the impact of an A+B→C reaction on such density profiles in the host phase and classify them in a parameter space spanned by the ratios of relative contributions to density and diffusion coefficients of the chemical species. While the density profile is either monotonically increasing or decreasing in the nonreactive case, reactions combined with differential diffusivity can create eight different types of density profiles featuring up to two extrema in density, at the reaction front or below it. We use this framework to predict various possible hydrodynamic instability scenarios inducing buoyancy-driven convection around such reaction fronts when they propagate parallel to the gravity field.

A minimally-resolved immersed boundary model for reaction-diffusion problems

NASA Astrophysics Data System (ADS)

Pal Singh Bhalla, Amneet; Griffith, Boyce E.; Patankar, Neelesh A.; Donev, Aleksandar

2013-12-01

We develop an immersed boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a minimally-resolved "blob" using many fewer degrees of freedom per particle than standard discretization approaches. More complicated or more highly resolved particle shapes can be built out of a collection of reactive blobs. We demonstrate numerically that the blob model can provide an accurate representation at low to moderate packing densities of the reactive particles, at a cost not much larger than solving a Poisson equation in the same domain. Unlike multipole expansion methods, our method does not require analytically computed Green's functions, but rather, computes regularized discrete Green's functions on the fly by using a standard grid-based discretization of the Poisson equation. This allows for great flexibility in implementing different boundary conditions, coupling to fluid flow or thermal transport, and the inclusion of other effects such as temporal evolution and even nonlinearities. We develop multigrid-based preconditioners for solving the linear systems that arise when using implicit temporal discretizations or studying steady states. In the diffusion-limited case the resulting linear system is a saddle-point problem, the efficient solution of which remains a challenge for suspensions of many particles. We validate our method by comparing to published results on reaction-diffusion in ordered and disordered suspensions of reactive spheres.

Nonlinear Chemical Dynamics and Synchronization

NASA Astrophysics Data System (ADS)

Li, Ning

Alan Turing's work on morphogenesis, more than half a century ago, continues to motivate and inspire theoretical and experimental biologists even today. That said, there are very few experimental systems for which Turing's theory is applicable. In this thesis we present an experimental reaction-diffusion system ideally suited for testing Turing's ideas in synthetic "cells" consisting of microfluidically produced surfactant-stabilized emulsions in which droplets containing the Belousov-Zhabotinsky (BZ) oscillatory chemical reactants are dispersed in oil. The BZ reaction has become the prototype of nonlinear dynamics in chemistry and a preferred system for exploring the behavior of coupled nonlinear oscillators. Our system consists of a surfactant stabilized monodisperse emulsion of drops of aqueous BZ solution dispersed in a continuous phase of oil. In contrast to biology, here the chemistry is understood, rate constants are measured and interdrop coupling is purely diffusive. We explore a large set of parameters through control of rate constants, drop size, spacing, and spatial arrangement of the drops in lines and rings in one-dimension (1D) and hexagonal arrays in two-dimensions (2D). The Turing model is regarded as a metaphor for morphogenesis in biology but not for prediction. Here, we develop a quantitative and falsifiable reaction-diffusion model that we experimentally test with synthetic cells. We quantitatively establish the extent to which the Turing model in 1D describes both stationary pattern formation and temporal synchronization of chemical oscillators via reaction-diffusion and in 2D demonstrate that chemical morphogenesis drives physical differentiation in synthetic cells.

Lead electrowinning in a fluoborate medium. Use of hydrogen diffusion anodes

NASA Astrophysics Data System (ADS)

Expósito, E.; González-García, J.; Bonete, P.; Montiel, V.; Aldaz, A.

The results of an investigation of the electrowinning of lead employing a fluoboric acid bath are reported. The electrodeposition lead reaction was studied by voltammetric methods and scanning electron microscopy (SEM) microphotographs of the electrodeposited lead were taken. The effects of current density, temperature, catholyte flow and H + concentration were investigated on a laboratory scale to optimise operating conditions. Finally, the substitution of the traditionally used Dimensionally Stable Anode (DSA) by a Hydrogen Diffusion Electrode (HDE) was made in order to decrease the energy consumption (EC) of the overall process.

Interfacial reactions between metal and gallium arsenide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, J.C.; Schulz, K.J.; Hsieh, K.C.

1989-10-01

The phase formation sequence for GaAs/metal ternary diffusion couples is discussed. The diffusion path concept is introduced and is used with the phase diagram to understand interfacial reactions between GaAs and metal. The correlation between growth kinetics and interface morphology is discussed. Studies of bulk and thin film couples in two systems, GaAs/Pd and GaAs/Pt, are given to illustrate these concepts.

Nonlinear waves in reaction-diffusion systems: The effect of transport memory

NASA Astrophysics Data System (ADS)

Manne, K. K.; Hurd, A. J.; Kenkre, V. M.

2000-04-01

Motivated by the problem of determining stress distributions in granular materials, we study the effect of finite transport correlation times on the propagation of nonlinear wave fronts in reaction-diffusion systems. We obtain results such as the possibility of spatial oscillations in the wave-front shape for certain values of the system parameters and high enough wave-front speeds. We also generalize earlier known results concerning the minimum wave-front speed and shape-speed relationships stemming from the finiteness of the correlation times. Analytic investigations are made possible by a piecewise linear representation of the nonlinearity.

Spatiotemporal chaos of self-replicating spots in reaction-diffusion systems.

PubMed

Wang, Hongli; Ouyang, Qi

2007-11-23

The statistical properties of self-replicating spots in the reaction-diffusion Gray-Scott model are analyzed. In the chaotic regime of the system, the spots that dominate the spatiotemporal chaos grow and divide in two or decay into the background randomly and continuously. The rates at which the spots are created and decay are observed to be linearly dependent on the number of spots in the system. We derive a probabilistic description of the spot dynamics based on the statistical independence of spots and thus propose a characterization of the spatiotemporal chaos dominated by replicating spots.

Breathing pulses in singularly perturbed reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Veerman, Frits

2015-07-01

The weakly nonlinear stability of pulses in general singularly perturbed reaction-diffusion systems near a Hopf bifurcation is determined using a centre manifold expansion. A general framework to obtain leading order expressions for the (Hopf) centre manifold expansion for scale separated, localised structures is presented. Using the scale separated structure of the underlying pulse, directly calculable expressions for the Hopf normal form coefficients are obtained in terms of solutions to classical Sturm-Liouville problems. The developed theory is used to establish the existence of breathing pulses in a slowly nonlinear Gierer-Meinhardt system, and is confirmed by direct numerical simulation.

Synchronization of generalized reaction-diffusion neural networks with time-varying delays based on general integral inequalities and sampled-data control approach.

PubMed

Dharani, S; Rakkiyappan, R; Cao, Jinde; Alsaedi, Ahmed

2017-08-01

This paper explores the problem of synchronization of a class of generalized reaction-diffusion neural networks with mixed time-varying delays. The mixed time-varying delays under consideration comprise of both discrete and distributed delays. Due to the development and merits of digital controllers, sampled-data control is a natural choice to establish synchronization in continuous-time systems. Using a newly introduced integral inequality, less conservative synchronization criteria that assure the global asymptotic synchronization of the considered generalized reaction-diffusion neural network and mixed delays are established in terms of linear matrix inequalities (LMIs). The obtained easy-to-test LMI-based synchronization criteria depends on the delay bounds in addition to the reaction-diffusion terms, which is more practicable. Upon solving these LMIs by using Matlab LMI control toolbox, a desired sampled-data controller gain can be acuqired without any difficulty. Finally, numerical examples are exploited to express the validity of the derived LMI-based synchronization criteria.

A Nonequilibrium Rate Formula for Collective Motions of Complex Molecular Systems

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2010-09-01

We propose a compact reaction rate formula that accounts for a non-equilibrium distribution of residence times of complex molecules, based on a detailed study of the coarse-grained phase space of a reaction coordinate. We take the structural transition dynamics of a six-atom Morse cluster between two isomers as a prototype of multi-dimensional molecular reactions. Residence time distribution of one of the isomers shows an exponential decay, while that of the other isomer deviates largely from the exponential form and has multiple peaks. Our rate formula explains such equilibrium and non-equilibrium distributions of residence times in terms of the rates of diffusions of energy and the phase of the oscillations of the reaction coordinate. Rapid diffusions of energy and the phase generally give rise to the exponential decay of residence time distribution, while slow diffusions give rise to a non-exponential decay with multiple peaks. We finally make a conjecture about a general relationship between the rates of the diffusions and the symmetry of molecular mass distributions.

Global dynamics of a nonlocal delayed reaction-diffusion equation on a half plane

NASA Astrophysics Data System (ADS)

Hu, Wenjie; Duan, Yueliang

2018-04-01

We consider a delayed reaction-diffusion equation with spatial nonlocality on a half plane that describes population dynamics of a two-stage species living in a semi-infinite environment. A Neumann boundary condition is imposed accounting for an isolated domain. To describe the global dynamics, we first establish some a priori estimate for nontrivial solutions after investigating asymptotic properties of the nonlocal delayed effect and the diffusion operator, which enables us to show the permanence of the equation with respect to the compact open topology. We then employ standard dynamical system arguments to establish the global attractivity of the nontrivial equilibrium. The main results are illustrated by the diffusive Nicholson's blowfly equation and the diffusive Mackey-Glass equation.

Rule-based spatial modeling with diffusing, geometrically constrained molecules.

PubMed

Gruenert, Gerd; Ibrahim, Bashar; Lenser, Thorsten; Lohel, Maiko; Hinze, Thomas; Dittrich, Peter

2010-06-07

We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly.

Rule-based spatial modeling with diffusing, geometrically constrained molecules

PubMed Central

2010-01-01

Background We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Results Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. Conclusions We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly. PMID:20529264

An electromechanical based deformable model for soft tissue simulation.

PubMed

Zhong, Yongmin; Shirinzadeh, Bijan; Smith, Julian; Gu, Chengfan

2009-11-01

Soft tissue deformation is of great importance to surgery simulation. Although a significant amount of research efforts have been dedicated to simulating the behaviours of soft tissues, modelling of soft tissue deformation is still a challenging problem. This paper presents a new deformable model for simulation of soft tissue deformation from the electromechanical viewpoint of soft tissues. Soft tissue deformation is formulated as a reaction-diffusion process coupled with a mechanical load. The mechanical load applied to a soft tissue to cause a deformation is incorporated into the reaction-diffusion system, and consequently distributed among mass points of the soft tissue. Reaction-diffusion of mechanical load and non-rigid mechanics of motion are combined to govern the simulation dynamics of soft tissue deformation. An improved reaction-diffusion model is developed to describe the distribution of the mechanical load in soft tissues. A three-layer artificial cellular neural network is constructed to solve the reaction-diffusion model for real-time simulation of soft tissue deformation. A gradient based method is established to derive internal forces from the distribution of the mechanical load. Integration with a haptic device has also been achieved to simulate soft tissue deformation with haptic feedback. The proposed methodology does not only predict the typical behaviours of living tissues, but it also accepts both local and large-range deformations. It also accommodates isotropic, anisotropic and inhomogeneous deformations by simple modification of diffusion coefficients.

Perfluoroalkyl phosphonic and phosphinic acids as proton conductors for anhydrous proton-exchange membranes.

PubMed

Herath, Mahesha B; Creager, Stephen E; Kitaygorodskiy, Alex; DesMarteau, Darryl D

2010-09-10

A study of proton-transport rates and mechanisms under anhydrous conditions using a series of acid model compounds, analogous to comb-branch perfluorinated ionomers functionalized with phosphonic, phosphinic, sulfonic, and carboxylic acid protogenic groups, is reported. Model compounds are characterized with respect to proton conductivity, viscosity, proton, and anion (conjugate base) self-diffusion coefficients, and Hammett acidity. The highest conductivities, and also the highest viscosities, are observed for the phosphonic and phosphinic acid model compounds. Arrhenius analysis of conductivity and viscosity for these two acids reveals much lower activation energies for ion transport than for viscous flow. Additionally, the proton self-diffusion coefficients are much higher than the conjugate-base self-diffusion coefficients for these two acids. Taken together, these data suggest that anhydrous proton transport in the phosphonic and phosphinic acid model compounds occurs primarily by a structure-diffusion, hopping-based mechanism rather than a vehicle mechanism. Further analysis of ionic conductivity and ion self-diffusion rates by using the Nernst-Einstein equation reveals that the phosphonic and phosphinic acid model compounds are relatively highly dissociated even under anhydrous conditions. In contrast, sulfonic and carboxylic acid-based systems exhibit relatively low degrees of dissociation under anhydrous conditions. These findings suggest that fluoroalkyl phosphonic and phosphinic acids are good candidates for further development as anhydrous, high-temperature proton conductors.

Hopping Conduction and Bacteria: Transport Properties of Disordered Reaction-Diffusion Systems

NASA Astrophysics Data System (ADS)

Missel, Andrew; Dahmen, Karin

2008-03-01

Reaction-diffusion (RD) systems are used to model everything from the formation of animal coat patterns to the spread of genes in a population to the seasonal variation of plankton density in the ocean. In all of these problems, disorder plays a large role, but determining its effects on transport properties in RD systems has been a challenge. We present here both analytical and numerical studies of a particular disordered RD system consisting of particles which are allowed to diffuse and compete for resources (2A->A) with spatially homogeneous rates, reproduce (A->2A) in certain areas (``oases''), and die (A->0) everywhere else (the ``desert''). In the low oasis density regime, transport is mediated through rare ``hopping events'' in which a small number of particles diffuse through the desert from one oasis to another; the situation is mathematically analogous to hopping conduction in doped semiconductors, and this analogy, along with some ideas from first passage percolation theory, allows us to make some quantitative predictions about the transport properties of the system on a large scale.

Study on copper kinetics in processing sulphide ore mixed with copper and zinc with sulfuric acid leaching under pressure

NASA Astrophysics Data System (ADS)

Wen-bo, LUO; Ji-kun, WANG; Yin, GAN

2018-01-01

Sulphide ore mixed with copper and zinc is processed with pressure acid leaching. Research is conducted on the copper kinetic. The stirring rate is set at 600 rpm which could eliminate the influence of external diffusions. Research is conducted on the factors affecting the copper leaching kinetic are temperature, pressure, concentration of sulfuric acid, particle size. The result shows that the apparent activity energy is 50.7 KJ/mol. We could determine that the copper leaching process is shrinking core model of chemical reaction control and work out the leaching equation.

pH Wave-Front Propagation in the Urea-Urease Reaction

PubMed Central

Wrobel, Magdalena M.; Bánsági, Tamás; Scott, Stephen K.; Taylor, Annette F.; Bounds, Chris O.; Carranza, Arturo; Pojman, John A.

2012-01-01

The urease-catalyzed hydrolysis of urea displays feedback that results in a switch from acid (pH ∼3) to base (pH ∼9) after a controllable period of time (from 10 to >5000 s). Here we show that the spatially distributed reaction can support pH wave fronts propagating with a speed of the order of 0.1−1 mm min−1. The experimental results were reproduced qualitatively in reaction-diffusion simulations including a Michaelis-Menten expression for the urease reaction with a bell-shaped rate-pH dependence. However, this model fails to predict that at lower enzyme concentrations, the unstirred reaction does not always support fronts when the well-stirred reaction still rapidly switches to high pH. PMID:22947878

Chemistry with spatial control using particles and streams†

PubMed Central

Kalinin, Yevgeniy V.; Murali, Adithya

2012-01-01

Spatial control of chemical reactions, with micro- and nanometer scale resolution, has important consequences for one pot synthesis, engineering complex reactions, developmental biology, cellular biochemistry and emergent behavior. We review synthetic methods to engineer this spatial control using chemical diffusion from spherical particles, shells and polyhedra. We discuss systems that enable both isotropic and anisotropic chemical release from isolated and arrayed particles to create inhomogeneous and spatially patterned chemical fields. In addition to such finite chemical sources, we also discuss spatial control enabled with laminar flow in 2D and 3D microfluidic networks. Throughout the paper, we highlight applications of spatially controlled chemistry in chemical kinetics, reaction-diffusion systems, chemotaxis and morphogenesis. PMID:23145348

Mode-locking in advection-reaction-diffusion systems: An invariant manifold perspective

NASA Astrophysics Data System (ADS)

Locke, Rory A.; Mahoney, John R.; Mitchell, Kevin A.

2018-01-01

Fronts propagating in two-dimensional advection-reaction-diffusion systems exhibit a rich topological structure. When the underlying fluid flow is periodic in space and time, the reaction front can lock to the driving frequency. We explain this mode-locking phenomenon using the so-called burning invariant manifolds (BIMs). In fact, the mode-locked profile is delineated by a BIM attached to a relative periodic orbit (RPO) of the front element dynamics. Changes in the type (and loss) of mode-locking can be understood in terms of local and global bifurcations of the RPOs and their BIMs. We illustrate these concepts numerically using a chain of alternating vortices in a channel geometry.

Curved fronts in the Belousov-Zhabotinskii reaction-diffusion systems in R2

NASA Astrophysics Data System (ADS)

Niu, Hong-Tao; Wang, Zhi-Cheng; Bu, Zhen-Hui

2018-05-01

In this paper we consider a diffusion system with the Belousov-Zhabotinskii (BZ for short) chemical reaction. Following Brazhnik and Tyson [4] and Pérez-Muñuzuri et al. [45], who predicted V-shaped fronts theoretically and discovered V-shaped fronts by experiments respectively, we give a rigorous mathematical proof of their results. We establish the existence of V-shaped traveling fronts in R2 by constructing a proper supersolution and a subsolution. Furthermore, we establish the stability of the V-shaped front in R2.

Reaction-diffusion processes and metapopulation models on duplex networks

NASA Astrophysics Data System (ADS)

Xuan, Qi; Du, Fang; Yu, Li; Chen, Guanrong

2013-03-01

Reaction-diffusion processes, used to model various spatially distributed dynamics such as epidemics, have been studied mostly on regular lattices or complex networks with simplex links that are identical and invariant in transferring different kinds of particles. However, in many self-organized systems, different particles may have their own private channels to keep their purities. Such division of links often significantly influences the underlying reaction-diffusion dynamics and thus needs to be carefully investigated. This article studies a special reaction-diffusion process, named susceptible-infected-susceptible (SIS) dynamics, given by the reaction steps β→α and α+β→2β, on duplex networks where links are classified into two groups: α and β links used to transfer α and β particles, which, along with the corresponding nodes, consist of an α subnetwork and a β subnetwork, respectively. It is found that the critical point of particle density to sustain reaction activity is independent of the network topology if there is no correlation between the degree sequences of the two subnetworks, and this critical value is suppressed or extended if the two degree sequences are positively or negatively correlated, respectively. Based on the obtained results, it is predicted that epidemic spreading may be promoted on positive correlated traffic networks but may be suppressed on networks with modules composed of different types of diffusion links.

Consumption and diffusion of dissolved oxygen in sedimentary rocks.

PubMed

Manaka, M; Takeda, M

2016-10-01

Fe(II)-bearing minerals (e.g., biotite, chlorite, and pyrite) are a promising reducing agent for the consumption of atmospheric oxygen in repositories for the geological disposal of high-level radioactive waste. To estimate effective diffusion coefficients (D e , in m 2 s -1 ) for dissolved oxygen (DO) and the reaction rates for the oxidation of Fe(II)-bearing minerals in a repository environment, we conducted diffusion-chemical reaction experiments using intact rock samples of Mizunami sedimentary rock. In addition, we conducted batch experiments on the oxidation of crushed sedimentary rock by DO in a closed system. From the results of the diffusion-chemical reaction experiments, we estimated the values of D e for DO to lie within the range 2.69×10 -11

Finite element procedures for time-dependent convection-diffusion-reaction systems

NASA Technical Reports Server (NTRS)

Tezduyar, T. E.; Park, Y. J.; Deans, H. A.

1988-01-01

New finite element procedures based on the streamline-upwind/Petrov-Galerkin formulations are developed for time-dependent convection-diffusion-reaction equations. These procedures minimize spurious oscillations for convection-dominated and reaction-dominated problems. The results obtained for representative numerical examples are accurate with minimal oscillations. As a special application problem, the single-well chemical tracer test (a procedure for measuring oil remaining in a depleted field) is simulated numerically. The results show the importance of temperature effects on the interpreted value of residual oil saturation from such tests.

Nicotine-selective radiation-induced poly(acrylamide/maleic acid) hydrogels

NASA Astrophysics Data System (ADS)

Saraydin, D.; Karadağ, E.; Çaldiran, Y.; Güven, O.

2001-02-01

Nicotine-selective poly(acrylamide/maleic acid) (AAm/MA) hydrogels prepared by γ-irradiation were used in experiments on swelling, diffusion, and interactions of the pharmaceuticals nicotine, nicotinic acid, nicotinamide, and nikethamide. For AAm/MA hydrogel containing 60 mg maleic acid and irradiated at 5.2 kGy, the studies indicated that swelling increased in the following order; nicotine>nicotinamide>nikethamide>nicotinic acid>water. Diffusions of water and the pharmaceuticals within the hydrogels were found to be non-Fickian in character. AAm/MA hydrogel sorbed only nicotine and did not sorb nicotinamide, nikethamide and nicotinic acid in the binding experiments. S-type adsorption in Giles's classification system was observed. Some binding and thermodynamic parameters for AAm/MA hydrogel-nicotine system were calculated using the Scatchard method. The values of adsorption heat and free energy of this system were found to be negative whereas adsorption entropy was found to be positive.

Product interactions and feedback in diffusion-controlled reactions

NASA Astrophysics Data System (ADS)

Roa, Rafael; Siegl, Toni; Kim, Won Kyu; Dzubiella, Joachim

2018-02-01

Steric or attractive interactions among reactants or between reactants and inert crowders can substantially influence the total rate of a diffusion-influenced reaction in the liquid phase. However, the role of the product species, which has typically different physical properties than the reactant species, has been disregarded so far. Here we study the effects of reactant-product and product-product interactions as well as asymmetric diffusion properties on the rate of diffusion-controlled reactions in the classical Smoluchowski-setup for chemical transformations at a perfect catalytic sphere. For this, we solve the diffusion equation with appropriate boundary conditions coupled by a mean-field approach on the second virial level to account for the particle interactions. We find that all particle spatial distributions and the total rate can change significantly, depending on the diffusion and interaction properties of the accumulated products. Complex competing and self-regulating (homeostatic) or self-amplifying effects are observed for the system, leading to both decrease and increase in the rates, as the presence of interacting products feeds back to the reactant flux and thus the rate with which the products are generated.

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

PubMed Central

Chevalier, Michael W.; El-Samad, Hana

2014-01-01

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled. PMID:25481130

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

NASA Astrophysics Data System (ADS)

Chevalier, Michael W.; El-Samad, Hana

2014-12-01

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.

Scalar dissipation rates in non-conservative transport systems

PubMed Central

Engdahl, Nicholas B.; Ginn, Timothy R.; Fogg, Graham E.

2014-01-01

This work considers how the inferred mixing state of diffusive and advective-diffusive systems will vary over time when the solute masses are not constant over time. We develop a number of tools that allow the scalar dissipation rate to be used as a mixing measure in these systems without calculating local concentration gradients. The behavior of dissipation rates are investigated for single and multi-component kinetic reactions and a commonly studied equilibrium reaction. The scalar dissipation rate of a tracer experiencing first order decay can be determined exactly from the decay constant and the dissipation rate of a passive tracer, and the mixing rate of a conservative component is not the superposition of the solute specific mixing rates. We then show how the behavior of the scalar dissipation rate can be determined from a limited subset of an infinite domain. Corrections are derived for constant and time dependent limits of integration the latter is used to approximate dissipation rates in advective-diffusive systems. Several of the corrections exhibit similarities to the previous work on mixing, including non-Fickian mixing. This illustrates the importance of accounting for the effects that reaction systems or limited monitoring areas may have on the inferred mixing state. PMID:23584457

Reactive multi-particle collision dynamics with reactive boundary conditions

NASA Astrophysics Data System (ADS)

Sayyidmousavi, Alireza; Rohlf, Katrin

2018-07-01

In the present study, an off-lattice particle-based method called the reactive multi-particle collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian Dynamics. The main advantages of the RMPC compared to other molecular based methods are less computational cost as well as conservation of mass, energy and momentum in the collision and free streaming steps. The proposed approach is tested on three reaction-diffusion systems and very good agreement with the solutions to their corresponding partial differential equations is observed.

Convergence to a pulsating travelling wave for an epidemic reaction-diffusion system with non-diffusive susceptible population.

PubMed

Ducrot, Arnaud; Giletti, Thomas

2014-09-01

In this work we study the asymptotic behaviour of the Kermack-McKendrick reaction-diffusion system in a periodic environment with non-diffusive susceptible population. This problem was proposed by Kallen et al. as a model for the spatial spread for epidemics, where it can be reasonable to assume that the susceptible population is motionless. For arbitrary dimensional space we prove that large classes of solutions of such a system have an asymptotic spreading speed in large time, and that the infected population has some pulse-like asymptotic shape. The analysis of the one-dimensional problem is more developed, as we are able to uncover a much more accurate description of the profile of solutions. Indeed, we will see that, for some initially compactly supported infected population, the profile of the solution converges to some pulsating travelling wave with minimal speed, that is to some entire solution moving at a constant positive speed and whose profile's shape is periodic in time.

Polybenzimidazole-membrane-based PEM fuel cell in the temperature range of 120-200 °C

NASA Astrophysics Data System (ADS)

Zhang, Jianlu; Tang, Yanghua; Song, Chaojie; Zhang, Jiujun

Phosphoric acid-doped polybenzimidazole-membrane-based PEM fuel cells were tested in the temperature range of 120-200 °C, with ambient backpressure and 0% RH. AC impedance spectroscopy, surface cyclic voltammetry and fuel cell performance simulation were used to obtain the exchange current densities for the cathodic oxygen reduction reaction (ORR) and anodic hydrogen oxidation reaction (HOR) on platinum-based catalysts at such high temperatures. The activation energies for ORR, HOR and membrane conductivity were also obtained separately. The results showed that temperature significantly affects the charger transfer and gas (O 2 and H 2) diffusion resistances. The effect of O 2 stoichiometry (ST air) on fuel cell performance was also investigated. Increasing ST air can effectively increase the O 2 partial pressure in the feed air, leading to improvements in both the thermodynamics and the kinetics of the fuel cell reactions. In addition, it was observed that increasing ST air could also improve the gas diffusion processes.

Structure, hydrolysis, and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics

NASA Astrophysics Data System (ADS)

Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

2016-09-01

A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries. Here, we employ Car-Parrinello molecular dynamics simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction, and diffusion of aqueous V2+, V3+, VO2+, and VO 2+ ions at 300 K. The results indicate that the first hydration shell of both V2+ and V3+ contains six water molecules, while VO2+ is coordinated to five and VO 2+ to three water ligands. The first acidity constants (pKa) estimated using metadynamics simulations are 2.47, 3.06, and 5.38 for aqueous V3+, VO 2+ , and VO2+, respectively, while V2+ is predicted to be a fairly weak acid in aqueous solution with a pKa value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO 2+ ion has a significant impact on water hydrolysis leading to a much higher pKa value of 4.8. This should result in a lower propensity of aqueous VO 2+ for oxide precipitation reaction in agreement with experimental observations for chloride-based electrolyte solutions. The computed diffusion coefficients of vanadium species in water at room temperature are found to increase as V 3 + < VO 2 + < V O 2 + < V 2 + and thus correlate with the simulated hydrolysis constants, namely, the higher the pKa value, the greater the diffusion coefficient.

Metallated porphyrin based porous organic polymers as efficient electrocatalysts

NASA Astrophysics Data System (ADS)

Lu, Guolong; Zhu, Youlong; Xu, Kongliang; Jin, Yinghua; Ren, Zhiyong Jason; Liu, Zhenning; Zhang, Wei

2015-10-01

Developing efficient, stable and low-cost catalysts for Oxygen Reduction Reaction (ORR) is of great significance to many emerging technologies including fuel cells and metal-air batteries. Herein, we report the development of a cobalt(ii) porphyrin based porous organic polymer (CoPOP) and its pyrolyzed derivatives as highly active ORR catalysts. The as-synthesized CoPOP exhibits high porosity and excellent catalytic performance stability, retaining ~100% constant ORR current over 50 000 s in both alkaline and acidic media. Pyrolysis of CoPOP at various temperatures (600 °C, 800 °C, and 1000 °C) yields the materials consisting of graphitic carbon layers and cobalt nanoparticles, which show greatly enhanced catalytic activity compared to the as-synthesized CoPOP. Among them, CoPOP-800/C pyrolyzed at 800 °C shows the highest specific surface area and ORR activity, displaying the most positive half-wave potential (0.825 V vs. RHE) and the largest limited diffusion current density (5.35 mA cm-2) in an alkaline medium, which are comparable to those of commercial Pt/C (20 wt%) (half-wave potential 0.829 V vs. RHE, limited diffusion current density 5.10 mA cm-2). RDE and RRDE experiments indicate that CoPOP-800/C directly reduces molecular oxygen to water through a 4-e- pathway in both alkaline and acidic media. More importantly, CoPOP-800/C exhibits excellent durability and methanol-tolerance under acidic and alkaline conditions, which surpass the Pt/C (20 wt%) system.Developing efficient, stable and low-cost catalysts for Oxygen Reduction Reaction (ORR) is of great significance to many emerging technologies including fuel cells and metal-air batteries. Herein, we report the development of a cobalt(ii) porphyrin based porous organic polymer (CoPOP) and its pyrolyzed derivatives as highly active ORR catalysts. The as-synthesized CoPOP exhibits high porosity and excellent catalytic performance stability, retaining ~100% constant ORR current over 50 000 s in both alkaline and acidic media. Pyrolysis of CoPOP at various temperatures (600 °C, 800 °C, and 1000 °C) yields the materials consisting of graphitic carbon layers and cobalt nanoparticles, which show greatly enhanced catalytic activity compared to the as-synthesized CoPOP. Among them, CoPOP-800/C pyrolyzed at 800 °C shows the highest specific surface area and ORR activity, displaying the most positive half-wave potential (0.825 V vs. RHE) and the largest limited diffusion current density (5.35 mA cm-2) in an alkaline medium, which are comparable to those of commercial Pt/C (20 wt%) (half-wave potential 0.829 V vs. RHE, limited diffusion current density 5.10 mA cm-2). RDE and RRDE experiments indicate that CoPOP-800/C directly reduces molecular oxygen to water through a 4-e- pathway in both alkaline and acidic media. More importantly, CoPOP-800/C exhibits excellent durability and methanol-tolerance under acidic and alkaline conditions, which surpass the Pt/C (20 wt%) system. Electronic supplementary information (ESI) available: Details of the experimental section, powder X-ray diffraction (PXRD) data, scanning electron microscopy (FE-SEM) images, Fourier transform infrared spectroscopy (FT-IR) data, and additional electrochemical data. See DOI: 10.1039/c5nr05324b

Traveling wave solutions to a reaction-diffusion equation

NASA Astrophysics Data System (ADS)

Feng, Zhaosheng; Zheng, Shenzhou; Gao, David Y.

2009-07-01

In this paper, we restrict our attention to traveling wave solutions of a reaction-diffusion equation. Firstly we apply the Divisor Theorem for two variables in the complex domain, which is based on the ring theory of commutative algebra, to find a quasi-polynomial first integral of an explicit form to an equivalent autonomous system. Then through this first integral, we reduce the reaction-diffusion equation to a first-order integrable ordinary differential equation, and a class of traveling wave solutions is obtained accordingly. Comparisons with the existing results in the literature are also provided, which indicates that some analytical results in the literature contain errors. We clarify the errors and instead give a refined result in a simple and straightforward manner.

Multi-scale modeling of diffusion-controlled reactions in polymers: renormalisation of reactivity parameters.

PubMed

Everaers, Ralf; Rosa, Angelo

2012-01-07

The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-controlled reactions in polymers developed by Wilemski, Fixman, and Doi to discuss the renormalisation of the reactivity parameters in polymer models with varying spatial resolution. In particular, we show that the adjustments are independent of chain length. As a consequence, it is possible to match reactions times between descriptions with different resolution for relatively short reference chains and to use the coarse-grained model to make quantitative predictions for longer chains. We illustrate our results by a detailed discussion of the classical problem of chain cyclization in the Rouse model, which offers the simplest example of a multi-scale descriptions, if we consider differently discretized Rouse models for the same physical system. Moreover, we are able to explore different combinations of compact and non-compact diffusion in the local and large-scale dynamics by varying the embedding dimension.

Investigation and kinetic evaluation of the reactions of hydroxymethylfurfural with amino and thiol groups of amino acids.

PubMed

Hamzalıoğlu, Aytül; Gökmen, Vural

2018-02-01

In this study, reactions of hydroxymethylfurfural (HMF) with selected amino acids (arginine, cysteine and lysine) were investigated in HMF-amino acid (high moisture) and Coffee-amino acid (low moisture) model systems at 5, 25 and 50°C. The results revealed that HMF reacted efficiently and effectively with amino acids in both high and low moisture model systems. High-resolution mass spectrometry (HRMS) analyses of the reaction mixtures confirmed the formations of Michael adduct and Schiff base of HMF with amino acids. Calculated pseudo-first order reaction rate constants were in the following order; k Cysteine >k Arginine >k Lysine for high moisture model systems. Comparing to these rate constants, the k Cysteine decreased whereas, k Arginine and k Lysine increased under the low moisture conditions of Coffee-amino acid model systems. The temperature dependence of the rate constants was found to obey the Arrhenius law in a temperature range of 5-50°C under both low and high moisture conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Peroxyl radicals are potential agents of lignin biodegradation

Treesearch

Alexander N. Kapich; Kenneth A. Jensen; Kenneth E. Hammel

1999-01-01

Past work has shown that the extracellular manganese- dependent peroxidases (MnPs) of ligninolytic fungi degrade the principal non-phenolic structures of lignin when they peroxidize unsaturated fatty acids. This reaction is likely to be relevant to ligninolysis in sound wood, where enzymes cannot penetrate, only if it employs a small, diffusible lipid radical as the...

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals.

PubMed

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-04-08

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

PubMed Central

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-01-01

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems. DOI: http://dx.doi.org/10.7554/eLife.14022.001 PMID:27058171

The chemisorption and reactions of formic acid on Cu films on ZnO (000 overline1)-O

NASA Astrophysics Data System (ADS)

Ludviksson, A.; Zhang, R.; Campbell, Charles T.; Griffiths, K.

1994-06-01

The adsorption and reactions of formic acid (HCOOD : HCOOH = 3:1) on the oxygen-terminated ZnO(0001¯)-O surface and on thin Cu films deposited on the ZnO(0001¯)-O surface have been studied with temperature programmed desorption (TPD) and XPS. Small amounts of formic acid dissociate at defect sites on clean ZnO(0001¯)-O to yield surface formate (HCOO). The acid D(H) from this dissociation does not reappear in TPD, and is lost to the ZnO bulk, as confirmed by nuclear reaction analysis. The surface HCOO decomposes to yield nearly simultaneous CO 2 (37%), CO (63%) and H 2 TPD peaks at 560 K. Substantial amounts of D (˜ 20%) are incorporated in this hydrogen TPD peak resulting from formate decomposition at ZnO defects, indicating that bulk D is readily accessible. Submonolayer and multilayer Cu films that are deposited at 130 K and partially cover the ZnO surface as 2D and 3D islands adsorb formic acid and decompose it into formate and hydrogen much like the Cu(110) surface. The surface formate from the Cu film decomposes at 470-500 K to give primarily CO 2 and H 2, also much like Cu(110), although atom-thin Cu islands also give ˜ 40% CO. Annealed Cu films give formate decomposition peaks at 25-50 K lower in temperature, attributed to thickening and ordering of the Cu islands to form Cu(111)-like sites. The acid D(H) atom from the formic acid is partially lost by hydrogen spillover from the Cu islands into the ZnO substrate, especially for thin Cu films. This effect partially desorbs and is enhanced upon preannealing the Cu layers, due to increased H diffusion rates across the annealed Cu islands, and/or the decrease in island size. Bulk D(H) is slowly removed as D 2, HD and H 2 above 400 K in diffusion-limited desorption, catalyzed by Cu.

The reaction of iodobenzene-p-sulphonyl chloride (pipsyl chloride) with certain amino acids and peptides, and with insulin

PubMed Central

Fletcher, J. C.

1967-01-01

1. A system of separation using buffered Celite columns is described that enables the pipsyl derivatives of most of the common amino acids to be separated. 2. The reaction of pipsyl chloride with several amino acids not included in previous studies has been investigated. In particular, knowledge of the acid-soluble pipsyl derivatives of arginine, histidine, lysine, tyrosine and cysteic acid has been extended. 3. Reproducible factors have been obtained that enable corrections to be applied for the breakdown of pipsylamino acids on acid hydrolysis. 4. The reaction of pipsyl chloride with peptides has been studied under various conditions. 5. The extent of the reaction between pipsyl chloride and insulin depends on the nature of the solvent–buffer system, and under the best conditions so far found is about 75% complete. 6. In an Appendix, the separation of pipsylamino acids by thin-layer chromatography is described. PMID:16742498

The effects of temperature and aeration on the corrosion of A508III low alloy steel in boric acid solutions at 25-95 °C

NASA Astrophysics Data System (ADS)

Xiao, Qian; Lu, Zhanpeng; Chen, Junjie; Yao, Meiyi; Chen, Zhen; Ejaz, Ahsan

2016-11-01

The effects of temperature, solution composition and dissolved oxygen on the corrosion rate and electrochemical behavior of an A508III low alloy steel in boric acid solution with lithium hydroxide at 25-95 °C are investigated. In aerated solutions, increasing the boric acid concentration increases the corrosion rate and the anodic current density. The corrosion rate in deaerated solutions increases with increasing temperature. A corrosion rate peak value is found at approximately 75 °C in aerated solutions. Increasing temperature increases the oxygen diffusion coefficient, decreases the dissolved oxygen concentration, accelerates the hydrogen evolution reaction, and accelerates both the active dissolution and the film forming reactions. Increasing dissolved oxygen concentration does not significantly affect the corrosion rate at 50 and 60 °C, increases the corrosion rate at 70 and 80 °C, and decreases the corrosion rate at 87.5 and 95 °C in a high concentration boric acid solution with lithium hydroxide.

Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK.

PubMed

Wang, Kaier; Steyn-Ross, Moira L; Steyn-Ross, D Alistair; Wilson, Marcus T; Sleigh, Jamie W; Shiraishi, Yoichi

2014-04-11

Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system's set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This "code-based" approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming skills, and the graphical interface lends itself to easy modification and use by non-experts.

Ordered mesoporous silica prepared by quiescent interfacial growth method - effects of reaction chemistry

PubMed Central

2013-01-01

Acidic interfacial growth can provide a number of industrially important mesoporous silica morphologies including fibers, spheres, and other rich shapes. Studying the reaction chemistry under quiescent (no mixing) conditions is important for understanding and for the production of the desired shapes. The focus of this work is to understand the effect of a number of previously untested conditions: acid type (HCl, HNO3, and H2SO4), acid content, silica precursor type (TBOS and TEOS), and surfactant type (CTAB, Tween 20, and Tween 80) on the shape and structure of products formed under quiescent two-phase interfacial configuration. Results show that the quiescent growth is typically slow due to the absence of mixing. The whole process of product formation and pore structuring becomes limited by the slow interfacial diffusion of silica source. TBOS-CTAB-HCl was the typical combination to produce fibers with high order in the interfacial region. The use of other acids (HNO3 and H2SO4), a less hydrophobic silica source (TEOS), and/or a neutral surfactant (Tweens) facilitate diffusion and homogenous supply of silica source into the bulk phase and give spheres and gyroids with low mesoporous order. The results suggest two distinct regions for silica growth (interfacial region and bulk region) in which the rate of solvent evaporation and local concentration affect the speed and dimension of growth. A combined mechanism for the interfacial bulk growth of mesoporous silica under quiescent conditions is proposed. PMID:24237719

Existence and exponential stability of traveling waves for delayed reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Hsu, Cheng-Hsiung; Yang, Tzi-Sheng; Yu, Zhixian

2018-03-01

The purpose of this work is to investigate the existence and exponential stability of traveling wave solutions for general delayed multi-component reaction-diffusion systems. Following the monotone iteration scheme via an explicit construction of a pair of upper and lower solutions, we first obtain the existence of monostable traveling wave solutions connecting two different equilibria. Then, applying the techniques of weighted energy method and comparison principle, we show that all solutions of the Cauchy problem for the considered systems converge exponentially to traveling wave solutions provided that the initial perturbations around the traveling wave fronts belong to a suitable weighted Sobolev space.

[Removal Kinetics and Mechanism of Aniline by Manganese-oxide-modified Diatomite].

PubMed

Xiao, Shao-dan; Liu, Lu; Jiang, Li-ying; Chen, Jian-meng

2015-06-01

A novel rapid green one-step method was developed for the preparation of manganese modified diatomite (Mn-D) by treating roasted diatomite with an acidic permanganate solution. The effects of calcination temperature and mass ratio of KMnO4 and diatomite (p) on aniline removal efficiency of Mn-D were investigated. The removal kinetics and mechanism of aniline by Mn-D were also discussed. The results showed that when the optimal calcination temperature was 450 degrees C, p was 1.6, and the loading amounts of δ-MnO2 was 0.82 g x g(-1), Mn-D had a great performance for aniline removal, and more than 80% of aniline was adsorbed within 10 minutes, accompanied with the release of Mn2+. In acidic conditions, the adsorption process on Mn-D followed pseudo-second-order and was mainly controlled by intra-particle diffusion. The best fitting of the experimental adsorption data was given by the Freundlich equation. Gas chromatograph-mass spectrometer was applied to identify the reaction intermediates at different times, and azobenzene was found to be the main reaction intermediate in the degradation system. Based on the above observations, the possible degradation pathway of aniline by Mn-D was proposed.

Volatile Emissions from Hot Spring Basin, Yellowstone National Park, USA

NASA Astrophysics Data System (ADS)

Werner, C.; Hurwitz, S.; Bergfeld, D.; Evans, W. C.; Lowenstern, J. B.; Jaworowski, C.; Heasler, H.

2007-12-01

The flux and composition of magmatic volatiles were characterized for Hot Spring Basin (HSB), Yellowstone National Park, in August 2006. Diffuse fluxes of CO2 (228 sites) from thermal soil were elevated, with a population distribution similar to that of other acid-sulfate areas in Yellowstone. Thus the estimated diffuse emission rate at HSB is proportionately larger than other areas due to its large area, and could be as high as 1000 td-1 CO2. The diffuse flux of H2S was only above detection limits at 20 of the 31 sites measured. The estimated diffuse H2S emission rate was ~ 4 td-1. Good correlation exists between the log of CO2 flux and shallow soil temperatures, indicating linked steam and gas upflow in the subsurface. The correlation between CO2 and H2S fluxes is weak, and the CO2 / H2S diffuse flux ratio was higher than in fumarolic ratios of CO2 to H2S. This suggests that various reactions, e.g., native sulfur deposition, act to remove H2S from the original gas stream in the diffuse low- temperature environment. Dissolved sulfate flux through Shallow Creek, which drains part of HSB, was ~ 4 td-1. Comparing dissolved sulfate flux to estimates of primary emission of H2S based on fumarolic gas geochemistry gives first order estimates of the sulfur consumed in surficial or subsurface mineral deposition. Total C and S outputs from HSB are comparable to other active volcanic systems.

Semi-implicit integration factor methods on sparse grids for high-dimensional systems

NASA Astrophysics Data System (ADS)

Wang, Dongyong; Chen, Weitao; Nie, Qing

2015-07-01

Numerical methods for partial differential equations in high-dimensional spaces are often limited by the curse of dimensionality. Though the sparse grid technique, based on a one-dimensional hierarchical basis through tensor products, is popular for handling challenges such as those associated with spatial discretization, the stability conditions on time step size due to temporal discretization, such as those associated with high-order derivatives in space and stiff reactions, remain. Here, we incorporate the sparse grids with the implicit integration factor method (IIF) that is advantageous in terms of stability conditions for systems containing stiff reactions and diffusions. We combine IIF, in which the reaction is treated implicitly and the diffusion is treated explicitly and exactly, with various sparse grid techniques based on the finite element and finite difference methods and a multi-level combination approach. The overall method is found to be efficient in terms of both storage and computational time for solving a wide range of PDEs in high dimensions. In particular, the IIF with the sparse grid combination technique is flexible and effective in solving systems that may include cross-derivatives and non-constant diffusion coefficients. Extensive numerical simulations in both linear and nonlinear systems in high dimensions, along with applications of diffusive logistic equations and Fokker-Planck equations, demonstrate the accuracy, efficiency, and robustness of the new methods, indicating potential broad applications of the sparse grid-based integration factor method.

Enhanced hydroxyl radical generation in the combined ozonation and electrolysis process using carbon nanotubes containing gas diffusion cathode.

PubMed

Wu, Donghai; Lu, Guanghua; Zhang, Ran; Lin, Qiuhong; Yan, Zhenhua; Liu, Jianchao; Li, Yi

2015-10-01

Combination of ozone together with electrolysis (ozone-electrolysis) is a promising wastewater treatment technology. This work investigated the potential use of carbon nanotube (CNT)-based gas diffusion cathode (GDC) for ozone-electrolysis process employing hydroxyl radicals (·OH) production as an indicator. Compared with conventional active carbon (AC)-polytetrafluoroethylene (PTFE) and carbon black (CB)-PTFE cathodes, the production of ·OH in the coupled process was improved using CNTs-PTFE GDC. Appropriate addition of acetylene black (AB) and pore-forming agent Na2SO4 could enhance the efficiency of CNTs-PTFE GDC. The optimum GDC composition was obtained by response surface methodology (RSM) analysis and was determined as CNTs 31.2 wt%, PTFE 60.6 wt%, AB 3.5 wt%, and Na2SO4 4.7 wt%. Moreover, the optimized CNT-based GDC exhibited much more effective than traditional Ti and graphite cathodes in Acid Orange 7 (AO7) mineralization and possessed the desirable stability without performance decay after ten times reaction. The comparison tests revealed that peroxone reaction was the main pathway of ·OH production in the present system, and cathodic reduction of ozone could significantly promote ·OH generation. These results suggested that application of CNT-based GDC offers considerable advantages in ozone-electrolysis of organic wastewater.

Removal of dieldrin from aqueous solution by a novel triolein-embedded composite adsorbent.

PubMed

Ru, Jia; Liu, Huijuan; Qu, Jiuhui; Wang, Aimin; Dai, Ruihua

2007-03-06

In this study, a novel triolein-embedded activated carbon composite adsorbent (CA-T) was prepared and applied for the adsorption and removal of dieldrin from aqueous systems. Experiments were carried out to investigate the adsorption behavior of dieldrin on CA-T, including adsorption isotherms, adsorption kinetics, the influence of initial concentration, temperature, shaking speed, pH and the addition of humic acid (HA) on adsorption. The adsorption isotherms accorded with Freundlich equation. Three kinetics models, including pseudo-first-order, pseudo-second-order and intraparticle diffusion models, were used to fit the experimental data. By comparing the correlation coefficients, it was found that both pseudo-second-order and intraparticle diffusion models were used to well describe the adsorption of dieldrin on CA-T. The addition of HA had little effect on dieldrin adsorption by CA-T. Results indicated that CA-T appeared to be a promising adsorbent for removing lipophilic dieldrin in trace amount, which was advantageous over pure granular activated carbon (GAC). The adsorption rate increased with increasing shaking speed, initial concentration and temperature, and remained almost unchanged in the pH range of 4-8. Thermodynamic calculations indicated that the adsorption reaction was spontaneous with a high affinity and the adsorption was an endothermic reaction.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santhanagopalan, Shriram; White, Ralph E.

Rotating ring disc electrode (RRDE) experiments are a classic tool for investigating kinetics of electrochemical reactions. Several standardized methods exist for extracting transport parameters and reaction rate constants using RRDE measurements. Here in this work, we compare some approximate solutions to the convective diffusion used popularly in the literature to a rigorous numerical solution of the Nernst-Planck equations coupled to the three dimensional flow problem. In light of these computational advancements, we explore design aspects of the RRDE that will help improve sensitivity of our parameter estimation procedure to experimental data. We use the oxygen reduction in acidic media involvingmore » three charge transfer reactions and a chemical reaction as an example, and identify ways to isolate reaction currents for the individual processes in order to accurately estimate the exchange current densities.« less

Extracellular Electron Transfer and Survival Strategies in Acid Mine Drainage Impacted Soils

NASA Astrophysics Data System (ADS)

Gorby, Y. A.; Senko, J.

2011-12-01

Acid mine drainage (AMD) is a prominent and increasing problem in the greater Appalachian region of the United States and throughout the world. Recognition of the importance of extracellular electron transfer (EET) in microbial communities has provided a fertile research environment for multidisciplinary collaborations to emerge and effectively address complex questions with important environmental implications. Our research focuses on the components, strategies and mechanisms of EET in soil systems impacted by AMD and extends to other biogeochemical systems typified by steep redox gradients. Organisms within acid mine drainage use Fe(II) as their primary electron donor and couple Fe(II) oxidation to the reduction of oxygen as the terminal electron acceptor. Biogenic minerals formed by this process completely encase microbes in think deposits that would seem to limit diffusion of both Fe(II) and O2 for access by the organisms. We have developed methods for catalytically removing biogenic minerals revealing microorganisms and a fine network of filamentous extracellular material. Here we present a status report of our efforts to characterize the molecular and electronic properties of these filaments and to address the hypothesis that at least some of these filaments are electrically conductive microbial nanowires that facilitate electron transfer reactions within this complex biogeochemical system.

Nanoparticle bioconjugates as "bottom-up" assemblies of artifical multienzyme complexes

NASA Astrophysics Data System (ADS)

Keighron, Jacqueline D.

2010-11-01

The sequential enzymes of several metabolic pathways have been shown to exist in close proximity with each other in the living cell. Although not proven in all cases, colocalization may have several implications for the rate of metabolite formation. Proximity between the sequential enzymes of a metabolic pathway has been proposed to have several benefits for the overall rate of metabolite formation. These include reduced diffusion distance for intermediates, sequestering of intermediates from competing pathways and the cytoplasm. Restricted diffusion in the vicinity of an enzyme can also cause the pooling of metabolites, which can alter reaction equilibria to control the rate of reaction through inhibition. Associations of metabolic enzymes are difficult to isolate ex vivo due to the weak interactions believed to colocalize sequential enzymes within the cell. Therefore model systems in which the proximity and diffusion of intermediates within the experiment system are controlled are attractive alternatives to explore the effects of colocalization of sequential enzymes. To this end three model systems for multienzyme complexes have been constructed. Direct adsorption enzyme:gold nanoparticle bioconjugates functionalized with malate dehydrogenase (MDH) and citrate synthase (CS) allow for proximity between to the enzymes to be controlled from the nanometer to micron range. Results show that while the enzymes present in the colocalized and non-colocalized systems compared here behaved differently overall the sequential activity of the pathway was improved by (1) decreasing the diffusion distance between active sites, (2) decreasing the diffusion coefficient of the reaction intermediate to prevent escape into the bulk solution, and (3) decreasing the overall amount of bioconjugate in the solution to prevent the pathway from being inhibited by the buildup of metabolite over time. Layer-by-layer (LBL) assemblies of MDH and CS were used to examine the layering effect of sequential enzymes found in multienzyme complexes such as the pyruvate dehydrogenase complex (PDC). By controlling the orientation of enzymes in the complex (i.e. how deeply embedded each enzyme is) it was hypothesized that differences in sequential activity would determine an optimal orientation for a multienzyme complex. It was determined during the course of these experiments that the polyelectrolyte (PE) assembly itself served to slow diffusion of intermediates, leading to a buildup of oxaloacetate within the PE layers to form a pool of metabolite that equalized the rate of sequential reaction between the different orientations tested. Hexahistidine tag -- Ni(II) nitriliotriacetic acid (NTA) chemistry is an attractive method to control the proximity between sequential enzymes because each enzyme can be bound in a specific orientation, with minimal loss of activity, and the interaction is reversible. Modifying gold nanoparticles or large unilamellar vesicles with this functionality allows for another class of model to be constructed in which proximity between enzymes is dynamic. Some metabolic pathways (such as the de novo purine biosynthetic pathway), have demonstrated dynamic proximity of sequential enzymes in response to specific cellular stimuli. Results indicate that Ni(II)NTA scaffolds immobilize histidine-tagged enzymes non-destructively, with a near 100% reversibility. This model can be used to demonstrate the possible implications of dynamic proximity such as pathway regulation. Insight into the benefits and mechanisms of sequential enzyme colocalization can enhance the general understanding of cellular processes, as well as allow for the development of new and innovative ways to modulate pathway activity. This may provide new designs for treatments of metabolic diseases and cancer, where metabolic pathways are altered.

[Alcohol intake--a two-edged sword. Part 1: metabolism and pathogenic effects of alcohol].

PubMed

Ströhle, Alexander; Wolters, Maike; Hahn, Andreas

2012-08-01

From the biomedical point of view alcohol is a Janus-faced dietary component with a dose-dependent effect varying from cardiovascular protection to cytotoxicity. Alcohol is absorbed in the upper gastrointestinal tract by passive diffusion, is quickly distributed throughout body water and is mostly eliminated through oxidation. The enzymatically-catalyzed oxidative degradation to acetaldehyde and further to acetate is primarily localized in the liver. In case of a low blood alcohol concentration (<0.5 per thousand) alcohol is predominantely metabolized by the enzyme aldehyde dehydrogenase; higher blood concentrations (>0.5 per thousand) are increasingly oxidized by the microsomal ethanoloxidizing system (MEOS). Alcohol consumption induces several metabolic reactions as well as acute effects on the central nervous system. Chronic alcohol consumption to some extent irreparably damages nearly every organ with the liver being particularly concerned. There are three stages of alcohol-induced liver disease (fatty liver, alcohol hepatitis, liver cirrhosis) and the liver damages mainly result from reaction products of alcohol degradation (acetaldehyde, NADH and reactive oxygen species). An especially dreaded clinical complication of the alcohol-induced liver disease is the hepatic encephalopathy. Its pathogenesis is a multifactorial and self-perpetuating process with the swelling of astrocytes being a crucial point. Swollen astrocytes induce several reactions such as oxidative/nitrosative stress, impaired signal transduction, protein modifications and a modified gene expression profile. The swelling of astrocytes and the change in neuronal activity are attributed to several neurotoxins, especially ammonia and aromatic amino acids. In alcohol addicted subjects multiple micronutrient deficiencies are common. The status of folic acid, thiamine, pyridoxine and zinc is especially critical.

Chemical ageing and transformation of diffusivity in semi-solid multi-component organic aerosol particles

NASA Astrophysics Data System (ADS)

Pfrang, C.; Shiraiwa, M.; Pöschl, U.

2011-04-01

Recent experimental evidence underlines the importance of reduced diffusivity in amorphous semi-solid or glassy atmospheric aerosols. This paper investigates the impact of diffusivity on the ageing of multi-component reactive organic particles representative of atmospheric cooking aerosols. We apply and extend the recently developed KM-SUB model in a study of a 12-component mixture containing oleic and palmitoleic acids. We demonstrate that changes in the diffusivity may explain the evolution of chemical loss rates in ageing semi-solid particles, and we resolve surface and bulk processes under transient reaction conditions considering diffusivities altered by oligomerisation. This new model treatment allows prediction of the ageing of mixed organic multi-component aerosols over atmospherically relevant time scales and conditions. We illustrate the impact of changing diffusivity on the chemical half-life of reactive components in semi-solid particles, and we demonstrate how solidification and crust formation at the particle surface can affect the chemical transformation of organic aerosols.

Chemical ageing and transformation of diffusivity in semi-solid multi-component organic aerosol particles

NASA Astrophysics Data System (ADS)

Pfrang, C.; Shiraiwa, M.; Pöschl, U.

2011-07-01

Recent experimental evidence underlines the importance of reduced diffusivity in amorphous semi-solid or glassy atmospheric aerosols. This paper investigates the impact of diffusivity on the ageing of multi-component reactive organic particles approximating atmospheric cooking aerosols. We apply and extend the recently developed KM-SUB model in a study of a 12-component mixture containing oleic and palmitoleic acids. We demonstrate that changes in the diffusivity may explain the evolution of chemical loss rates in ageing semi-solid particles, and we resolve surface and bulk processes under transient reaction conditions considering diffusivities altered by oligomerisation. This new model treatment allows prediction of the ageing of mixed organic multi-component aerosols over atmospherically relevant timescales and conditions. We illustrate the impact of changing diffusivity on the chemical half-life of reactive components in semi-solid particles, and we demonstrate how solidification and crust formation at the particle surface can affect the chemical transformation of organic aerosols.

Surface acid-base behaviors of Chinese loess.

PubMed

Chu, Zhaosheng; Liu, Wenxin; Tang, Hongxiao; Qian, Tianwei; Li, Shushen; Li, Zhentang; Wu, Guibin

2002-08-15

Acid-base titration was applied to investigate the surface acid-base properties of a Chinese loess sample at different ionic strengths. The acidimetric supernatant was regarded as the system blank of titration to correct the influence of particle dissolution on the estimation of proton consumption. The titration behavior of the system blank could be described by the hydrolysis of Al3+ and Si(OH)4 in aqueous solution as well as the production of hydroxyaluminosilicates. The formation of Al-Si species on homogeneous surface sites by hydrous aluminum and silicic acid, released from solid substrate during the acidic titration, was considered in the model description of the back-titration procedure. A surface reaction model was suggested as follows: >SOH<-->SO(-)+H+, pK(a)(int)=3.48-3.98;>SOH+Al(3+)+H4SiO4<-->SOAl(OSi(OH)3(+)+2H+, pK(SC)=3.48-4.04. Two simple surface complexation models accounted for the interfacial structure, i.e., the constant capacitance model (CCM) and the diffuse layer model (DLM), and gave a satisfactory description of the experimental data. Considering the effect of ionic strength on the electrostatic profile at the solid-aqueous interface, the DLM was appropriate at the low concentrations (0.01 and 0.005 mol/L) of background electrolyte (NaNO3 in this study), while the CCM was preferable in the case of high ionic strength (0.1 mol/L).

An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Padgett, Jill M. A.; Ilie, Silvana, E-mail: silvana@ryerson.ca

2016-03-15

Stochastic modelling is critical for studying many biochemical processes in a cell, in particular when some reacting species have low population numbers. For many such cellular processes the spatial distribution of the molecular species plays a key role. The evolution of spatially heterogeneous biochemical systems with some species in low amounts is accurately described by the mesoscopic model of the Reaction-Diffusion Master Equation. The Inhomogeneous Stochastic Simulation Algorithm provides an exact strategy to numerically solve this model, but it is computationally very expensive on realistic applications. We propose a novel adaptive time-stepping scheme for the tau-leaping method for approximating themore » solution of the Reaction-Diffusion Master Equation. This technique combines effective strategies for variable time-stepping with path preservation to reduce the computational cost, while maintaining the desired accuracy. The numerical tests on various examples arising in applications show the improved efficiency achieved by the new adaptive method.« less

Spatiotemporal patterns in reaction-diffusion system and in a vibrated granular bed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swinney, H.L.; Lee, K.J.; McCormick, W.D.

Experiments on a quasi-two-dimensional reaction-diffusion system reveal transitions from a uniform state to stationary hexagonal, striped, and rhombic spatial patterns. For other reactor conditions lamellae and self-replicating spot patterns are observed. These patterns form in continuously fed thin gel reactors that can be maintained indefinitely in well-defined nonequilibrium states. Reaction-diffusion models with two chemical species yield patterns similar to those observed in the experiments. Pattern formation is also being examined in vertically oscillated thin granular layers (typically 3-30 particle diameters deep). For small acceleration amplitudes, a granular layer is flat, but above a well-defined critical acceleration amplitude, spatial patterns spontaneouslymore » form. Disordered time-dependent granular patterns are observed as well as regular patterns of squares, stripes, and hexagons. A one-dimensional model consisting of a completely inelastic ball colliding with a sinusoidally oscillating platform provides a semi-quantitative description of most of the observed bifurcations between the different spatiotemporal regimes.« less

Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling

PubMed Central

Kekenes-Huskey, Peter M.; Eun, Changsun; McCammon, J. A.

2015-01-01

Biochemical reaction networks consisting of coupled enzymes connect substrate signaling events with biological function. Substrates involved in these reactions can be strongly influenced by diffusion “barriers” arising from impenetrable cellular structures and macromolecules, as well as interactions with biomolecules, especially within crowded environments. For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non-specific crowders, and specific-binders (buffers) strongly controls the temporal and spatial reaction kinetics. In this study, we use two prototypical biochemical reactions, a Goodwin oscillator, and a reaction with a periodic source/sink term to examine how a diffusion barrier that partitions substrates controls reaction behavior. Namely, we examine how conditions representative of a densely packed cytosol, including reduced accessible volume fraction, non-specific interactions, and buffers, impede diffusion over nanometer length-scales. We find that diffusion barriers can modulate the frequencies and amplitudes of coupled diffusion-influenced reaction networks, as well as give rise to “compartments” of decoupled reactant populations. These effects appear to be intensified in the presence of buffers localized to the diffusion barrier. These findings have strong implications for the role of the cellular environment in tuning the dynamics of signaling pathways. PMID:26342355

Numerical simulation of the interaction of transport, diffusion and chemical reactions in an urban plume

NASA Technical Reports Server (NTRS)

Vogel, Bernhard; Vogel, Heike; Fiedler, Franz

1994-01-01

A model system is presented that takes into account the main physical and chemical processes on the regional scale here in an area of 100x100 sq km. The horizontal gridsize used is 2x2 sq km. For a case study, it is demonstrated how the model system can be used to separate the contributions of the processes advection, turbulent diffusion, and chemical reactions to the diurnal cycle of ozone. In this way, typical features which are visible in observations and are reproduced by the numerical simulations can be interpreted.

Square Turing patterns in reaction-diffusion systems with coupled layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jing; Wang, Hongli, E-mail: hlwang@pku.edu.cn, E-mail: qi@pku.edu.cn; Center for Quantitative Biology, Peking University, Beijing 100871

Square Turing patterns are usually unstable in reaction-diffusion systems and are rarely observed in corresponding experiments and simulations. We report here an example of spontaneous formation of square Turing patterns with the Lengyel-Epstein model of two coupled layers. The squares are found to be a result of the resonance between two supercritical Turing modes with an appropriate ratio. Besides, the spatiotemporal resonance of Turing modes resembles to the mode-locking phenomenon. Analysis of the general amplitude equations for square patterns reveals that the fixed point corresponding to square Turing patterns is stationary when the parameters adopt appropriate values.

Efficient numerical simulation of non-integer-order space-fractional reaction-diffusion equation via the Riemann-Liouville operator

NASA Astrophysics Data System (ADS)

Owolabi, Kolade M.

2018-03-01

In this work, we are concerned with the solution of non-integer space-fractional reaction-diffusion equations with the Riemann-Liouville space-fractional derivative in high dimensions. We approximate the Riemann-Liouville derivative with the Fourier transform method and advance the resulting system in time with any time-stepping solver. In the numerical experiments, we expect the travelling wave to arise from the given initial condition on the computational domain (-∞, ∞), which we terminate in the numerical experiments with a large but truncated value of L. It is necessary to choose L large enough to allow the waves to have enough space to distribute. Experimental results in high dimensions on the space-fractional reaction-diffusion models with applications to biological models (Fisher and Allen-Cahn equations) are considered. Simulation results reveal that fractional reaction-diffusion equations can give rise to a range of physical phenomena when compared to non-integer-order cases. As a result, most meaningful and practical situations are found to be modelled with the concept of fractional calculus.

Molecules in motion: influences of diffusion on metabolic structure and function in skeletal muscle.

PubMed

Kinsey, Stephen T; Locke, Bruce R; Dillaman, Richard M

2011-01-15

Metabolic processes are often represented as a group of metabolites that interact through enzymatic reactions, thus forming a network of linked biochemical pathways. Implicit in this view is that diffusion of metabolites to and from enzymes is very fast compared with reaction rates, and metabolic fluxes are therefore almost exclusively dictated by catalytic properties. However, diffusion may exert greater control over the rates of reactions through: (1) an increase in reaction rates; (2) an increase in diffusion distances; or (3) a decrease in the relevant diffusion coefficients. It is therefore not surprising that skeletal muscle fibers have long been the focus of reaction-diffusion analyses because they have high and variable rates of ATP turnover, long diffusion distances, and hindered metabolite diffusion due to an abundance of intracellular barriers. Examination of the diversity of skeletal muscle fiber designs found in animals provides insights into the role that diffusion plays in governing both rates of metabolic fluxes and cellular organization. Experimental measurements of metabolic fluxes, diffusion distances and diffusion coefficients, coupled with reaction-diffusion mathematical models in a range of muscle types has started to reveal some general principles guiding muscle structure and metabolic function. Foremost among these is that metabolic processes in muscles do, in fact, appear to be largely reaction controlled and are not greatly limited by diffusion. However, the influence of diffusion is apparent in patterns of fiber growth and metabolic organization that appear to result from selective pressure to maintain reaction control of metabolism in muscle.

Combined cross-linked enzyme aggregates of horseradish peroxidase and glucose oxidase for catalyzing cascade chemical reactions.

PubMed

Nguyen, Le Truc; Yang, Kun-Lin

2017-05-01

Cascade reactions involved unstable intermediates are often encountered in biological systems. In this study, we developed combined cross-linked enzyme aggregates (combi-CLEA) to catalyze a cascade reaction which involves unstable hydrogen peroxide as an intermediate. The combi-CLEA contains two enzymes̶ glucose oxidase (GOx) and horseradish peroxidase (HRP) which are cross-linked together as solid aggregates. The first enzyme GOx catalyzes the oxidation of glucose and produces hydrogen peroxide, which is used by the second enzyme HRP to oxidize 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). The apparent reaction rate of the cascade reaction reaches 10.5±0.5μM/min when the enzyme ratio is 150:1 (GOx:HRP). Interestingly, even in the presence of catalase, an enzyme that quickly decomposes hydrogen peroxide, the reaction rate only decreases by 18.7% to 8.3±0.3μM/min. This result suggests that the intermediate hydrogen peroxide is not decomposed by catalase due to a short diffusion distance between GOx and HRP in the combi-CLEA. Scanning electron microscopy images suggest that combi-CLEA particles are hollow spheres and have an average diameter around 250nm. Because of their size, combi-CLEA particles can be entrapped inside a nylon membrane for detecting glucose by using the cascade reaction. Copyright © 2017 Elsevier Inc. All rights reserved.

The chemistry and diffusion of aircraft exhausts in the lower stratosphere during the first few hours after fly-by. [with attention to ozone depletion by SST exhaust plumes

NASA Technical Reports Server (NTRS)

Hilst, G. R.

1974-01-01

An analysis of the hydrogen-nitrogen-oxygen reaction systems in the lower stratosphere as they are initially perturbed by individual aircraft engine exhaust plumes was conducted in order to determine whether any significant chemical reactions occur, either among exhaust chemical species, or between these species and the environmental ozone, while the exhaust products are confined to intact plume segments at relatively high concentrations. The joint effects of diffusive mixing and chemical kinetics on the reactions were also studied, using the techniques of second-order closure diffusion/chemistry models. The focus of the study was on the larger problem of the potential depletion of ozone by supersonic transport aircraft exhaust materials emitted into the lower stratosphere.

A numerical solution for a variable-order reaction-diffusion model by using fractional derivatives with non-local and non-singular kernel

NASA Astrophysics Data System (ADS)

Coronel-Escamilla, A.; Gómez-Aguilar, J. F.; Torres, L.; Escobar-Jiménez, R. F.

2018-02-01

A reaction-diffusion system can be represented by the Gray-Scott model. The reaction-diffusion dynamic is described by a pair of time and space dependent Partial Differential Equations (PDEs). In this paper, a generalization of the Gray-Scott model by using variable-order fractional differential equations is proposed. The variable-orders were set as smooth functions bounded in (0 , 1 ] and, specifically, the Liouville-Caputo and the Atangana-Baleanu-Caputo fractional derivatives were used to express the time differentiation. In order to find a numerical solution of the proposed model, the finite difference method together with the Adams method were applied. The simulations results showed the chaotic behavior of the proposed model when different variable-orders are applied.

Unimolecular diffusion-mediated reactions with a nonrandom time-modulated absorbing barrier

NASA Technical Reports Server (NTRS)

Bashford, D.; Weaver, D. L.

1986-01-01

A diffusion-reaction model with time-dependent reactivity is formulated and applied to unimolecular reactions. The model is solved exactly numerically and approximately analytically for the unreacted fraction as a function of time. It is shown that the approximate analytical solution is valid even when the system is far from equilibrium, and when the reactivity probability is more complicated than a square-wave function of time. A discussion is also given of an approach to problems of this type using a stochastically fluctuating reactivity, and the first-passage time for a particular example is derived.

Resist image quality control via acid diffusion constant and/or photodecomposable quencher concentration in the fabrication of 11 nm half-pitch line-and-space patterns using extreme-ultraviolet lithography

NASA Astrophysics Data System (ADS)

Kozawa, Takahiro; Santillan, Julius Joseph; Itani, Toshiro

2018-05-01

Extreme-ultraviolet (EUV) lithography will be applied to the high-volume production of semiconductor devices with 16 nm half-pitch resolution and is expected to be extended to that of devices with 11 nm half-pitch resolution. With the reduction in the feature sizes, the control of acid diffusion becomes a significant concern. In this study, the dependence of resist image quality on T PEB D acid and photodecomposable quencher concentration was investigated by the Monte Carlo method on the basis of the sensitization and reaction mechanisms of chemically amplified EUV resists. Here, T PEB and D acid are the postexposure baking (PEB) time and the acid diffusion constant, respectively. The resist image quality of 11 nm line-and-space patterns is discussed in terms of line edge roughness (LER) and stochastic defect generation. For the minimization of LER, it is necessary to design and control not only the photodecomposable quencher concentration but also T PEB D acid. In this case, D acid should be adjusted to be 0.3–1.5 nm2 s‑1 for a PEB time of 60 s with optimization of the balance among LER and stochastic pinching and bridging. Even if it is difficult to decrease D acid to the range of 0.3–1.5 nm2 s‑1, the image quality can still be controlled via only the photodecomposable quencher concentration, although LER and stochastic pinching and bridging are slightly increased. In this case, accurate control of the photodecomposable quencher concentration and the reduction in the initial standard deviation of the number of protected units are required.

System for chemically digesting low level radioactive, solid waste material

DOEpatents

Cowan, Richard G.; Blasewitz, Albert G.

1982-01-01

An improved method and system for chemically digesting low level radioactive, solid waste material having a high through-put. The solid waste material is added to an annular vessel (10) substantially filled with concentrated sulfuric acid. Concentrated nitric acid or nitrogen dioxide is added to the sulfuric acid within the annular vessel while the sulfuric acid is reacting with the solid waste. The solid waste is mixed within the sulfuric acid so that the solid waste is substantilly fully immersed during the reaction. The off gas from the reaction and the products slurry residue is removed from the vessel during the reaction.

A generalized reaction diffusion model for spatial structure formed by motile cells.

PubMed

Ochoa, F L

1984-01-01

A non-linear stability analysis using a multi-scale perturbation procedure is carried out on a model of a generalized reaction diffusion mechanism which involves only a single equation but which nevertheless exhibits bifurcation to non-uniform states. The patterns generated by this model by variation in a parameter related to the scalar dimensions of domain of definition, indicate its capacity to represent certain key morphogenetic features of multicellular systems formed by motile cells.

Changes in Effective Thermal Conductivity During the Carbothermic Reduction of Magnetite Using Graphite

NASA Astrophysics Data System (ADS)

Kiamehr, Saeed; Ahmed, Hesham; Viswanathan, Nurni; Seetharaman, Seshadri

2017-06-01

Knowledge of the effective thermal diffusivity changes of systems undergoing reactions where heat transfer plays an important role in the reaction kinetics is essential for process understanding and control. Carbothermic reduction process of magnetite containing composites is a typical example of such systems. The reduction process in this case is highly endothermic and hence, the overall rate of the reaction is greatly influenced by the heat transfer through composite compact. Using Laser-Flash method, the change of effective thermal diffusivity of magnetite-graphite composite pellet was monitored in the dynamic mode over a pre-defined thermal cycle (heating at the rate of 7 K/min to 1423 K (1150 °C), holding the sample for 270 minutes at this temperature and then cooling it down to the room temperature at the same rate as heating). These measurements were supplemented by Thermogravimetric Analysis under comparable experimental conditions as well as quenching tests of the samples in order to combine the impact of various factors such as sample dilatations and changes in apparent density on the progress of the reaction. The present results show that monitoring thermal diffusivity changes during the course of reduction would be a very useful tool in a total understanding of the underlying physicochemical phenomena. At the end, effort is made to estimate the apparent thermal conductivity values based on the measured thermal diffusivity and dilatations.

Kinetics of intercalation of fluorescent probes in magnesium-aluminium layered double hydroxide within a multiscale reaction-diffusion framework

NASA Astrophysics Data System (ADS)

Saliba, Daniel; Al-Ghoul, Mazen

2016-11-01

We report the synthesis of magnesium-aluminium layered double hydroxide (LDH) using a reaction-diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium-aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK

PubMed Central

2014-01-01

Background Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system’s set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This “code-based” approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. Results As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. Conclusions The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming skills, and the graphical interface lends itself to easy modification and use by non-experts. PMID:24725437

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chevalier, Michael W., E-mail: Michael.Chevalier@ucsf.edu; El-Samad, Hana, E-mail: Hana.El-Samad@ucsf.edu

Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation timesmore » of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.« less

Experimental and modeling study of a two-stage pilot scale high solid anaerobic digester system.

PubMed

Yu, Liang; Zhao, Quanbao; Ma, Jingwei; Frear, Craig; Chen, Shulin

2012-11-01

This study established a comprehensive model to configure a new two-stage high solid anaerobic digester (HSAD) system designed for highly degradable organic fraction of municipal solid wastes (OFMSW). The HSAD reactor as the first stage was naturally separated into two zones due to biogas floatation and low specific gravity of solid waste. The solid waste was retained in the upper zone while only the liquid leachate resided in the lower zone of the HSAD reactor. Continuous stirred-tank reactor (CSTR) and advective-diffusive reactor (ADR) models were constructed in series to describe the whole system. Anaerobic digestion model No. 1 (ADM1) was used as reaction kinetics and incorporated into each reactor module. Compared with the experimental data, the simulation results indicated that the model was able to well predict the pH, volatile fatty acid (VFA) and biogas production. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes.

PubMed

Ovchinnikov, Victor; Nam, Kwangho; Karplus, Martin

2016-08-25

A method is developed to obtain simultaneously free energy profiles and diffusion constants from restrained molecular simulations in diffusive systems. The method is based on low-order expansions of the free energy and diffusivity as functions of the reaction coordinate. These expansions lead to simple analytical relationships between simulation statistics and model parameters. The method is tested on 1D and 2D model systems; its accuracy is found to be comparable to or better than that of the existing alternatives, which are briefly discussed. An important aspect of the method is that the free energy is constructed by integrating its derivatives, which can be computed without need for overlapping sampling windows. The implementation of the method in any molecular simulation program that supports external umbrella potentials (e.g., CHARMM) requires modification of only a few lines of code. As a demonstration of its applicability to realistic biomolecular systems, the method is applied to model the α-helix ↔ β-sheet transition in a 16-residue peptide in implicit solvent, with the reaction coordinate provided by the string method. Possible modifications of the method are briefly discussed; they include generalization to multidimensional reaction coordinates [in the spirit of the model of Ermak and McCammon (Ermak, D. L.; McCammon, J. A. J. Chem. Phys. 1978, 69, 1352-1360)], a higher-order expansion of the free energy surface, applicability in nonequilibrium systems, and a simple test for Markovianity. In view of the small overhead of the method relative to standard umbrella sampling, we suggest its routine application in the cases where umbrella potential simulations are appropriate.

Anomalous diffusion with linear reaction dynamics: from continuous time random walks to fractional reaction-diffusion equations.

PubMed

Henry, B I; Langlands, T A M; Wearne, S L

2006-09-01

We have revisited the problem of anomalously diffusing species, modeled at the mesoscopic level using continuous time random walks, to include linear reaction dynamics. If a constant proportion of walkers are added or removed instantaneously at the start of each step then the long time asymptotic limit yields a fractional reaction-diffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps then the long time asymptotic limit has a standard linear reaction kinetics term but a fractional order temporal derivative operating on a nonstandard diffusion term. Results from the above two models are compared with a phenomenological model with standard linear reaction kinetics and a fractional order temporal derivative operating on a standard diffusion term. We have also developed further extensions of the CTRW model to include more general reaction dynamics.

Reaction-diffusion controlled growth of complex structures

NASA Astrophysics Data System (ADS)

Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

2013-03-01

Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support

Management of the diffusion of 4-methylumbelliferone across phases in microdroplet-based systems for in vitro protein evolution.

PubMed

Wu, Nan; Courtois, Fabienne; Zhu, Yonggang; Oakeshott, John; Easton, Chris; Abell, Chris

2010-09-01

Fluorongenic reagents based on 4-methylumbelliferone (4-MU) have been widely used for the detection of phosphatase, sulfatase, esterase, lipase and glycosidase activities in conventionally formatted enzyme assay systems. However, the sensitivity of assays based on these substrates is also potentially very useful in the microdroplet formats now being developed for high throughput in vitro evolution experiments. In this article, we report the investigation of diffusion of 4-MU as a model dye from water-in-oil droplets and the internal aqueous phase of water-in-oil-in-water droplets in microfluidics. The effect of BSA in the aqueous phase on the diffusion of 4-MU is also discussed. Based on these results, we provided here proof-of-concept of the reaction of the enzyme OpdA with the substrate coumaphos in water-in-oil-in-water droplets. In this double-emulsion system, the reaction of OpdA and coumaphos was achieved by allowing coumaphos to diffuse from the continuous aqueous phase across the oil phase into the internal aqueous droplets.

Separation of the Stern and diffuse layer in coarse-grained models: the cases of phosphatidyl serine, phosphatidic acid, and PIP2 monolayers.

PubMed

Vangaveti, S; Travesset, A

2014-12-28

We present here a method to separate the Stern and diffuse layer in general systems into two regions that can be analyzed separately. The Stern layer can be described in terms of Bjerrum pairing and the diffuse layer in terms of Poisson-Boltzmann theory (monovalent) or strong coupling theory plus a slowly decaying tail (divalent). We consider three anionic phospholipids: phosphatidyl serine, phosphatidic acid, and phosphatidylinositol(4,5)bisphosphate (PIP2), which we describe within a minimal coarse-grained model as a function of ionic concentration. The case of mixed lipid systems is also considered, which shows a high level of binding cooperativity as a function of PIP2 localization. Implications for existing experimental systems of lipid heterogeneities are also discussed.

Separation of the Stern and diffuse layer in coarse-grained models: The cases of phosphatidyl serine, phosphatidic acid, and PIP2 monolayers

NASA Astrophysics Data System (ADS)

Vangaveti, S.; Travesset, A.

2014-12-01

We present here a method to separate the Stern and diffuse layer in general systems into two regions that can be analyzed separately. The Stern layer can be described in terms of Bjerrum pairing and the diffuse layer in terms of Poisson-Boltzmann theory (monovalent) or strong coupling theory plus a slowly decaying tail (divalent). We consider three anionic phospholipids: phosphatidyl serine, phosphatidic acid, and phosphatidylinositol(4,5)bisphosphate (PIP2), which we describe within a minimal coarse-grained model as a function of ionic concentration. The case of mixed lipid systems is also considered, which shows a high level of binding cooperativity as a function of PIP2 localization. Implications for existing experimental systems of lipid heterogeneities are also discussed.

Difluoro-and Trifluoromethylation of Electron-Deficient Alkenes in an Electrochemical Microreactor.

PubMed

Arai, Kenta; Watts, Kevin; Wirth, Thomas

2014-02-01

Electrochemical microreactors, which have electrodes integrated into the flow path, can afford rapid and efficient electrochemical reactions without redox reagents due to the intrinsic properties of short diffusion distances. Taking advantage of electrochemical microreactors, Kolbe electrolysis of di-and trifluoroacetic acid in the presence of various electron-deficient alkenes was performed under constant current at continuous flow at room temperature. As a result, di-and trifluoromethylated compounds were effectively produced in either equal or higher yields than identical reactions under batch conditions previously reported by Uneyamas group. The strategy of using electrochemical microreactor technology is useful for an effective fluoromethylation of alkenes based on Kolbe electrolysis in significantly shortened reaction times.

Global solutions to a class of multi-species reaction-diffusion systems with cross-diffusions arising in population dynamics

NASA Astrophysics Data System (ADS)

Wen, Zijuan; Fu, Shengmao

2009-08-01

In this paper, an n-species strongly coupled cooperating diffusive system is considered in a bounded smooth domain, subject to homogeneous Neumann boundary conditions. Employing the method of energy estimates, we obtain some conditions on the diffusion matrix and inter-specific cooperatives to ensure the global existence and uniform boundedness of a nonnegative solution. The globally asymptotical stability of the constant positive steady state is also discussed. As a consequence, all the results hold true for multi-species Lotka-Volterra type competition model and prey-predator model.

Introduction to the Focus Issue: Chemo-Hydrodynamic Patterns and Instabilities

NASA Astrophysics Data System (ADS)

De Wit, A.; Eckert, K.; Kalliadasis, S.

2012-09-01

Pattern forming instabilities are often encountered in a wide variety of natural phenomena and technological applications, from self-organization in biological and chemical systems to oceanic or atmospheric circulation and heat and mass transport processes in engineering systems. Spatio-temporal structures are ubiquitous in hydrodynamics where numerous different convective instabilities generate pattern formation and complex spatiotemporal dynamics, which have been much studied both theoretically and experimentally. In parallel, reaction-diffusion processes provide another large family of pattern forming instabilities and spatio-temporal structures which have been analyzed for several decades. At the intersection of these two fields, "chemo-hydrodynamic patterns and instabilities" resulting from the coupling of hydrodynamic and reaction-diffusion processes have been less studied. The exploration of the new instability and symmetry-breaking scenarios emerging from the interplay between chemical reactions, diffusion and convective motions is a burgeoning field in which numerous exciting problems have emerged during the last few years. These problems range from fingering instabilities of chemical fronts and reactive fluid-fluid interfaces to the dynamics of reaction-diffusion systems in the presence of chaotic mixing. The questions to be addressed are at the interface of hydrodynamics, chemistry, engineering or environmental sciences to name a few and, as a consequence, they have started to draw the attention of several communities including both the nonlinear chemical dynamics and hydrodynamics communities. The collection of papers gathered in this Focus Issue sheds new light on a wide range of phenomena in the general area of chemo-hydrodynamic patterns and instabilities. It also serves as an overview of the current research and state-of-the-art in the field.

Nonlinear Systems.

ERIC Educational Resources Information Center

Seider, Warren D.; Ungar, Lyle H.

1987-01-01

Describes a course in nonlinear mathematics courses offered at the University of Pennsylvania which provides an opportunity for students to examine the complex solution spaces that chemical engineers encounter. Topics include modeling many chemical processes, especially those involving reaction and diffusion, auto catalytic reactions, phase…

Citric Acid-Modified Fenton's Reaction for the Oxidation of Chlorinated Ethylenes in Soil Solution Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seol, Yongkoo; Javandel, Iraj

Fenton's reagent, a solution of hydrogen peroxide and ferrous iron catalyst, is used for an in-situ chemical oxidation of organic contaminants. Sulfuric acid is commonly used to create an acidic condition needed for catalytic oxidation. Fenton's reaction often involves pressure buildup and precipitation of reaction products, which can cause safety hazards and diminish efficiency. We selected citric acid, a food-grade substance, as an acidifying agent to evaluate its efficiencies for organic contaminant removal in Fenton's reaction, and examined the impacts of using citric acid on the unwanted reaction products. A series of batch and column experiments were performed with varyingmore » H{sub 2}O{sub 2} concentrations to decompose selected chlorinated ethylenes. Either dissolved iron from soil or iron sulfate salt was added to provide the iron catalyst in the batch tests. Batch experiments revealed that both citric and sulfuric acid systems achieved over 90% contaminant removal rates, and the presence of iron catalyst was essential for effective decontamination. Batch tests with citric acid showed no signs of pressure accumulation and solid precipitations, however the results suggested that an excessive usage of H{sub 2}O{sub 2} relative to iron catalysts (Fe{sup 2+}/H{sub 2}O{sub 2} < 1/330) would result in lowering the efficiency of contaminant removal by iron chelations in the citric acid system. Column tests confirmed that citric acid could provide suitable acidic conditions to achieve higher than 55% contaminant removal rates.« less

Citric acid-modified Fenton's reaction for the oxidation of chlorinated ethylenes in soil solution systems.

PubMed

Seol, Yongkoo; Javandel, Iraj

2008-06-01

Fenton's reagent, a solution of hydrogen peroxide and ferrous iron catalyst, is used for an in situ chemical oxidation of organic contaminants. Sulfuric acid is commonly used to create an acidic condition needed for catalytic oxidation. Fenton's reaction often involves pressure buildup and precipitation of reaction products, which can cause safety hazards and diminish efficiency. We selected citric acid, a food-grade substance, as an acidifying agent to evaluate its efficiencies for organic contaminant removal in Fenton's reaction, and examined the impacts of using citric acid on the unwanted reaction products. A series of batch and column experiments were performed with varying H2O2 concentrations to decompose selected chlorinated ethylenes. Either dissolved iron from soil or iron sulfate salt was added to provide the iron catalyst in the batch tests. Batch experiments revealed that both citric and sulfuric acid systems achieved over 90% contaminant removal rates, and the presence of iron catalyst was essential for effective decontamination. Batch tests with citric acid showed no signs of pressure accumulation and solid precipitations, however the results suggested that an excessive usage of H2O2 relative to iron catalysts (Fe2+/H2O2<1/330) would result in lowering the efficiency of contaminant removal by iron chelation in the citric acid system. Column tests confirmed that citric acid could provide suitable acidic conditions to achieve higher than 55% contaminant removal rates.

A Generalized Model for Transport of Contaminants in Soil by Electric Fields

PubMed Central

Paz-Garcia, Juan M.; Baek, Kitae; Alshawabkeh, Iyad D.; Alshawabkeh, Akram N.

2012-01-01

A generalized model applicable to soils contaminated with multiple species under enhanced boundary conditions during treatment by electric fields is presented. The partial differential equations describing species transport are developed by applying the law of mass conservation to their fluxes. Transport, due to migration, advection and diffusion, of each aqueous component and complex species are combined to produce one partial differential equation hat describes transport of the total analytical concentrations of component species which are the primary dependent variables. This transport couples with geochemical reactions such as aqueous equilibrium, sorption, precipitation and dissolution. The enhanced model is used to simulate electrokinetic cleanup of lead and copper contaminants at an Army Firing Range. Acid enhancement is achieved by the use of adipic acid to neutralize the basic front produced for the cathode electrochemical reaction. The model is able to simulate enhanced application of the process by modifying the boundary conditions. The model showed that kinetics of geochemical reactions, such as metals dissolution/leaching and redox reactions might be significant for realistic prediction of enhanced electrokinetic extraction of metals in real world applications. PMID:22242884

Thermomyces lanuginosus lipase-catalyzed synthesis of natural flavor esters in a continuous flow microreactor.

PubMed

Gumel, Ahmad Mohammed; Annuar, M S M

2016-06-01

Enzymatic catalysis is considered to be among the most environmental friendly processes for the synthesis of fine chemicals. In this study, lipase from Thermomyces lanuginosus (Lecitase Ultra™) was used to catalyze the synthesis of flavor esters, i.e., methyl butanoate and methyl benzoate by esterification of the acids with methanol in a microfluidic system. Maximum reaction rates of 195 and 115 mM min -1 corresponding to catalytic efficiencies (k cat /K M ) of 0.30 and 0.24 min -1  mM -1 as well as yield conversion of 54 and 41 % were observed in methyl butanoate and methyl benzoate synthesis, respectively. Catalytic turnover (k cat ) was higher for methyl butanoate synthesis. Rate of synthesis and yield decreased with increasing flow rates. For both esters, increase in microfluidic flow rate resulted in increased advective transport over molecular diffusion and reaction rate, thus lower conversion. In microfluidic synthesis using T. lanuginosus lipase, the following reaction conditions were 40 °C, flow rate 0.1 mL min -1 , and 123 U g -1 enzyme loading found to be the optimum operating limits. The work demonstrated the application of enzyme(s) in a microreactor system for the synthesis of industrially important esters.

Estimating parameters from rotating ring disc electrode measurements

DOE PAGES

Santhanagopalan, Shriram; White, Ralph E.

2017-10-21

Rotating ring disc electrode (RRDE) experiments are a classic tool for investigating kinetics of electrochemical reactions. Several standardized methods exist for extracting transport parameters and reaction rate constants using RRDE measurements. Here in this work, we compare some approximate solutions to the convective diffusion used popularly in the literature to a rigorous numerical solution of the Nernst-Planck equations coupled to the three dimensional flow problem. In light of these computational advancements, we explore design aspects of the RRDE that will help improve sensitivity of our parameter estimation procedure to experimental data. We use the oxygen reduction in acidic media involvingmore » three charge transfer reactions and a chemical reaction as an example, and identify ways to isolate reaction currents for the individual processes in order to accurately estimate the exchange current densities.« less

Acid generation mechanism in anion-bound chemically amplified resists used for extreme ultraviolet lithography

NASA Astrophysics Data System (ADS)

Komuro, Yoshitaka; Yamamoto, Hiroki; Kobayashi, Kazuo; Ohomori, Katsumi; Kozawa, Takahiro

2015-03-01

Extreme ultraviolet (EUV) lithography is the most promising candidate for the high-volume production of semiconductor devices with half-pitches of sub 10nm. An anion-bound polymer(ABP), in which at the anion part of onium salts is polymerized, has attracted much attention from the viewpoint of the control of acid diffusion. In this study, the acid generation mechanism in ABP films was investigated using γ and EUV radiolysis. On the basis of experimental results, the acid generation mechanism in anion-bound chemically amplified resists was proposed. The protons of acids are considered to be mainly generated through the reaction of phenyl radicals with diphenylsulfide radical cations that are produced through the hole transfer to the decomposition products of onium salts.

Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer

NASA Astrophysics Data System (ADS)

Chen, Mohan; Zheng, Lixin; Santra, Biswajit; Ko, Hsin-Yu; DiStasio, Robert A., Jr.; Klein, Michael L.; Car, Roberto; Wu, Xifan

2018-03-01

Proton transfer via hydronium and hydroxide ions in water is ubiquitous. It underlies acid-base chemistry, certain enzyme reactions, and even infection by the flu. Despite two centuries of investigation, the mechanism underlying why hydroxide diffuses slower than hydronium in water is still not well understood. Herein, we employ state-of-the-art density-functional-theory-based molecular dynamics—with corrections for non-local van der Waals interactions, and self-interaction in the electronic ground state—to model water and hydrated water ions. At this level of theory, we show that structural diffusion of hydronium preserves the previously recognized concerted behaviour. However, by contrast, proton transfer via hydroxide is less temporally correlated, due to a stabilized hypercoordination solvation structure that discourages proton transfer. Specifically, the latter exhibits non-planar geometry, which agrees with neutron-scattering results. Asymmetry in the temporal correlation of proton transfer leads to hydroxide diffusing slower than hydronium.

Let the substrate flow, not the enzyme: Practical immobilization of d-amino acid oxidase in a glass microreactor for effective biocatalytic conversions.

PubMed

Bolivar, Juan M; Tribulato, Marco A; Petrasek, Zdenek; Nidetzky, Bernd

2016-11-01

Exploiting enzymes for chemical synthesis in flow microreactors necessitates their reuse for multiple rounds of conversion. To achieve this goal, immobilizing the enzymes on microchannel walls is a promising approach, but practical methods for it are lacking. Using fusion to a silica-binding module to engineer enzyme adsorption to glass surfaces, we show convenient immobilization of d-amino acid oxidase on borosilicate microchannel plates. In confocal laser scanning microscopy, channel walls appeared uniformly coated with target protein. The immobilized enzyme activity was in the range expected for monolayer coverage of the plain surface with oxidase (2.37 × 10(-5)  nmol/mm(2) ). Surface attachment of the enzyme was completely stable under flow. The operational half-life of the immobilized oxidase (25°C, pH 8.0; soluble catalase added) was 40 h. Enzymatic oxidation of d-Met into α-keto-γ-(methylthio)butyric acid was characterized in single-pass and recycle reactor configurations, employing in-line measurement of dissolved O2 , and off-line determination of the keto-acid product. Reaction-diffusion time-scale analysis for different flow conditions showed that the heterogeneously catalyzed reaction was always slower than diffusion of O2 to the solid surface (DaII  ≤ 0.3). Potential of the microreactor for intensifying O2 -dependent biotransformations restricted by mass transfer in conventional reactors is thus revealed. Biotechnol. Bioeng. 2016;113: 2342-2349. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Catalytic conversion in nanoporous materials: Concentration oscillations and spatial correlations due to inhibited transport and intermolecular interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia, Andres; Evans, James W.

2016-11-03

We show that steady-state catalytic conversion in nanoporous materials can occur in a quasi-counter-diffusion mode with the reactant (product) concentration strongly decaying (growing) into the pore, but also with oscillations in the total concentration. These oscillations reflect the response of the fluid to the transition from an extended to a confined environment near the pore opening. We focus on the regime of strongly inhibited transport in narrow pores corresponding to single-file diffusion. Here, limited penetration of the reactant into the pores and the associated low reaction yield is impacted by strong spatial correlations induced by both reaction (non-equilibrium correlations) andmore » also by intermolecular interactions (thermodynamic correlations). We develop a generalized hydrodynamic formulation to effectively describe inhibited transport accounting for the effect of these correlations, and incorporate this description of transport into appropriate reaction-diffusion equations. These equations accurately describe both shorter-range concentration oscillations near the pore opening and the longer-range mesoscale variation of concentration profiles in the pore (and thus also describe reaction yield). Success of the analytic theory is validated by comparison with a precise kinetic Monte Carlo simulation of an appropriate molecular-level stochastic reaction-diffusion model. As a result, this work elucidates unconventional chemical kinetics in interacting confined systems.« less

Invariantly propagating dissolution fingers in finite-width systems

NASA Astrophysics Data System (ADS)

Dutka, Filip; Szymczak, Piotr

2016-04-01

Dissolution fingers are formed in porous medium due to positive feedback between transport of reactant and chemical reactions [1-4]. We investigate two-dimensional semi-infinite systems, with constant width W in one direction. In numerical simulations we solve the Darcy flow problem combined with advection-dispersion-reaction equation for the solute transport to track the evolving shapes of the fingers and concentration of reactant in the system. We find the stationary, invariantly propagating finger shapes for different widths of the system, flow and reaction rates. Shape of the reaction front, turns out to be controlled by two dimensionless numbers - the (width-based) Péclet number PeW = vW/Dφ0 and Damköhler number DaW = ksW/v, where k is the reaction rate, s - specific reactive surface area, v - characteristic flow rate, D - diffusion coefficient of the solute, and φ0 - initial porosity of the rock matrix. Depending on PeW and DaW stationary shapes can be divided into seperate classes, e.g. parabolic-like and needle-like structures, which can be inferred from theoretical predictions. In addition we determine velocity of propagating fingers in time and concentration of reagent in the system. Our simulations are compared with natural forms (solution pipes). P. Ortoleva, J. Chadam, E. Merino, and A. Sen, Geochemical self-organization II: the reactive-infiltration instability, Am. J. Sci, 287, 1008-1040 (1987). M. L. Hoefner, and H. S. Fogler. Pore evolution and channel formation during flow and reaction in porous media, AIChE Journal 34, 45-54 (1988). C. E. Cohen, D. Ding, M. Quintard, and B. Bazin, From pore scale to wellbore scale: impact of geometry on wormhole growth in carbonate acidization, Chemical Engineering Science 63, 3088-3099 (2008). P. Szymczak and A. J. C. Ladd, Reactive-infiltration nstabilities in rocks. Part II: Dissolution of a porous matrix, J. Fluid Mech. 738, 591-630 (2014).

Step-by-Step Simulation of Radiation of Radiation Chemistry Using Green Functions for Diffusion-Influenced Reactions

NASA Technical Reports Server (NTRS)

Plante, Ianik; Cucinotta, Francis A.

2011-01-01

The irradiation of biological systems leads to the formation of radiolytic species such as H(raised dot), (raised dot)OH, H2, H2O2, e(sup -)(sub aq), etc.[1]. These species react with neighboring molecules, which result in damage in biological molecules such as DNA. Radiation chemistry is there for every important to understand the radiobiological consequences of radiation[2]. In this work, we discuss an approach based on the exact Green Functions for diffusion-influenced reactions which may be used to simulate radiation chemistry and eventually extended to study more complex systems, including DNA.

Buoyancy-driven convection around chemical fronts traveling in covered horizontal solution layers.

PubMed

Rongy, L; Goyal, N; Meiburg, E; De Wit, A

2007-09-21

Density differences across an autocatalytic chemical front traveling horizontally in covered thin layers of solution trigger hydrodynamic flows which can alter the concentration profile. We theoretically investigate the spatiotemporal evolution and asymptotic dynamics resulting from such an interplay between isothermal chemical reactions, diffusion, and buoyancy-driven convection. The studied model couples the reaction-diffusion-convection evolution equation for the concentration of an autocatalytic species to the incompressible Stokes equations ruling the evolution of the flow velocity in a two-dimensional geometry. The dimensionless parameter of the problem is a solutal Rayleigh number constructed upon the characteristic reaction-diffusion length scale. We show numerically that the asymptotic dynamics is one steady vortex surrounding, deforming, and accelerating the chemical front. This chemohydrodynamic structure propagating at a constant speed is quite different from the one obtained in the case of a pure hydrodynamic flow resulting from the contact between two solutions of different density or from the pure reaction-diffusion planar traveling front. The dynamics is symmetric with regard to the middle of the layer thickness for positive and negative Rayleigh numbers corresponding to products, respectively, lighter or heavier than the reactants. A parametric study shows that the intensity of the flow, the propagation speed, and the deformation of the front are increasing functions of the Rayleigh number and of the layer thickness. In particular, the asymptotic mixing length and reaction-diffusion-convection speed both scale as square root Ra for Ra>5. The velocity and concentration fields in the asymptotic dynamics are also found to exhibit self-similar properties with Ra. A comparison of the dynamics in the case of a monostable versus bistable kinetics is provided. Good agreement is obtained with experimental data on the speed of iodate-arsenous acid fronts propagating in horizontal capillaries. We furthermore compare the buoyancy-driven dynamics studied here to Marangoni-driven deformation of traveling chemical fronts in solution open to the air in the absence of gravity previously studied in the same geometry [L. Rongy and A. De Wit, J. Chem. Phys. 124, 164705 (2006)].

Controlling mechanisms of metals release form cement-based waste form in acetic acid solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Kuang Ye.

1991-01-01

The purpose of this dissertation is to identify the individual leaching mechanisms of metals by knowing the pH profile within the leached specimen and the physical and chemical properties of the leached material. Leaching of cement-based waste form in acetic acid solutions with different acidic strengths has been investigated in this work. The pH profile along the acid penetration route in the cement-based waste form was identified by various pH color indicators. The pH in the surface altered layer varies from 5.0 to 6.0, which is very close to the pH in the bulk leachate. A reacting zone, where themore » pH abruptly changes from 6 to 12, sharply divides the altered surface layer from the remaining unleached waste form or kernel. Leaching of metals is controlled by the acidity available in the leachant. Dissolution of alkaline materials leaves a silica-rich layer on the surface of the cement-based waste form. This surface layer exhibits different properties than those of the unleached material. The surface layer has a higher water content, is lighter weight, and is soft and friable. Furthermore, the abundant silicate content on the solid surface detains portion of the leached metals, while they are moving through the leached layer into bulk solution. The leaching of metals is a consequence of acid penetration. The distance from the solid/solution interface to the front of the leaching boundary can be regarded as the depth of leaching zone, where the metals dissolve and diffuse out of the waste form. The metal ions diffuse through the leached layer may be retarded on the solid surface by the pH-dependent adsorption reactions. It is found that the leaching process through the leached layer is diffusion-controlled for calcium and cadmium, whereas diffusion and adsorption occur simultaneously in the leached layer for lead and arsenic.« less

Label-free electrical detection of pyrophosphate generated from DNA polymerase reactions on field-effect devices.

PubMed

Credo, Grace M; Su, Xing; Wu, Kai; Elibol, Oguz H; Liu, David J; Reddy, Bobby; Tsai, Ta-Wei; Dorvel, Brian R; Daniels, Jonathan S; Bashir, Rashid; Varma, Madoo

2012-03-21

We introduce a label-free approach for sensing polymerase reactions on deoxyribonucleic acid (DNA) using a chelator-modified silicon-on-insulator field-effect transistor (SOI-FET) that exhibits selective and reversible electrical response to pyrophosphate anions. The chemical modification of the sensor surface was designed to include rolling-circle amplification (RCA) DNA colonies for locally enhanced pyrophosphate (PPi) signal generation and sensors with immobilized chelators for capture and surface-sensitive detection of diffusible reaction by-products. While detecting arrays of enzymatic base incorporation reactions is typically accomplished using optical fluorescence or chemiluminescence techniques, our results suggest that it is possible to develop scalable and portable PPi-specific sensors and platforms for broad biomedical applications such as DNA sequencing and microbe detection using surface-sensitive electrical readout techniques.

Mathematical modeling of degradation for bulk-erosive polymers: applications in tissue engineering scaffolds and drug delivery systems.

PubMed

Chen, Yuhang; Zhou, Shiwei; Li, Qing

2011-03-01

The degradation of polymeric biomaterials, which are widely exploited in tissue engineering and drug delivery systems, has drawn significant attention in recent years. This paper aims to develop a mathematical model that combines stochastic hydrolysis and mass transport to simulate the polymeric degradation and erosion process. The hydrolysis reaction is modeled in a discrete fashion by a fundamental stochastic process and an additional autocatalytic effect induced by the local carboxylic acid concentration in terms of the continuous diffusion equation. Illustrative examples of microparticles and tissue scaffolds demonstrate the applicability of the model. It is found that diffusive transport plays a critical role in determining the degradation pathway, whilst autocatalysis makes the degradation size dependent. The modeling results show good agreement with experimental data in the literature, in which the hydrolysis rate, polymer architecture and matrix size actually work together to determine the characteristics of the degradation and erosion processes of bulk-erosive polymer devices. The proposed degradation model exhibits great potential for the design optimization of drug carriers and tissue scaffolds. Copyright © 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

[Study on X-ray powder diffraction of various structured zinc titanate prepared by the method of direct precipitation].

PubMed

Guo, Jian; Wang, Zhi-hua; Tao, Dong-liang; Guo, Guang-sheng

2007-05-01

Zinc titanate powders were prepared from Ti(SO4)2, Zn(NO3)2 x (6)H2O and (NH4)2CO3 by the method of direct precipitation. The effects of reaction conditions on the structure of zinc titanate were studied. The sample was analyzed by means of XRD and TG-DTA. The structure of zinc titanate was affected by the reaction subsequence of the formation of titanic acid and zinc carbonate. In the reaction system where titanic acid was generated earlier, collision reaction occurred between the generated zinc carbonate molecule and the surrounding titanic acid molecule. When titanic acid was generated earlier and precipitant (NH4)2CO3 was sufficient, Zn2Ti3O8 was obtained because of the sufficient collision reaction and superfluous titanic acid. In the reaction system where zinc carbonate was generated earlier, collision reaction occurred between the generated titanic acid molecule and the surrounding zinc carbonate molecule. When zinc carbonate was generated earlier and precipitant (NH4)2CO3 was sufficient, Zn2TiO4 was obtained because of the sufficient collision reaction and superfluous zinc carbonate. In addition, the kinds and structure of the production were affected by the dosage of precipitant and the reaction temperature. Zn2Ti3O8 or Zn2TiO4 could be obtained easier when using more precipitant or higher reaction temperature which could cause more sufficient collision reaction. ZnTiO3 could be obtained under the conditions of less precipitant and lower reaction temperature.

A Computational Approach to Increase Time Scales in Brownian Dynamics–Based Reaction-Diffusion Modeling

PubMed Central

Frazier, Zachary

2012-01-01

Abstract Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling. PMID:22697237

Experimental identification of the active sites in pyrolyzed carbon-supported cobalt-polypyrrole-4-toluenesulfinic acid as electrocatalysts for oxygen reduction reaction

NASA Astrophysics Data System (ADS)

Sha, Hao-Dong; Yuan, Xianxia; Li, Lin; Ma, Zhong; Ma, Zi-Feng; Zhang, Lei; Zhang, Jiujun

2014-06-01

A series of carbon supported cobalt-polypyrrole-4-toluenesulfinic acid have been pyrolyzed in an argon atmosphere at 800 °C, then structurally characterized and electrochemically evaluated as oxygen reduction reaction (ORR) catalysts in aqueous 0.5 M sulfuric acid. The structures are cobalt bonded to nitrogen species (Co-Nx) along with metallic cobalt and cobalt oxide. When the cobalt loading in the compound is less than 1.0 wt%, the predominate form is Co-Nx, when the loading is higher than 1.0 wt%, metallic Co and Co oxide particles co-exist with the Co-Nx compound. At a Co loading of ∼1.0 wt%, the catalyst gives the best ORR activity. Both metallic Co and Co oxide are not active for catalyzing ORR, and block the catalytically active Co-Nx species from the surface and reduce the catalytic activity since the diffusion limiting current density on a rotating disk electrode (RDE) increases when the electrode blocking agents are washed away with acid.

Drosophila segmentation: supercomputer simulation of prepattern hierarchy.

PubMed

Hunding, A; Kauffman, S A; Goodwin, B C

1990-08-09

Spontaneous prepattern formation in a two level hierarchy of reaction-diffusion systems is simulated in three space co-ordinates and time, mimicking gap gene and primary pair-rule gene expression. The model rests on the idea of Turing systems of the second kind, in which one prepattern generates position dependent rate constants for a subsequent reaction-diffusion system. Maternal genes are assumed responsible for setting up gradients from the anterior and posterior ends, one of which is needed to stabilize a double period prepattern suggested to underly the read out of the gap genes. The resulting double period pattern in turn stabilizes the next prepattern in the hierarchy, which has a short wavelength with many characteristics of the stripes seen in actual primary pair-rule gene expression. Without such hierarchical stabilization, reaction-diffusion mechanisms yield highly patchy short wave length patterns, and thus unreliable stripes. The model yields seven stable stripes located in the middle of the embryo, with the potential for additional expression near the poles, as observed experimentally. The model does not rely on specific chemical reaction kinetics, rather the effect is general to many such kinetic schemes. This makes it robust to parameter changes, and it has good potential for adapting to size and shape changes as well. The study thus suggests that the crucial organizing principle in early Drosophila embryogenesis is based on global field mechanisms, not on particular local interactions.

Studies on the mucin derived from human colloid breast carcinoma

PubMed Central

Adams, J. B.

1965-01-01

1. A non-diffusible mucoid, showing a single peak in the ultracentrifuge, was isolated from human colloid breast carcinoma by treatment with trypsin and pepsin. The material contained threonine, leucine (isoleucine), valine, proline, glycine and glutamic acid in the approximate molar proportions 5:1:1:2:1:1. Smaller amounts of aspartic acid and serine were also found. For each 5 threonine residues, 6 N-acetylgalactosamine and 3–4 galactose residues were present. 2. The mucoid possessed reducing properties by the Park & Johnson (1949) procedure; these were attributable to the action of mild alkali, as employed in this procedure. Mild alkaline treatment by the Aminoff, Morgan & Watkins (1952) procedure gave rise to a diffusible N-acetylgalactosamine chromophore that gave an enhanced colour with Ehrlich's reagent. That galactosyl-(1→3)-N-acetylgalactosamine residues were liberated was supported by periodate studies. 3. Alkaline liberation of hexosamine residues was accompanied by a specific destruction of threonine. After 40 min. at 100° in 0·18 n-lithium hydroxide, both moieties had almost completely disappeared from the ninhydrin-positive components formed on subsequent acid hydrolysis. Glycine and α-oxobutyric acid were present in the acid hydrolysate, showing that both possible pathways of a β-elimination reaction were involved. Formation of diffusible peptide on very mild alkaline treatment was attributable to the rupture of the original peptide core, necessitated by the second of these two pathways. 4. Hydroxamate formation on treatment with hydroxylamine showed the presence of carbohydrate linkage to glutamic acid or aspartic acid residues or both. This could account for the single N-acetylgalactosamine residue not linked to threonine. 5. The native mucin contained sialic acid, which was cleaved by the acid environment used in the treatment with pepsin. A statistical model of the mucin would require each prosthetic group to be linked, via N-acetylgalactosamine, to threonine, which would occupy every alternate position among the amino acids in the peptide core. ImagesFig. 1.Fig. 4. PMID:14348196

Mapping Ionic Currents and Reactivity on the Nanoscale: Electrochemical Strain Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalinin, S.V.

2010-10-19

Solid-state electrochemical processes in oxides underpin a broad spectrum of energy and information storage devices, ranging from Li-ion and Li-air batteries, to solid oxide fuel cells (SOFC) to electroresistive and memristive systems. These functionalities are controlled by the bias-driven diffusive and electromigration transport of mobile ionic species, as well as intricate a set of electrochemical and defect-controlled reactions at interfaces and in bulk. Despite the wealth of device-level and atomistic studies, little is known on the mesoscopic mechanisms of ion diffusion and electronic transport on the level of grain clusters, individual grains, and extended defects. The development of the capabilitymore » for probing ion transport on the nanometer scale is a key to deciphering complex interplay between structure, functionality, and performance in these systems. Here we introduce Electrochemical Strain Microscopy, a scanning probe microscopy technique based on strong strain-bias coupling in the systems in which local ion concentrations are changed by electrical fields. The imaging capability, as well as time- and voltage spectroscopies analogous to traditional current based electrochemical characterization methods are developed. The reversible intercalation of Li and mapping electrochemical activity in LiCoO2 is demonstrated, illustrating higher Li diffusivity at non-basal planes and grain boundaries. In Si-anode device structure, the direct mapping of Li diffusion at extended defects and evolution of Li-activity with charge state is explored. The electrical field-dependence of Li mobility is studied to determine the critical bias required for the onset of electrochemical transformation, allowing reaction and diffusion processes in the battery system to be separated at each location. Finally, the applicability of ESM for probing oxygen vacancy diffusion and oxygen reduction/evolution reactions is illustrated, and the high resolution ESM maps are correlated with aberration corrected scanning transmission electron microscopy imaging. The future potential for deciphering mechanisms of electrochemical transformations on an atomically-defined single-defect level is discussed.« less

A deterministic particle method for one-dimensional reaction-diffusion equations

NASA Technical Reports Server (NTRS)

Mascagni, Michael

1995-01-01

We derive a deterministic particle method for the solution of nonlinear reaction-diffusion equations in one spatial dimension. This deterministic method is an analog of a Monte Carlo method for the solution of these problems that has been previously investigated by the author. The deterministic method leads to the consideration of a system of ordinary differential equations for the positions of suitably defined particles. We then consider the time explicit and implicit methods for this system of ordinary differential equations and we study a Picard and Newton iteration for the solution of the implicit system. Next we solve numerically this system and study the discretization error both analytically and numerically. Numerical computation shows that this deterministic method is automatically adaptive to large gradients in the solution.

Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates

PubMed Central

Yogurtcu, Osman N.; Johnson, Margaret E.

2015-01-01

The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute to dense systems. PMID:26328828

Radiation-induced reductive modifications of sulfur-containing amino acids within peptides and proteins.

PubMed

Chatgilialoglu, Chryssostomos; Ferreri, Carla; Torreggiani, Armida; Salzano, Anna Maria; Renzone, Giovanni; Scaloni, Andrea

2011-10-19

The complex scenario of radical stress reactions affecting peptides/proteins can be better elucidated through the design of biomimetic studies simulating the consequences of the different free radicals attacking amino acids. In this context, ionizing radiations allowed to examine the specific damages caused by H-atoms and electrons coupled with protons, thus establishing the molecular basis of reductive radical stress. This is an innovative concept that complements the well-known oxidative stress also in view of a complete understanding of the global consequences of radical species reactivities on living systems. This review summarizes the knowledge of the chemical changes present in sulfur-containing amino acids occurring in polypeptides under reductive radical conditions, in particular the transformation of Met and Cys residues into α-amino butyric acid and alanine, respectively. Reductive radical stress causing a desulfurization process, is therefore coupled with the formation of S-centered radicals, which in turn can diffuse apart and become responsible of the damage transfer from proteins to lipids. These reductive modifications assayed in different peptide/protein sequences constitute an integration of the molecular inventories that up to now take into account only oxidative transformations. They can be useful to achieve an integrated vision of the free radical reactivities in a multifunctional system and, overall, for wider applications in the redox proteomics field. Copyright © 2011 Elsevier B.V. All rights reserved.

Sorption specificity and desorption hysteresis of gibberellic acid on ferrihydrite compared to goethite, hematite, montmorillonite, and kaolinite.

PubMed

Zhang, Li; Liu, Fei; Chen, Liang

2017-08-01

The pesticide gibberellic acid (GA 3 ) is a potential endocrine disruptor and environmental toxin; therefore, research into its environmental fate is warranted. Batch studies were conducted to investigate the sorption and desorption characteristics of GA 3 on aquifer media. The results demonstrated special sorption characteristic of GA 3 on ferrihydrite compared to goethite, hematite, montmorillonite, and kaolinite, where the sorption kinetics of GA 3 on ferrihydrite was fitted well with the pseudo-second-order, Elovich, and intra-particle diffusion models. The sorption kinetics of GA 3 on ferrihydrite indicated an initial high sorption rate followed by a slow reaction process. The initial high GA 3 sorption rate may be related to electrostatic sorption and surface complexation reactions on the outer surfaces and at the macropore entrances of ferrihydrite. While the slow step was controlled by GA 3 diffusion into mesopore of ferrihydrite. Analysis of the desorption hysteresis indicated a high hysteresis index (HI) ranging from 0.68 to 17.32, and a low desorption percentage ranging from 18 to 48%. After sufficient desorption, the calculated maximum residual GA 3 quantity due to surface complexation reactions with the ferrihydrite coordinated unsaturated sites was 9.05 ± 0.12 mg g -1 . The calculated maximum quantity of GA 3 trapped within the mesopore was 16.23 ± 0.91 mg g -1 . Graphical Abstract Schematic overview of GA 3 sorption and desorption on five minerals in groundwater.

Boron Nitride-supported Sub-nanometer Pd 6 Clusters for Formic Acid Decomposition: A DFT Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schimmenti, Roberto; Cortese, Remedios; Duca, Dario

A periodic, self-consistent planewave DFT study was carried out to explore the potential use of Pd 6 clusters supported on a boron nitride sheet as a catalyst for the selective decomposition of formic acid (HCOOH) to CO 2 and H 2. The competition between formate (HCOO) and carboxyl (COOH) paths on catalytic sites, with different proximities to the support, was studied. Based on energetics alone, the reaction may mainly follow the HCOO route. Slightly lower activation energies were found at the lateral sites of the cluster as compared to top face sites. This is particularly true for the bidentate tomore » monodentate HCOO conversion. Through comparison of results with similar studies on HCOOH decomposition on extended Pd surfaces, it was demonstrated that the existence of undercoordinated sites in the sub-nanometer cluster could play a key role in preferentially stabilizing HCOO over COOH, which is a common CO precursor in this reaction. A hydrogen spillover mechanism was also investigated; migration toward the boron nitride support is not favorable, at least in the early stages of the reaction. However, hydrogen diffusion on the cluster has low barriers compared to those involved in formic acid decomposition.« less

Boron Nitride-supported Sub-nanometer Pd 6 Clusters for Formic Acid Decomposition: A DFT Study

DOE PAGES

Schimmenti, Roberto; Cortese, Remedios; Duca, Dario; ...

2017-04-25

A periodic, self-consistent planewave DFT study was carried out to explore the potential use of Pd 6 clusters supported on a boron nitride sheet as a catalyst for the selective decomposition of formic acid (HCOOH) to CO 2 and H 2. The competition between formate (HCOO) and carboxyl (COOH) paths on catalytic sites, with different proximities to the support, was studied. Based on energetics alone, the reaction may mainly follow the HCOO route. Slightly lower activation energies were found at the lateral sites of the cluster as compared to top face sites. This is particularly true for the bidentate tomore » monodentate HCOO conversion. Through comparison of results with similar studies on HCOOH decomposition on extended Pd surfaces, it was demonstrated that the existence of undercoordinated sites in the sub-nanometer cluster could play a key role in preferentially stabilizing HCOO over COOH, which is a common CO precursor in this reaction. A hydrogen spillover mechanism was also investigated; migration toward the boron nitride support is not favorable, at least in the early stages of the reaction. However, hydrogen diffusion on the cluster has low barriers compared to those involved in formic acid decomposition.« less

A selection criterion for patterns in reaction–diffusion systems

PubMed Central

2014-01-01

Background Alan Turing’s work in Morphogenesis has received wide attention during the past 60 years. The central idea behind his theory is that two chemically interacting diffusible substances are able to generate stable spatial patterns, provided certain conditions are met. Ever since, extensive work on several kinds of pattern-generating reaction diffusion systems has been done. Nevertheless, prediction of specific patterns is far from being straightforward, and a great deal of interest in deciphering how to generate specific patterns under controlled conditions prevails. Results Techniques allowing one to predict what kind of spatial structure will emerge from reaction–diffusion systems remain unknown. In response to this need, we consider a generalized reaction diffusion system on a planar domain and provide an analytic criterion to determine whether spots or stripes will be formed. Our criterion is motivated by the existence of an associated energy function that allows bringing in the intuition provided by phase transitions phenomena. Conclusions Our criterion is proved rigorously in some situations, generalizing well-known results for the scalar equation where the pattern selection process can be understood in terms of a potential. In more complex settings it is investigated numerically. Our work constitutes a first step towards rigorous pattern prediction in arbitrary geometries/conditions. Advances in this direction are highly applicable to the efficient design of Biotechnology and Developmental Biology experiments, as well as in simplifying the analysis of morphogenetic models. PMID:24476200

Reaction Kernel Structure of a Slot Jet Diffusion Flame in Microgravity

NASA Technical Reports Server (NTRS)

Takahashi, F.; Katta, V. R.

2001-01-01

Diffusion flame stabilization in normal earth gravity (1 g) has long been a fundamental research subject in combustion. Local flame-flow phenomena, including heat and species transport and chemical reactions, around the flame base in the vicinity of condensed surfaces control flame stabilization and fire spreading processes. Therefore, gravity plays an important role in the subject topic because buoyancy induces flow in the flame zone, thus increasing the convective (and diffusive) oxygen transport into the flame zone and, in turn, reaction rates. Recent computations show that a peak reactivity (heat-release or oxygen-consumption rate) spot, or reaction kernel, is formed in the flame base by back-diffusion and reactions of radical species in the incoming oxygen-abundant flow at relatively low temperatures (about 1550 K). Quasi-linear correlations were found between the peak heat-release or oxygen-consumption rate and the velocity at the reaction kernel for cases including both jet and flat-plate diffusion flames in airflow. The reaction kernel provides a stationary ignition source to incoming reactants, sustains combustion, and thus stabilizes the trailing diffusion flame. In a quiescent microgravity environment, no buoyancy-induced flow exits and thus purely diffusive transport controls the reaction rates. Flame stabilization mechanisms in such purely diffusion-controlled regime remain largely unstudied. Therefore, it will be a rigorous test for the reaction kernel correlation if it can be extended toward zero velocity conditions in the purely diffusion-controlled regime. The objectives of this study are to reveal the structure of the flame-stabilizing region of a two-dimensional (2D) laminar jet diffusion flame in microgravity and develop a unified diffusion flame stabilization mechanism. This paper reports the recent progress in the computation and experiment performed in microgravity.

Acid-$beta$-glycerophosphatase reaction products in the central nervous system mitochondria following x-ray irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roizin, L.; Orlovskaja, D.; Liu, J.C.

A survey of the literature to date on the enzyme histochemistry of intracellular organelles has not yielded any reference to the presence of acid phosphatase reaction products in the mammalian mitochondria of the central nervous system. A combination of Gomori's acid phosphatase method, however, with standard electron microscopy has disclosed the presence of enzyme reaction products in the mitochondria of the central nervous system of rats from 2 hr to 22 weeks after x-ray irradiation, as well as in a cerebral biopsy performed on a patient affected by Huntington's chorea. No enzyme reaction products, on the other hand, were observedmore » in serial sections that had been incubated in substrates either containing sodium fluoride or lacking in $beta$- glycerophosphate. The abnormal mitochondrial enzyme reaction (chemical lesion) is considered to be the consequence of the pathologic process affecting the ultrastructural-chemical organization of the organelle. (auth)« less

A class of exact solutions for biomacromolecule diffusion-reaction in live cells.

PubMed

Sadegh Zadeh, Kouroush; Montas, Hubert J

2010-06-07

A class of novel explicit analytic solutions for a system of n+1 coupled partial differential equations governing biomolecular mass transfer and reaction in living organisms are proposed, evaluated, and analyzed. The solution process uses Laplace and Hankel transforms and results in a recursive convolution of an exponentially scaled Gaussian with modified Bessel functions. The solution is developed for wide range of biomolecular binding kinetics from pure diffusion to multiple binding reactions. The proposed approach provides solutions for both Dirac and Gaussian laser beam (or fluorescence-labeled biomacromolecule) profiles during the course of a Fluorescence Recovery After Photobleaching (FRAP) experiment. We demonstrate that previous models are simplified forms of our theory for special cases. Model analysis indicates that at the early stages of the transport process, biomolecular dynamics is governed by pure diffusion. At large times, the dominant mass transfer process is effective diffusion. Analysis of the sensitivity equations, derived analytically and verified by finite difference differentiation, indicates that experimental biologists should use full space-time profile (instead of the averaged time series) obtained at the early stages of the fluorescence microscopy experiments to extract meaningful physiological information from the protocol. Such a small time frame requires improved bioinstrumentation relative to that in use today. Our mathematical analysis highlights several limitations of the FRAP protocol and provides strategies to improve it. The proposed model can be used to study biomolecular dynamics in molecular biology, targeted drug delivery in normal and cancerous tissues, motor-driven axonal transport in normal and abnormal nervous systems, kinetics of diffusion-controlled reactions between enzyme and substrate, and to validate numerical simulators of biological mass transport processes in vivo. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Modeling the oxidation kinetics of sono-activated persulfate's process on the degradation of humic acid.

PubMed

Songlin, Wang; Ning, Zhou; Si, Wu; Qi, Zhang; Zhi, Yang

2015-03-01

Ultrasound degradation of humic acid has been investigated in the presence of persulfate anions at ultrasonic frequency of 40 kHz. The effects of persulfate anion concentration, ultrasonic power input, humic acid concentration, reaction time, solution pH and temperature on humic acid removal efficiency were studied. It is found that up to 90% humic acid removal efficiency was achieved after 2 h reaction. In this system, sulfate radicals (SO₄⁻·) were considered to be the mainly oxidant to mineralize humic acid while persulfate anion can hardly react with humic acid directly. A novel kinetic model based on sulfate radicals (SO₄⁻·) oxidation was established to describe the humic acid mineralization process mathematically and chemically in sono-activated persulfate system. According to the new model, ultrasound power, persulfate dosage, solution pH and reaction temperature have great influence on humic acid degradation. Different initial concentration of persulfate anions and humic acid, ultrasonic power, initial pH and reaction temperature have been discussed to valid the effectiveness of the model, and the simulated data showed new model had good agreement with the experiments data.

Comparative study on copper leaching from waste printed circuit boards by typical ionic liquid acids.

PubMed

Chen, Mengjun; Huang, Jinxiu; Ogunseitan, Oladele A; Zhu, Nengming; Wang, Yan-min

2015-07-01

Waste printed circuit boards (WPCBs) are attracting increasing concerns because the recovery of its content of valuable metallic resources is hampered by the presence of hazardous substances. In this study, we used ionic liquids (IL) to leach copper from WPCBs. [BSO3HPy]OTf, [BSO3HMIm]OTf, [BSO4HPy]HSO4, [BSO4HMim]HSO4 and [MIm]HSO4 were selected. Factors that affect copper leaching rate were investigated in detail and their leaching kinetics were also examined with the comparison of [Bmim]HSO4. The results showed that all six IL acids could successfully leach copper out, with near 100% recovery. WPCB particle size and leaching time had similar influences on copper leaching performance, while IL acid concentration, hydrogen peroxide addition, solid to liquid ratio, temperature, showed different influences. Moreover, IL acid with HSO4(-) was more efficient than IL acid with CF3SO3(-). These six IL acids indicate a similar behavior with common inorganic acids, except temperature since copper leaching rate of some IL acids decreases with its increase. The results of leaching kinetics studies showed that diffusion plays a more important role than surface reaction, whereas copper leaching by inorganic acids is usually controlled by surface reaction. This innovation provides a new option for recovering valuable materials such as copper from WPCBs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Enzymatic Synthesis of Glyserol-Coconut Oil Fatty Acid and Glycerol-Decanoic Acis Ester as Emulsifier and Antimicrobial Agents Using Candida rugosa Lipase EC 3.1.1.3

NASA Astrophysics Data System (ADS)

Handayani, Sri; Putri, Ayu Tanissa Tamara; Setiasih, Siswati; Hudiyono, Sumi

2018-01-01

In this research, enzymatic esterification was carried out between glycerol and fatty acid from coconut oil and decanoic acid using n-hexane as solvent. In this reaction Candida rugosa lipase was used as biocatalyst. Optimization esterification reaction was carried out for parameter of the substrate ratio. The mmol ratio between fatty acid and glycerol were used are 1:1, 1:2, 1:3, and 1: 4. The highest conversion percentage obtained at the mole ratio of 1: 4 with the value of 78.5% for the glycerol-decanoic acid ester and 55.4% for the glycerol coconut oil fatty acid ester. Esterification products were characterized by FT-IR. The FT-IR spectrum showed that the ester bond was formed as indicated by the wave number 1750-1739 cm-1. The esterification products were then examined by simple emulsion test and was proved to be an emulsifier. The glycerol-coconut oil fatty acid ester produced higher stability emulsion compare with glycerol decanoic ester. The antimicrobial activity assay using disc diffusion method showed that both glycerol-coconut oil fatty acid ester and glycerol-decanoic ester had the ability inhibiting the growth of Propionibacterium acnes and Staphylococcus epidermidis. Glycerol-decanoic ester shows higher antimicrobial activity than glycerol-coconut oil fatty acid ester.

An Experimental and Kinetic Modeling Study of Methyl Decanoate Combustion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarathy, S M; Thomson, M J; Pitz, W J

2009-12-04

Biodiesel is a mixture of long chain fatty acid methyl esters derived from fats and oils. This research study presents opposed-flow diffusion flame data for one large fatty acid methyl ester, methyl decanoate, and uses the experiments to validate an improved skeletal mechanism consisting of 648 species and 2998 reactions. The results indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular weight oxygenated compounds such as carbon monoxide, formaldehyde, and ketene.

Spatiotemporal pattern formation in a prey-predator model under environmental driving forces

NASA Astrophysics Data System (ADS)

Sirohi, Anuj Kumar; Banerjee, Malay; Chakraborti, Anirban

2015-09-01

Many existing studies on pattern formation in the reaction-diffusion systems rely on deterministic models. However, environmental noise is often a major factor which leads to significant changes in the spatiotemporal dynamics. In this paper, we focus on the spatiotemporal patterns produced by the predator-prey model with ratio-dependent functional response and density dependent death rate of predator. We get the reaction-diffusion equations incorporating the self-diffusion terms, corresponding to random movement of the individuals within two dimensional habitats, into the growth equations for the prey and predator population. In order to have the noise added model, small amplitude heterogeneous perturbations to the linear intrinsic growth rates are introduced using uncorrelated Gaussian white noise terms. For the noise added system, we then observe spatial patterns for the parameter values lying outside the Turing instability region. With thorough numerical simulations we characterize the patterns corresponding to Turing and Turing-Hopf domain and study their dependence on different system parameters like noise-intensity, etc.

Incorporating Geochemical And Microbial Kinetics In Reactive Transport Models For Generation Of Acid Rock Drainage

NASA Astrophysics Data System (ADS)

Andre, B. J.; Rajaram, H.; Silverstein, J.

2010-12-01

Acid mine drainage, AMD, results from the oxidation of metal sulfide minerals (e.g. pyrite), producing ferrous iron and sulfuric acid. Acidophilic autotrophic bacteria such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans obtain energy by oxidizing ferrous iron back to ferric iron, using oxygen as the electron acceptor. Most existing models of AMD do not account for microbial kinetics or iron geochemistry rigorously. Instead they assume that oxygen limitation controls pyrite oxidation and thus focus on oxygen transport. These models have been successfully used for simulating conditions where oxygen availability is a limiting factor (e.g. source prevention by capping), but have not been shown to effectively model acid generation and effluent chemistry under a wider range of conditions. The key reactions, oxidation of pyrite and oxidation of ferrous iron, are both slow kinetic processes. Despite being extensively studied for the last thirty years, there is still not a consensus in the literature about the basic mechanisms, limiting factors or rate expressions for microbially enhanced oxidation of metal sulfides. An indirect leaching mechanism (chemical oxidation of pyrite by ferric iron to produce ferrous iron, with regeneration of ferric iron by microbial oxidation of ferrous iron) is used as the foundation of a conceptual model for microbially enhanced oxidation of pyrite. Using literature data, a rate expression for microbial consumption of ferrous iron is developed that accounts for oxygen, ferrous iron and pH limitation. Reaction rate expressions for oxidation of pyrite and chemical oxidation of ferrous iron are selected from the literature. A completely mixed stirred tank reactor (CSTR) model is implemented coupling the kinetic rate expressions, speciation calculations and flow. The model simulates generation of AMD and effluent chemistry that qualitatively agrees with column reactor and single rock experiments. A one dimensional reaction diffusion model at the scale of a single rock is developed incorporating the proposed kinetic rate expressions. Simulations of initiation, washout and AMD flows are discussed to gain a better understanding of the role of porosity, effective diffusivity and reactive surface area in generating AMD. Simulations indicate that flow boundary conditions control generation of acid rock drainage as porosity increases.

Measuring Hydrogen Concentrations in Metals

NASA Technical Reports Server (NTRS)

Danford, M. D.

1985-01-01

Commercial corrosion-measurement system adapted to electrochemical determination of hydrogen concentrations in metals. New technique based on diffusion of hydrogen through foil specimen of metal. In sample holder, hydrogen produced on one side of foil, either by corrosion reaction or by cathodic current. Hydrogen diffused through foil removed on other side by constant anode potential, which leads to oxidation of hydrogen to water. Anode current is measure of concentration of hydrogen diffusing through foil. System used to study hydrogen uptake, hydrogen elimination by baking, effect of heat treatment, and effect of electroplating on high-strength steels.

Fungal bioleaching of WPCBs using Aspergillus niger: Observation, optimization and kinetics.

PubMed

Faraji, Fariborz; Golmohammadzadeh, Rabeeh; Rashchi, Fereshteh; Alimardani, Navid

2018-07-01

In this study, Aspergillus niger (A. niger) as an environmentally friendly agent for fungal bioleaching of waste printed circuit boards (WPCBs) was employed. D-optimal response surface methodology (RSM) was utilized for optimization of the bioleaching parameters including bioleaching method (one step, two step and spent medium) and pulp densities (0.5 g L -1 to 20 g L -1 ) to maximize the recovery of Zn, Ni and Cu from WPCBs. According to the high performance liquid chromatography analysis, citric, oxalic, malic and gluconic acids were the most abundant organic acids produced by A.niger in 21 days experiments. Maximum recoveries of 98.57% of Zn, 43.95% of Ni and 64.03% of Cu were achieved based on acidolysis and complexolysis dissolution mechanisms of organic acids. Based on the kinetic studies, the rate controlling mechanism for Zn dissolution at one step approach was found to be diffusion through liquid film, while it was found to be mixed control for both two step and spent medium. Furthermore, rate of Cu dissolution which is controlled by diffusion in one step and two step approaches, detected to be controlled by chemical reaction at spent medium. It was shown that for Ni, the rate is controlled by chemical reaction for all the methods studied. Eventually, it was understood that A. niger is capable of leaching 100% of Zn, 80.39% of Ni and 85.88% of Cu in 30 days. Copyright © 2018 Elsevier Ltd. All rights reserved.

Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species

NASA Astrophysics Data System (ADS)

Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar

2018-02-01

The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.

Asynchronous discrete event schemes for PDEs

NASA Astrophysics Data System (ADS)

Stone, D.; Geiger, S.; Lord, G. J.

2017-08-01

A new class of asynchronous discrete-event simulation schemes for advection-diffusion-reaction equations is introduced, based on the principle of allowing quanta of mass to pass through faces of a (regular, structured) Cartesian finite volume grid. The timescales of these events are linked to the flux on the face. The resulting schemes are self-adaptive, and local in both time and space. Experiments are performed on realistic physical systems related to porous media flow applications, including a large 3D advection diffusion equation and advection diffusion reaction systems. The results are compared to highly accurate reference solutions where the temporal evolution is computed with exponential integrator schemes using the same finite volume discretisation. This allows a reliable estimation of the solution error. Our results indicate a first order convergence of the error as a control parameter is decreased, and we outline a framework for analysis.

Kinetics of browning and correlations between browning degree and pyrazine compounds in l-ascorbic acid/acidic amino acid model systems.

PubMed

Yu, Ai-Nong; Zhou, Yong-Yan; Yang, Yi-Ni

2017-04-15

The kinetics of browning and the correlation between browning products (BPs) and pyrazine compounds were investigated by heating equimolar l-ascorbic acid (ASA)/acidic amino acids under weak alkaline conditions at 120-150°C for 10-120min. The formations of BPs and pyrazine compounds from the reaction were monitored by UV-vis and SPME-GC-FID, respectively. The formation of BPs in both ASA/l-glutamic acid and ASA/l-aspartic acid model reaction systems followed zero order reaction kinetics with activation energies (E a ) of 90.13 and 93.38kJ/mol, respectively. ASA/l-aspartic acid browned at a slightly higher rate than ASA/l-glutamic acid. The total concentration of pyrazine compounds was highly and positively correlated with that of BPs. Based on the observed kinetic data, the formation mechanisms of BPs and pyrazine compounds were proposed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Lateral diffusion study of the Pt-Al system using the NAC nuclear microprobe.

NASA Astrophysics Data System (ADS)

de Waal, H.; Pretorius, R.

1999-10-01

In this study a nuclear microprobe (NMP) was used to analyse phase formation during reaction in Pt-Al lateral diffusion couples. Phase identification was done by Rutherford backscattering spectroscopy. These results were compared with phase formation during conventional thin film Pt-Al interactions. The co-existence of multiple phases in lateral diffusion couples is discussed with reference to the effective heat of formation (EHF) model.

Effect of Cr contents on the diffusion behavior of Te in Ni-based alloy

NASA Astrophysics Data System (ADS)

Jia, Yanyan; Li, Zhefu; Ye, Xiangxi; Liu, Renduo; Leng, Bin; Qiu, Jie; Liu, Min; Li, Zhijun

2017-12-01

The embrittlement of Ni-based structural alloys caused by fission production Te is one of the major challenges for molten salt reactors. It has been reported that solution element Cr can prevent the situation of intergranular cracks caused by Te. However, there is no detailed mechanism explanation on this phenomenon. In this study, the effect of Cr on Te diffusion in Ni-Cr binary system was investigated by diffusion experiments at 800 °C for 100 h. Results show that Te reacts with the alloy mainly forming Ni3Te2, and strip shaped Cr3Te4 is only found on the surface of Ni-15%Cr alloy. According to the discussion of thermodynamic chemical reaction process, Cr3Te4 exhibits the best stability and preferential formation compound in Te/Ni-Cr system as its Gibbs free energy of formation is the lowest. With the increase of Cr content in the alloy, the diffusion depth of Te along grain boundaries significantly decreases. Moreover, the formation process of reaction product and diffusion process are described. The diffusion of Te can be suppressed by high content of Cr in Ni-Cr alloy due to the formation of Cr3Te4 and thus the grain boundary is protected from Te corroding.

Influence of Pb 2+ ions in the H 2 oxidation on Pt catalyzed hydrogen diffusion anodes in sulfuric acid: presence of oscillatory phenomena

NASA Astrophysics Data System (ADS)

Expósito, E.; Sánchez-Sánchez, C. M.; Solla-Gullón, J.; Montiel, V.

The influence of Pb 2+ ions in sulfuric acid medium on the behavior of a platinum catalyzed hydrogen diffusion electrode (HDE) in a filter press reactor has been studied. A voltammetric study of the H 2 oxidation reaction on a polyoriented platinum electrode and a platinum rotating disk electrode (RDE) in presence of lead ions in solution has also been carried out. Potential oscillations were found in galvanostatic experiments of H 2 oxidation using a HDE catalyzed with platinum when Pb 2+ ions are present in solution. This oscillatory phenomenon was also observed when hydrogen oxidation was carried out in presence of Pb 2+ ions using a platinum RDE. The oscillatory behavior observed has been attributed to an adsorption-oxidation-desorption process of lead on the platinum surface. Due to the low solubility of Pb 2+ in sulfuric acid, at high values of coverage, lead is oxidised to insoluble lead sulfate that blocks the Pt surface. The coupling of the dissolution of lead sulfate and the Pb electrochemical adsorption-oxidation processes cause the oscillatory phenomenon.

Wave Phenomena in Reaction-Diffusion Systems

NASA Astrophysics Data System (ADS)

Steinbock, Oliver; Engel, Harald

2013-12-01

Pattern formation in excitable and oscillatory reaction-diffusion systems provides intriguing examples for the emergence of macroscopic order from molecular reaction events and Brownian motion. Here we review recent results on several aspects of excitation waves including anomalous dispersion, vortex pinning, and three-dimensional scroll waves. Anomalies in the speed-wavelength dependence of pulse trains include nonmonotonic behavior, bistability, and velocity gaps. We further report on the hysteresis effects during the pinning-depinning transition of twodimensional spiral waves. The pinning of three-dimensional scroll waves shows even richer dynamic complexity, partly due to the possibility of geometric and topological mismatches between the unexcitable, pinning heterogeneities and the one-dimensional rotation backbone of the vortex. As examples we present results on the pinning of scroll rings to spherical, C-shaped, and genus-2-type heterogeneities. We also review the main results of several experimental studies employing the Belousov-Zhabotinsky reaction and briefly discuss the biomedical relevance of this research especially in the context of cardiology.

Diffusion Flame Stabilization

NASA Technical Reports Server (NTRS)

Takahashi, Fumiaki; Katta, V. R.

2006-01-01

Diffusion flames are commonly used for industrial burners in furnaces and flares. Oxygen/fuel burners are usually diffusion burners, primarily for safety reasons, to prevent flashback and explosion in a potentially dangerous system. Furthermore, in most fires, condensed materials pyrolyze, vaporize, and burn in air as diffusion flames. As a result of the interaction of a diffusion flame with burner or condensed-fuel surfaces, a quenched space is formed, thus leaving a diffusion flame edge, which plays an important role in flame holding in combustion systems and fire spread through condensed fuels. Despite a long history of jet diffusion flame studies, lifting/blowoff mechanisms have not yet been fully understood, compared to those of premixed flames. In this study, the structure and stability of diffusion flames of gaseous hydrocarbon fuels in coflowing air at normal earth gravity have been investigated experimentally and computationally. Measurements of the critical mean jet velocity (U(sub jc)) of methane, ethane, or propane at lifting or blowoff were made as a function of the coflowing air velocity (U(sub a)) using a tube burner (i.d.: 2.87 mm). By using a computational fluid dynamics code with 33 species and 112 elementary reaction steps, the internal chemical-kinetic structures of the stabilizing region of methane and propane flames were investigated. A peak reactivity spot, i.e., reaction kernel, is formed in the flame stabilizing region due to back-diffusion of heat and radical species against an oxygen-rich incoming flow, thus holding the trailing diffusion flame. The simulated flame base moved downstream under flow conditions close to the measured stability limit.

Diffusion Flame Stabilization

NASA Technical Reports Server (NTRS)

Takahashi, Fumiaki; Katta, Viswanath R.

2007-01-01

Diffusion flames are commonly used for industrial burners in furnaces and flares. Oxygen/fuel burners are usually diffusion burners, primarily for safety reasons, to prevent flashback and explosion in a potentially dangerous system. Furthermore, in most fires, condensed materials pyrolyze, vaporize, and burn in air as diffusion flames. As a result of the interaction of a diffusion flame with burner or condensed-fuel surfaces, a quenched space is formed, thus leaving a diffusion flame edge, which plays an important role in flame holding in combustion systems and fire spread through condensed fuels. Despite a long history of jet diffusion flame studies, lifting/blowoff mechanisms have not yet been fully understood, compared to those of premixed flames. In this study, the structure and stability of diffusion flames of gaseous hydrocarbon fuels in coflowing air at normal earth gravity have been investigated experimentally and computationally. Measurements of the critical mean jet velocity (U(sub jc)) of methane, ethane, or propane at lifting or blowoff were made as a function of the coflowing air velocity (U(sub a)) using a tube burner (i.d.: 2.87 mm) (Fig. 1, left). By using a computational fluid dynamics code with 33 species and 112 elementary reaction steps, the internal chemical-kinetic structures of the stabilizing region of methane and propane flames were investigated (Fig. 1, right). A peak reactivity spot, i.e., reaction kernel, is formed in the flame stabilizing region due to back-diffusion of heat and radical species against an oxygen-rich incoming flow, thus holding the trailing diffusion flame. The simulated flame base moved downstream under flow conditions close to the measured stability limit.

STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python

PubMed Central

Wils, Stefan; Schutter, Erik De

2008-01-01

We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did not cleanly separate these phases, limiting modelers in how they could control the simulation and becoming increasingly complex as new features and new simulation algorithms were added. We solved all of these problems by tightly integrating STEPS with Python, using SWIG to expose our existing simulation code. PMID:19623245

Flow-Tube Investigations of Hypergolic Reactions of a Dicyanamide Ionic Liquid Via Tunable Vacuum Ultraviolet Aerosol Mass Spectrometry.

PubMed

Chambreau, Steven D; Koh, Christine J; Popolan-Vaida, Denisia M; Gallegos, Christopher J; Hooper, Justin B; Bedrov, Dmitry; Vaghjiani, Ghanshyam L; Leone, Stephen R

2016-10-07

The unusually high heats of vaporization of room-temperature ionic liquids (RTILs) complicate the utilization of thermal evaporation to study ionic liquid reactivity. Although effusion of RTILs into a reaction flow-tube or mass spectrometer is possible, competition between vaporization and thermal decomposition of the RTIL can greatly increase the complexity of the observed reaction products. In order to investigate the reaction kinetics of a hypergolic RTIL, 1-butyl-3-methylimidazolium dicyanamide (BMIM + DCA - ) was aerosolized and reacted with gaseous nitric acid, and the products were monitored via tunable vacuum ultraviolet photoionization time-of-flight mass spectrometry at the Chemical Dynamics Beamline 9.0.2 at the Advanced Light Source. Reaction product formation at m/z 42, 43, 44, 67, 85, 126, and higher masses was observed as a function of HNO 3 exposure. The identities of the product species were assigned to the masses on the basis of their ionization energies. The observed exposure profile of the m/z 67 signal suggests that the excess gaseous HNO 3 initiates rapid reactions near the surface of the RTIL aerosol. Nonreactive molecular dynamics simulations support this observation, suggesting that diffusion within the particle may be a limiting step. The mechanism is consistent with previous reports that nitric acid forms protonated dicyanamide species in the first step of the reaction.

Acid generation mechanism in anion-bound chemically amplified resists used for extreme ultraviolet lithography

NASA Astrophysics Data System (ADS)

Komuro, Yoshitaka; Yamamoto, Hiroki; Kobayashi, Kazuo; Utsumi, Yoshiyuki; Ohomori, Katsumi; Kozawa, Takahiro

2014-11-01

Extreme ultraviolet (EUV) lithography is the most promising candidate for the high-volume production of semiconductor devices with half-pitches of sub-10 nm. An anion-bound polymer (ABP), in which the anion part of onium salts is polymerized, has attracted much attention from the viewpoint of the control of acid diffusion. In this study, the acid generation mechanism in ABP films was investigated using electron (pulse), γ, and EUV radiolyses. On the basis of experimental results, the acid generation mechanism in anion-bound chemically amplified resists was proposed. The major path for proton generation in the absence of effective proton sources is considered to be the reaction of phenyl radicals with diphenylsulfide radical cations that are produced through hole transfer to the decomposition products of onium salts.

Cellular Automata for Spatiotemporal Pattern Formation from Reaction-Diffusion Partial Differential Equations

NASA Astrophysics Data System (ADS)

Ohmori, Shousuke; Yamazaki, Yoshihiro

2016-01-01

Ultradiscrete equations are derived from a set of reaction-diffusion partial differential equations, and cellular automaton rules are obtained on the basis of the ultradiscrete equations. Some rules reproduce the dynamical properties of the original reaction-diffusion equations, namely, bistability and pulse annihilation. Furthermore, other rules bring about soliton-like preservation and periodic pulse generation with a pacemaker, which are not obtained from the original reaction-diffusion equations.

Conformation-dependent chemical reaction of formic acid with an oxygen atom.

PubMed

Khriachtchev, Leonid; Domanskaya, Alexandra; Marushkevich, Kseniya; Räsänen, Markku; Grigorenko, Bella; Ermilov, Alexander; Andrijchenko, Natalya; Nemukhin, Alexander

2009-07-23

Conformation dictates many physical and chemical properties of molecules. The importance of conformation in the selectivity and function of biologically active molecules is widely accepted. However, clear examples of conformation-dependent bimolecular chemical reactions are lacking. Here we consider a case of formic acid (HCOOH) that is a valuable model system containing the -COOH carboxyl functional group, similar to many biomolecules including the standard amino acids. We have found a strong case of conformation-dependent reaction between formic acid and atomic oxygen obtained in cryogenic matrices. The reaction surprisingly leads to peroxyformic acid only from the ground-state trans conformer of formic acid, and it results in the hydrogen-bonded complex for the higher-energy cis conformer.

Micro/nanofabricated environments for synthetic biology.

PubMed

Collier, C Patrick; Simpson, Michael L

2011-08-01

A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.

Fe2P as a novel efficient catalyst promoter in Pd/C system for formic acid electro-oxidation in fuel cells reaction

NASA Astrophysics Data System (ADS)

Wang, Fulong; Xue, Huaiguo; Tian, Zhiqun; Xing, Wei; Feng, Ligang

2018-01-01

Developing catalyst promoter for Pd/C catalyst is significant for the catalytic ability improvement in energy transfer related electrochemical reactions. Herein, we demonstrate Fe2P as an efficient catalyst promoter in Pd/C catalyst system for formic acid electro-oxidation in fuel cells reactions. Adding Fe2P in the Pd/C catalyst system greatly increases the performances for formic acid oxidation by 3-4 times; the CO stripping technique displays two kinds of active sites formation in the Pd-Fe2P/C catalyst system coming from the interaction of Pd, Fe2P and Pd oxide species and both are more efficient for formic acid and CO-species electrooxidation. The smaller charge transfer resistance and Tafel slope for formic acid oxidation indicate the improvements in kinetics by Fe2P in the Pd-Fe2P/C system. The nanostructured hybrid units of Pd, Fe2P and carbon are evidently visible in the high resolution microscopy images and XPS technique confirmes the electronic effect in the catalyst system. The promotion effect of Fe2P in the catalyst system arising from the structure, composition and electronic effect changes is discussed with the help from multiple physical and electrochemical techniques. It is concluded that Fe2P as a significant catalyst promoter will have potential application in energy transfer related electrochemical reactions.

Study on monostable and bistable reaction-diffusion equations by iteration of travelling wave maps

NASA Astrophysics Data System (ADS)

Yi, Taishan; Chen, Yuming

2017-12-01

In this paper, based on the iterative properties of travelling wave maps, we develop a new method to obtain spreading speeds and asymptotic propagation for monostable and bistable reaction-diffusion equations. Precisely, for Dirichlet problems of monostable reaction-diffusion equations on the half line, by making links between travelling wave maps and integral operators associated with the Dirichlet diffusion kernel (the latter is NOT invariant under translation), we obtain some iteration properties of the Dirichlet diffusion and some a priori estimates on nontrivial solutions of Dirichlet problems under travelling wave transformation. We then provide the asymptotic behavior of nontrivial solutions in the space-time region for Dirichlet problems. These enable us to develop a unified method to obtain results on heterogeneous steady states, travelling waves, spreading speeds, and asymptotic spreading behavior for Dirichlet problem of monostable reaction-diffusion equations on R+ as well as of monostable/bistable reaction-diffusion equations on R.

Nonequilibrium Statistical Mechanics in One Dimension

NASA Astrophysics Data System (ADS)

Privman, Vladimir

2005-08-01

Part I. Reaction-Diffusion Systems and Models of Catalysis; 1. Scaling theories of diffusion-controlled and ballistically-controlled bimolecular reactions S. Redner; 2. The coalescence process, A+A->A, and the method of interparticle distribution functions D. ben-Avraham; 3. Critical phenomena at absorbing states R. Dickman; Part II. Kinetic Ising Models; 4. Kinetic ising models with competing dynamics: mappings, correlations, steady states, and phase transitions Z. Racz; 5. Glauber dynamics of the ising model N. Ito; 6. 1D Kinetic ising models at low temperatures - critical dynamics, domain growth, and freezing S. Cornell; Part III. Ordering, Coagulation, Phase Separation; 7. Phase-ordering dynamics in one dimension A. J. Bray; 8. Phase separation, cluster growth, and reaction kinetics in models with synchronous dynamics V. Privman; 9. Stochastic models of aggregation with injection H. Takayasu and M. Takayasu; Part IV. Random Sequential Adsorption and Relaxation Processes; 10. Random and cooperative sequential adsorption: exactly solvable problems on 1D lattices, continuum limits, and 2D extensions J. W. Evans; 11. Lattice models of irreversible adsorption and diffusion P. Nielaba; 12. Deposition-evaporation dynamics: jamming, conservation laws and dynamical diversity M. Barma; Part V. Fluctuations In Particle and Surface Systems; 13. Microscopic models of macroscopic shocks S. A. Janowsky and J. L. Lebowitz; 14. The asymmetric exclusion model: exact results through a matrix approach B. Derrida and M. R. Evans; 15. Nonequilibrium surface dynamics with volume conservation J. Krug; 16. Directed walks models of polymers and wetting J. Yeomans; Part VI. Diffusion and Transport In One Dimension; 17. Some recent exact solutions of the Fokker-Planck equation H. L. Frisch; 18. Random walks, resonance, and ratchets C. R. Doering and T. C. Elston; 19. One-dimensional random walks in random environment K. Ziegler; Part VII. Experimental Results; 20. Diffusion-limited exciton kinetics in one-dimensional systems R. Kroon and R. Sprik; 21. Experimental investigations of molecular and excitonic elementary reaction kinetics in one-dimensional systems R. Kopelman and A. L. Lin; 22. Luminescence quenching as a probe of particle distribution S. H. Bossmann and L. S. Schulman; Index.

Measurement of diffusion coefficients important in modeling the absorption rate of carbon dioxide into aqueous N-methyldiethanolamine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rowley, R.L.; Adams, M.E.; Marshall, T.L.

1997-03-01

Natural gas processors use amine treating processes to remove the acid gases H{sub 2}S and CO{sub 2} from gas streams. Absorption rates of gaseous CO{sub 2} into aqueous N-methyldiethanolamine (MDEA) solutions were measured in a quiescent, inverted-tube diffusiometer by monitoring the rate of pressure drop. The absorption rate was found to be insensitive to the diffusion coefficient of CO{sub 2} in solution but very sensitive to the diffusion rate of bicarbonate and protonated MDEA ions. Evidence also suggested that chemical reaction equilibrium is rapid relative to diffusion. A numerical model was developed on the basis of these observations. The modelmore » was used to regress diffusion coefficients of bicarbonate and protonated amine, which must be equivalent by electroneutrality arguments, from measured absorption rates. Complete modeling of the absorption process also required data for the diffusion coefficient of MDEA in water. These were measured using a Taylor dispersion apparatus. CO{sub 2} absorption rates and diffusion coefficients of bicarbonate and protonated MDEA were obtained at 298.2 K and 318.2 K in solutions containing 20, 35, and 50 mass % MDEA in water.« less

Soot Formation in Hydrocarbon/Air Laminar Jet Diffusion Flames

NASA Technical Reports Server (NTRS)

Sunderland, P. B.; Faeth, G. M.

1994-01-01

Soot processes within hydrocarbon/air diffusion flames are important because they affect the durability and performance of propulsion systems, the hazards of unwanted fires, the pollutant and particulate emissions from combustion processes, and the potential for developing computational combustion. Motivated by these observations, this investigation involved an experimental study of the structure and soot properties of round laminar jet diffusion flames, seeking an improved understanding of soot formation (growth and nucleation) within diffusion flames. The present study extends earlier work in this laboratory concerning laminar smoke points (l) and soot formation in acetylene/air laminar jet diffusion flames (2), emphasizing soot formation in hydrocarbon/air laminar jet diffusion flames for fuels other than acetylene. In the flame system, acetylene is the dominant gas species in the soot formation region and both nucleation and growth were successfully attributed to first-order reactions of acetylene, with nucleation exhibiting an activation energy of 32 kcal/gmol while growth involved negligible activation energy and a collision efficiency of O.53%. In addition, soot growth in the acetylene diffusion flames was comparable to new soot in premixed flame (which also has been attributed to first-order acetylene reactions). In view of this status, a major issue is the nature of soot formation processes in diffusion flame involving hydrocarbon fuels other than acetylene. In particular, information is needed about th dominant gas species in the soot formation region and the impact of gas species other than acetylene on soot nucleation and growth.

Molecules in motion: influences of diffusion on metabolic structure and function in skeletal muscle

PubMed Central

Kinsey, Stephen T.; Locke, Bruce R.; Dillaman, Richard M.

2011-01-01

Metabolic processes are often represented as a group of metabolites that interact through enzymatic reactions, thus forming a network of linked biochemical pathways. Implicit in this view is that diffusion of metabolites to and from enzymes is very fast compared with reaction rates, and metabolic fluxes are therefore almost exclusively dictated by catalytic properties. However, diffusion may exert greater control over the rates of reactions through: (1) an increase in reaction rates; (2) an increase in diffusion distances; or (3) a decrease in the relevant diffusion coefficients. It is therefore not surprising that skeletal muscle fibers have long been the focus of reaction–diffusion analyses because they have high and variable rates of ATP turnover, long diffusion distances, and hindered metabolite diffusion due to an abundance of intracellular barriers. Examination of the diversity of skeletal muscle fiber designs found in animals provides insights into the role that diffusion plays in governing both rates of metabolic fluxes and cellular organization. Experimental measurements of metabolic fluxes, diffusion distances and diffusion coefficients, coupled with reaction–diffusion mathematical models in a range of muscle types has started to reveal some general principles guiding muscle structure and metabolic function. Foremost among these is that metabolic processes in muscles do, in fact, appear to be largely reaction controlled and are not greatly limited by diffusion. However, the influence of diffusion is apparent in patterns of fiber growth and metabolic organization that appear to result from selective pressure to maintain reaction control of metabolism in muscle. PMID:21177946

Dynamics of localized structures in reaction-diffusion systems induced by delayed feedback

NASA Astrophysics Data System (ADS)

Gurevich, Svetlana V.

2013-05-01

We are interested in stability properties of a single localized structure in a three-component reaction-diffusion system subjected to the time-delayed feedback. We shall show that variation in the product of the delay time and the feedback strength leads to complex dynamical behavior of the system, including formation of target patterns, spontaneous motion, and spontaneous breathing as well as various complex structures, arising from combination of different oscillatory instabilities. In the case of spontaneous motion, we provide a bifurcation analysis of the delayed system and derive an order parameter equation for the position of the localized structure, explicitly describing its temporal evolution in the vicinity of the bifurcation point. This equation is a subject to a nonlinear delay differential equation, which can be transformed to the normal form of the pitchfork drift bifurcation.

Quasi elastic and inelastic neutron scattering study of vitamin C aqueous solutions

NASA Astrophysics Data System (ADS)

Migliardo, F.; Branca, C.; Magazù, S.; Migliardo, P.; Coppolino, S.; Villari, A.; Micali, N.

2002-02-01

In this paper, new results obtained by quasi elastic and inelastic neutron scattering experiments performed on vitamin C ( L-ascorbic acid)/H 2O mixtures are reported. The data analysis of the QENS measurements, by a separation of the diffusive dynamics of hydrated L-ascorbic acid from that of water, furnishes quantitative evidences of a random jump diffusion motion of vitamin C and shows that the water dynamics is strongly affected by the presence of L-ascorbic acid. Concerning the INS experiment, we are able, through the behaviour of neutron spectra across the glass transition temperature ( T g≈233 K for the vitamin C/water system), to collocate the investigated system in the Angell “strong-fragile” scheme.

Influence of post exposure bake time on EUV photoresist RLS trade-off

NASA Astrophysics Data System (ADS)

Vesters, Yannick; De Simone, Danilo; De Gendt, Stefan

2017-03-01

To achieve high volume manufacturing, EUV photoresists need to push back the "RLS trade-off" by simultaneously improving Resolution, Line-Width Roughness and Sensitivity (exposure dose). Acid diffusion in chemically amplified resist is known to impact these performances. This work studies the diffusion of acid in chemically amplified resist by varying the post exposure bake duration while monitoring the evolution of CD and LWR for 6 chemically amplified EUV photoresists (CAR). We observed a first regime where both CD and LWR quickly decrease during the first 30s of post exposure bake (PEB). This can be related to the deprotection reaction taking place in the exposed part of the resist. After 60s the decrease in CD and LWR slows down significantly, likely related to a regime of acid diffusion from exposed to unexposed region, and acid-quencher neutralization at the interface of these two regions. We tested two resists with different protecting group and the one having lower activation energy shows a faster CD change in the second regime, resulting in a worsening of LWR for longer PEB time. On the contrary, a resist with a high quencher loading shows reduced net diffusion of acid towards the unexposed region and controls the resist edge profile. In other words longer PEB does not degrade LWR, but as it reduces the line CD, sensitivity is impacted. With an appropriate ratio selection of quencher to PAG, an EUV dose reduction of up to 12% can be achieved with a change from a standard 60 second to a 240 second PEB time, while keeping LWR and resolution constant and therefore pushing the RLS performances. Finally, we confirmed that the observations on positive tone development (PTD) resist could be applied to negative tone development (NTD) resist: with a high quencher NTD resist we observed a dose reduction of 8% for longer PEB time, keeping LWR and resolution constant.

Mean-field hierarchical equations for some A+BC catalytic reaction models

NASA Astrophysics Data System (ADS)

Cortés, Joaquín; Puschmann, Heinrich; Valencia, Eliana

1998-10-01

A mean-field study of the (A+BC→AC+1/2B2) system is developed from hierarchical equations, considering mechanisms that include dissociation, reaction with finite rates, desorption, and diffusion of the adsorbed species. The phase diagrams are compared to Monte Carlo simulations.

Photoreverse Reaction Dynamics of Octopus Rhodopsin

PubMed Central

Inoue, Keiichi; Tsuda, Motoyuki; Terazima, Masahide

2007-01-01

Photoreverse reactions of octopus rhodopsin (Rh) from acid-metarhodopsin (Acid-Meta), which is the final product of the photoreaction of Rh, to Rh were studied by the time-resolved transient absorption and transient grating methods. The time course of the absorption signal showed a rapid change within 500 ns followed by one phase with a time constant of ∼470 μs, whereas the transient grating signal indicates three phases with time constants of <500 ns, ∼490 μs, and 2.6 ms. The faster two phases indicate the conformational change in the vicinity of the chromophore, and the slowest one represents conformational change far from the chromophore. The absorption spectrum of the first intermediate created just after the laser excitation (<500 ns) is already very similar to the final product, Rh. This behavior is quite different from that of the forward reaction from Rh to Acid-Meta, in which several intermediates with different absorption spectra are involved within 50 ns–500 μs. This result indicates that the conformation around the chromophore is easily adjusted from all-trans to 11-cis forms compared with that from 11-cis to all-trans forms. Furthermore, it was found that the protein energy is quickly relaxed after the excitation. One of the significantly different properties between Rh and Acid-Meta is the diffusion coefficient (D). D is reduced by about half the transformation from Rh to Acid-Meta. This large reduction was interpreted in terms of the helix opening of the Rh structure. PMID:17325000

Synchronization criteria for generalized reaction-diffusion neural networks via periodically intermittent control.

PubMed

Gan, Qintao; Lv, Tianshi; Fu, Zhenhua

2016-04-01

In this paper, the synchronization problem for a class of generalized neural networks with time-varying delays and reaction-diffusion terms is investigated concerning Neumann boundary conditions in terms of p-norm. The proposed generalized neural networks model includes reaction-diffusion local field neural networks and reaction-diffusion static neural networks as its special cases. By establishing a new inequality, some simple and useful conditions are obtained analytically to guarantee the global exponential synchronization of the addressed neural networks under the periodically intermittent control. According to the theoretical results, the influences of diffusion coefficients, diffusion space, and control rate on synchronization are analyzed. Finally, the feasibility and effectiveness of the proposed methods are shown by simulation examples, and by choosing different diffusion coefficients, diffusion spaces, and control rates, different controlled synchronization states can be obtained.

Consequences of acid strength for isomerization and elimination catalysis on solid acids.

PubMed

Macht, Josef; Carr, Robert T; Iglesia, Enrique

2009-05-13

We address here the manner in which acid catalysis senses the strength of solid acids. Acid strengths for Keggin polyoxometalate (POM) clusters and zeolites, chosen because of their accurately known structures, are described rigorously by their deprotonation energies (DPE). Mechanistic interpretations of the measured dynamics of alkane isomerization and alkanol dehydration are used to obtain rate and equilibrium constants and energies for intermediates and transition states and to relate them to acid strength. n-Hexane isomerization rates were limited by isomerization of alkoxide intermediates on bifunctional metal-acid mixtures designed to maintain alkane-alkene equilibrium. Isomerization rate constants were normalized by the number of accessible protons, measured by titration with 2,6-di-tert-butylpyridine during catalysis. Equilibrium constants for alkoxides formed by protonation of n-hexene increased slightly with deprotonation energies (DPE), while isomerization rate constants decreased and activation barriers increased with increasing DPE, as also shown for alkanol dehydration reactions. These trends are consistent with thermochemical analyses of the transition states involved in isomerization and elimination steps. For all reactions, barriers increased by less than the concomitant increase in DPE upon changes in composition, because electrostatic stabilization of ion-pairs at the relevant transition states becomes more effective for weaker acids, as a result of their higher charge density at the anionic conjugate base. Alkoxide isomerization barriers were more sensitive to DPE than for elimination from H-bonded alkanols, the step that limits 2-butanol and 1-butanol dehydration rates; the latter two reactions showed similar DPE sensitivities, despite significant differences in their rates and activation barriers, indicating that slower reactions are not necessarily more sensitive to acid strength, but instead reflect the involvement of more unstable organic cations at their transition states. These compensating effects from electrostatic stabilization depend on how similar the charge density in these organic cations is to that in the proton removed. Cations with more localized charge favor strong electrostatic interactions with anions and form more stable ionic structures than do cations with more diffuse charges. Ion-pairs at elimination transition states contain cations with higher local charge density at the sp(2) carbon than for isomerization transition states; as a result, these ion-pairs recover a larger fraction of the deprotonation energy, and, consequently, their reactions become less sensitive to acid strength. These concepts lead us to conclude that the energetic difficulty of a catalytic reaction, imposed by gas-phase reactant proton affinities in transition state analogues, does not determine its sensitivity to the acid strength of solid catalysts.

Application of gas diffusion electrodes in bioelectrochemical syntheses and energy conversion.

PubMed

Horst, Angelika E W; Mangold, Klaus-Michael; Holtmann, Dirk

2016-02-01

Combining the advantages of biological components (e.g., reaction specificity, self-replication) and electrochemical techniques in bioelectrochemical systems offers the opportunity to develop novel efficient and sustainable processes for the production of a number of valuable products. The choice of electrode material has a great impact on the performance of bioelectrochemical systems. In addition to the redox process at the electrodes, interactions of biocatalysts with electrodes (e.g., enzyme denaturation or biofouling) need to be considered. In recent years, gas diffusion electrodes (GDEs) have proved to be very attractive electrodes for bioelectrochemical purposes. GDEs are porous electrodes, that posses a large three-phase boundary surface. At this interface, a solid catalyst supports the electrochemical reaction between gaseous and liquid phase. This mini-review discusses the application of GDEs in microbial and enzymatic fuel cells, for microbial electrolysis, in biosensors and for electroenzymatic synthesis reactions. © 2015 Wiley Periodicals, Inc.

Production of sugars and levulinic acid from marine biomass Gelidium amansii.

PubMed

Jeong, Gwi-Taek; Park, Don-Hee

2010-05-01

This study focused on optimization of reaction conditions for formation of sugars and levulinic acid from marine algal biomass Gelidium amansii using acid catalyst and by using statistical approach. By this approach, optimal conditions for production of sugars and levulinic acid were found as follows: glucose (reaction temperature of 139.4 degrees C, reaction time of 15.0 min, and catalyst concentration of 3.0%), galactose (108.2 degrees C, 45.0 min, and 3.0%), and levulinic acid (160.0 degrees C, 43.1 min, and 3.0%). While trying to optimize the conditions for the production of glucose and galactose, levulinic acid production was found to be minimum. Similarly, the production of glucose and galactose were found to be minimum while optimizing the conditions for the production of levulinic acid. In addition, optimized production of glucose required a higher reaction temperature and shorter reaction time than that of galactose. Levulinic acid was formed at a high reaction temperature, long reaction time, and high catalyst concentration. The combined results of this study may provide useful information to develop more economical and efficient systems for production of sugars and chemicals from marine biomass.

Restoration of rhythmicity in diffusively coupled dynamical networks.

PubMed

Zou, Wei; Senthilkumar, D V; Nagao, Raphael; Kiss, István Z; Tang, Yang; Koseska, Aneta; Duan, Jinqiao; Kurths, Jürgen

2015-07-15

Oscillatory behaviour is essential for proper functioning of various physical and biological processes. However, diffusive coupling is capable of suppressing intrinsic oscillations due to the manifestation of the phenomena of amplitude and oscillation deaths. Here we present a scheme to revoke these quenching states in diffusively coupled dynamical networks, and demonstrate the approach in experiments with an oscillatory chemical reaction. By introducing a simple feedback factor in the diffusive coupling, we show that the stable (in)homogeneous steady states can be effectively destabilized to restore dynamic behaviours of coupled systems. Even a feeble deviation from the normal diffusive coupling drastically shrinks the death regions in the parameter space. The generality of our method is corroborated in diverse non-linear systems of diffusively coupled paradigmatic models with various death scenarios. Our study provides a general framework to strengthen the robustness of dynamic activity in diffusively coupled dynamical networks.

Iron Hydroxide Minerals Drive Organic and Phosphorus Chemistry in Subsurface Redox / pH Gradients

NASA Astrophysics Data System (ADS)

Flores, E.; Barge, L. M.; VanderVelde, D.; Baum, M.

2017-12-01

Iron minerals, particularly iron oxides and oxyhydroxides, are prevalent on Mars and may exist in mixed valence or even reduced states beneath the oxidized surface. Iron (II,III) hydroxides, including green rust, are reactive and potentially catalytic minerals that can absorb and concentrate charged species, while also driving chemical reactions. These minerals are highly redox-sensitive and the presence of organics and/or phosphorus species could affect their mineralogy and/or stability. Conversely, the minerals might be able to drive chemical processes such as amino acid formation, phosphorus oxyanion reactions, or could simply selectively preserve organic species via surface adsorption. In an open aqueous sediment column, soluble products of mineral-driven reactions could also diffuse to sites of different chemical conditions to react even further. We synthesized Fe-hydroxide minerals under various conditions relevant to early Earth and ancient Mars (>3.0 Gyr), anoxically and in the presence of salts likely to have been present in surface or ground waters. Using these minerals we conducted experiments to test whether iron hydroxides could promote amino acid formation, and how the reaction is affected by subsurface gradients of redox, pH, and temperature. We also tested the adsorption of organic and phosphorus species onto Fe-hydroxide minerals at different conditions within the gradients. The suite of organic or phosphorus signatures that may be found in a particular mineral system is a combination of what is synthesized there, what is preferentially concentrated / retained there, and what is preserved against degradation. Further work is needed to determine how these processes could have proceeded on Mars and what mineral-organic signatures, abiotic or otherwise, would be produced from such processes.

Study on US/O3 mechanism in p-chlorophenol decomposition

PubMed Central

Xu, Xian-wen; Xu, Xin-hua; Shi, Hui-xiang; Wang, Da-hui

2005-01-01

Study on the effects of sonolysis, ozonolysis and US/O3 system on the decomposition of p-chlorophenol in aqueous solutions indicated that in the cases of US/O3 system, individual ozonolysis and sonolysis, the decomposition rate of p-chlorophenol reached 78.78%, 56.20%, 2.79% after a 16-min reaction while its CODcr (chemical oxygen demand) removal rate was 97.02%, 62.17%, 3.67% after a 120-min reaction. The decomposition reaction of p-chlorophenol follows pseudo-first-order kinetics. The enhancement factors of p-chlorophenol and its CODcr under US/O3 system reached 63% and 237% respectively. The main intermediates during the decomposition include catechol, hydroquinone, p-benzoquinone, phenol, fumaric acid, maleic acid, oxalic acid and formic acid. The decomposition mechanism of p-chlorophenol was also discussed. PMID:15909343

The heat released during catalytic turnover enhances the diffusion of an enzyme

PubMed Central

Riedel, Clement; Gabizon, Ronen; Wilson, Christian A. M.; Hamadani, Kambiz; Tsekouras, Konstantinos; Marqusee, Susan; Pressé, Steve; Bustamante, Carlos

2015-01-01

Recent studies have shown that the diffusivity of enzymes increases in a substrate-dependent manner during catalysis1,2. Although this observation has been reported and characterized for several different systems3–10, the precise origin of this phenomenon is unknown. Calorimetric methods are often used to determine enthalpies from enzyme-catalysed reactions and can therefore provide important insight into their reaction mechanisms11,12. The ensemble averages involved in traditional bulk calorimetry cannot probe the transient effects that the energy exchanged in a reaction may have on the catalyst. Here we obtain single-molecule fluorescence correlation spectroscopy data and analyse them within the framework of a stochastic theory to demonstrate a mechanistic link between the enhanced diffusion of a single enzyme molecule and the heat released in the reaction. We propose that the heat released during catalysis generates an asymmetric pressure wave that results in a differential stress at the protein–solvent interface that transiently displaces the centre-of-mass of the enzyme (chemoacoustic effect). This novel perspective on how enzymes respond to the energy released during catalysis suggests a possible effect of the heat of reaction on the structural integrity and internal degrees of freedom of the enzyme. PMID:25487146

The heat released during catalytic turnover enhances the diffusion of an enzyme

DOE PAGES

Riedel, Clement; Gabizon, Ronen; Wilson, Christian A. M.; ...

2014-12-10

Recent studies have shown that the diffusivity of enzymes increases in a substrate-dependent manner during catalysis. Although this observation has been reported and characterized for several different systems, the precise origin of this phenomenon is unknown. Calorimetric methods are often used to determine enthalpies from enzyme-catalysed reactions and can therefore provide important insight into their reaction mechanisms. The ensemble averages involved in traditional bulk calorimetry cannot probe the transient effects that the energy exchanged in a reaction may have on the catalyst. Here we obtain single-molecule fluorescence correlation spectroscopy data and analyse them within the framework of a stochastic theorymore » to demonstrate a mechanistic link between the enhanced diffusion of a single enzyme molecule and the heat released in the reaction. We propose that the heat released during catalysis generates an asymmetric pressure wave that results in a differential stress at the protein-solvent interface that transiently displaces the centre-of-mass of the enzyme (chemoacoustic effect). We find this novel perspective on how enzymes respond to the energy released during catalysis suggests a possible effect of the heat of reaction on the structural integrity and internal degrees of freedom of the enzyme.« less

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

PubMed Central

2012-01-01

Background Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. Results We describe STEPS, a stochastic reaction–diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction–diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. Conclusion STEPS simulates models of cellular reaction–diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/ PMID:22574658

Unprecedented homotopy perturbation method for solving nonlinear equations in the enzymatic reaction of glucose in a spherical matrix.

PubMed

Saranya, K; Mohan, V; Kizek, R; Fernandez, C; Rajendran, L

2018-02-01

The theory of glucose-responsive composite membranes for the planar diffusion and reaction process is extended to a microsphere membrane. The theoretical model of glucose oxidation and hydrogen peroxide production in the chitosan-aliginate microsphere has been discussed in this manuscript for the first time. We have successfully reported an analytical derived methodology utilizing homotopy perturbation to perform the numerical simulation. The influence and sensitive analysis of various parameters on the concentrations of gluconic acid and hydrogen peroxide are also discussed. The theoretical results enable to predict and optimize the performance of enzyme kinetics.

Kinetics of DNA-mediated docking reactions between vesicles tethered to supported lipid bilayers

PubMed Central

Chan, Yee-Hung M.; Lenz, Peter; Boxer, Steven G.

2007-01-01

Membrane–membrane recognition and binding are crucial in many biological processes. We report an approach to studying the dynamics of such reactions by using DNA-tethered vesicles as a general scaffold for displaying membrane components. This system was used to characterize the docking reaction between two populations of tethered vesicles that display complementary DNA. Deposition of vesicles onto a supported lipid bilayer was performed by using a microfluidic device to prevent mixing of the vesicles in bulk during sample preparation. Once tethered onto the surface, vesicles mixed via two-dimensional diffusion. DNA-mediated docking of two reacting vesicles results in their colocalization after collision and their subsequent tandem motion. Individual docking events and population kinetics were observed via epifluorescence microscopy. A lattice-diffusion simulation was implemented to extract from experimental data the probability, Pdock, that a collision leads to docking. For individual vesicles displaying small numbers of docking DNA, Pdock shows a first-order relationship with copy number as well as a strong dependence on the DNA sequence. Both trends are explained by a model that includes both tethered vesicle diffusion on the supported bilayer and docking DNA diffusion over each vesicle's surface. These results provide the basis for the application of tethered vesicles to study other membrane reactions including protein-mediated docking and fusion. PMID:18025472

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers

PubMed Central

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation. PMID:28239346

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers.

PubMed

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation.

Theory of Neutron Chain Reactions: Extracts from Volume I, Diffusion and Slowing Down of Neutrons: Chapter I. Elementary Theory of Neutron Diffusion. Chapter II. Second Order Diffusion Theory. Chapter III. Slowing Down of Neutrons

DOE R&D Accomplishments Database

Weinberg, Alvin M.; Noderer, L. C.

1951-05-15

The large scale release of nuclear energy in a uranium fission chain reaction involves two essentially distinct physical phenomena. On the one hand there are the individual nuclear processes such as fission, neutron capture, and neutron scattering. These are essentially quantum mechanical in character, and their theory is non-classical. On the other hand, there is the process of diffusion -- in particular, diffusion of neutrons, which is of fundamental importance in a nuclear chain reaction. This process is classical; insofar as the theory of the nuclear chain reaction depends on the theory of neutron diffusion, the mathematical study of chain reactions is an application of classical, not quantum mechanical, techniques.

Miniaturized isothermal nucleic acid amplification, a review.

PubMed

Asiello, Peter J; Baeumner, Antje J

2011-04-21

Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.

Catalytic total hydrodeoxygenation of biomass-derived polyfunctionalized substrates to alkanes.

PubMed

Nakagawa, Yoshinao; Liu, Sibao; Tamura, Masazumi; Tomishige, Keiichi

2015-04-13

The total hydrodeoxygenation of carbohydrate-derived molecules to alkanes, a key reaction in the production of biofuel, was reviewed from the aspect of catalysis. Noble metals (or Ni) and acid are the main components of the catalysts, and group 6 or 7 metals such as Re are sometimes added as modifiers of the noble metal. The main reaction route is acid-catalyzed dehydration plus metal-catalyzed hydrogenation, and in some systems metal-catalyzed direct CO dissociation is involved. The appropriate active metal, acid strength, and reaction conditions depend strongly on the reactivity of the substrate. Reactions that use Pt or Pd catalysts supported on Nb-based acids or relatively weak acids are suitable for furanic substrates. Carbohydrates themselves and sugar alcohols undergo CC dissociation easily. The systems that use metal-catalyzed direct CO dissociations can give a higher yield of the corresponding alkane from carbohydrates and sugar alcohols. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of Reaction Mechanism on the Lime-Free Roasting of Chromium-Containing Slag

NASA Astrophysics Data System (ADS)

Yu, Kai-ping; Zhang, Hong-ling; Chen, Bo; Xu, Hong-bin; Zhang, Yi

2015-12-01

The lime-free roasting process of trivalent chromium-containing slag was investigated. The effect of Fe and liquid phase on the conversion reaction of chromium was discussed. The oxidation of trivalent chromium depends greatly on the diffusion of Na+ and O2. Both the raw material Na2CO3 and the intermediate product NaFeO2 serve as the carriers of Na+. The Na+ diffusion is improved by the binary liquid phase of Na2CrO4-Na2CO3, whereas excess liquid phase results in a low conversion rate of chromium by hindering the diffusion of oxygen towards the reaction interface. With the increasing of liquid volume, the controlled step of chromium oxidation changes from Na+ diffusion to oxygen diffusion. The mechanism study showed that the volume of liquid phase increased while raising the reaction temperature or prolonging the reaction time. Based on the role of both liquid phase and Fe, the oxidation process of chromium was summarized as a three-stage model: the Na+ diffusion-controlled stage, the O2 diffusion-controlled stage, and the oxidation reaction halted stage.

Production of alpha-hydroxy carboxylic acids and esters from higher sugars using tandem catalyst systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orazov, Marat; Davis, Mark E.

The present disclosure is directed to methods and composition used in the preparation of alpha-hydroxy carboxylic acids and esters from higher sugars using a tandem catalyst system comprising retro-aldol catalysts and Lewis acid catalysts. In some embodiments, these alpha-hydroxy carboxylic acids may be prepared from pentoses and hexoses. The retro-aldol and Lewis catalysts may be characterized by their respective ability to catalyze a 1,2-carbon shift reaction and a 1,2-hydride shift reaction on an aldose or ketose substrate.

Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions

PubMed Central

Johnson, Margaret E.; Hummer, Gerhard

2012-01-01

We explore the theoretical foundation of different string methods used to find dominant reaction pathways in high-dimensional configuration spaces. Pathways are assessed by the amount of reactive flux they carry and by their orientation relative to the committor function. By examining the effects of transforming between different collective coordinates that span the same underlying space, we unmask artificial coordinate dependences in strings optimized to follow the free energy gradient. In contrast, strings optimized to follow the drift vector produce reaction pathways that are significantly less sensitive to reparameterizations of the collective coordinates. The differences in these paths arise because the drift vector depends on both the free energy gradient and the diffusion tensor of the coarse collective variables. Anisotropy and position dependence of diffusion tensors arise commonly in spaces of coarse variables, whose generally slow dynamics are obtained by nonlinear projections of the strongly coupled atomic motions. We show here that transition paths constructed to account for dynamics by following the drift vector will (to a close approximation) carry the maximum reactive flux both in systems with isotropic position dependent diffusion, and in systems with constant but anisotropic diffusion. We derive a simple method for calculating the committor function along paths that follow the reactive flux. Lastly, we provide guidance for the practical implementation of the dynamic string method. PMID:22616575

Mode Reduction and Upscaling of Reactive Transport Under Incomplete Mixing

NASA Astrophysics Data System (ADS)

Lester, D. R.; Bandopadhyay, A.; Dentz, M.; Le Borgne, T.

2016-12-01

Upscaling of chemical reactions in partially-mixed fluid environments is a challenging problem due to the detailed interactions between inherently nonlinear reaction kinetics and complex spatio-temporal concentration distributions under incomplete mixing. We address this challenge via the development of an order reduction method for the advection-diffusion-reaction equation (ADRE) via projection of the reaction kinetics onto a small number N of leading eigenmodes of the advection-diffusion operator (the so-called "strange eigenmodes" of the flow) as an N-by-N nonlinear system, whilst mixing dynamics only are projected onto the remaining modes. For simple kinetics and moderate Péclet and Damkhöler numbers, this approach yields analytic solutions for the concentration mean, evolving spatio-temporal distribution and PDF in terms of the well-mixed reaction kinetics and mixing dynamics. For more complex kinetics or large Péclet or Damkhöler numbers only a small number of modes are required to accurately quantify the mixing and reaction dynamics in terms of the concentration field and PDF, facilitating greatly simplified approximation and analysis of reactive transport. Approximate solutions of this low-order nonlinear system provide quantiative predictions of the evolving concentration PDF. We demonstrate application of this method to a simple random flow and various mass-action reaction kinetics.

Gas-Phase Anionic σ-Adduct (Trans)formations in Heteroaromatic Systems1

NASA Astrophysics Data System (ADS)

Zimnicka, Magdalena; Danikiewicz, Witold

2015-07-01

Anions of nitroderivatives of thiophene and furan were subjected to the reactions with selected C-H acids in the gas phase. Various structures and reaction pathways were proposed for the observed ionic products. In general, the reactions of heteroaromatic anions with C-H acids may be divided into three groups, depending on the proton affinity difference between C-H acid's conjugate base and heteroaromatic anion (ΔPA). The proton transfer from C-H acid to heteroaromatic anion is a dominant process in the reactions for which ΔPA < 0 kcal mol-1, whereas the reactions with high ΔPA (ΔPA > 16 kcal mol-1) do not lead to any ionic products. The formation of σ-adducts and products of their further transformations according to the VNS, SNAr, cine, and tele substitution mechanisms have been proposed for reactions with moderate ΔPA. The other possible mechanisms as SN2 reaction, nucleophilic addition to the cyano group, ring-opening pathway, and halogenophilic reaction have also been discussed to contribute in the reactions between heteroaromatic anions and C-H acids.

Diffusive confinement of free radical intermediates in the OH radical oxidation of semisolid aerosols

DOE PAGES

Wiegel, Aaron A.; Liu, Matthew J.; Hinsberg, William D.; ...

2017-02-07

Multiphase chemical reactions (gas + solid/liquid) involve a complex interplay between bulk and interface chemistry, diffusion, evaporation, and condensation. Reactions of atmospheric aerosols are an important example of this type of chemistry: the rich array of particle phase states and multiphase transformation pathways produce diverse but poorly understood interactions between chemistry and transport. Their chemistry is of intrinsic interest because of their role in controlling climate. Their characteristics also make them useful models for the study of principles of reactivity of condensed materials under confined conditions. Previously, we have reported a computational study of the oxidation chemistry of a liquidmore » aliphatic aerosol. In this study, we extend the calculations to investigate nearly the same reactions at a semisolid gas-aerosol interface. A reaction-diffusion model for heterogeneous oxidation of triacontane by hydroxyl radicals (OH) is described, and its predictions are compared to measurements of aerosol size and composition, which evolve continuously during oxidation. Our results are also explicitly compared to those obtained for the corresponding liquid system, squalane, to pinpoint salient elements controlling reactivity. The diffusive confinement of the free radical intermediates at the interface results in enhanced importance of a few specific chemical processes such as the involvement of aldehydes in fragmentation and evaporation, and a significant role of radical-radical reactions in product formation. The simulations show that under typical laboratory conditions semisolid aerosols have highly oxidized nanometer-scale interfaces that encapsulate an unreacted core and may confer distinct optical properties and enhanced hygroscopicity. This highly oxidized layer dynamically evolves with reaction, which we propose to result in plasticization. The validated model is used to predict chemistry under atmospheric conditions, where the OH radical concentration is much lower. The oxidation reactions are more strongly influenced by diffusion in the particle, resulting in a more liquid-like character.« less

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

NASA Astrophysics Data System (ADS)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

Dynamics and Stabilization of Materials Possessing High Energy Content

DTIC Science & Technology

1991-10-31

Barton, Nucl. Acids Res., J2, 2595 (1991). 24. "Diffusion and Percolation of Radical Pairs in Zeolite Media. A Product Analysis Study," J. Am. Chem...Photobiol. A: Chem., i, 35 (1991). 33. "Effect of External Pressure on Photoinduced Electron-Transfer Reactions in the Marcus Inverted Region," W.-S. Chung...duPont (Towanda, PA), Unilever USA Research (Edgewater, NJ), IBM Almaden Research Labs (San Jose, CA), Hoeschst Chemical Company (Frankfurt, Germany

Cooperativity to increase Turing pattern space for synthetic biology.

PubMed

Diambra, Luis; Senthivel, Vivek Raj; Menendez, Diego Barcena; Isalan, Mark

2015-02-20

It is hard to bridge the gap between mathematical formulations and biological implementations of Turing patterns, yet this is necessary for both understanding and engineering these networks with synthetic biology approaches. Here, we model a reaction-diffusion system with two morphogens in a monostable regime, inspired by components that we recently described in a synthetic biology study in mammalian cells.1 The model employs a single promoter to express both the activator and inhibitor genes and produces Turing patterns over large regions of parameter space, using biologically interpretable Hill function reactions. We applied a stability analysis and identified rules for choosing biologically tunable parameter relationships to increase the likelihood of successful patterning. We show how to control Turing pattern sizes and time evolution by manipulating the values for production and degradation relationships. More importantly, our analysis predicts that steep dose-response functions arising from cooperativity are mandatory for Turing patterns. Greater steepness increases parameter space and even reduces the requirement for differential diffusion between activator and inhibitor. These results demonstrate some of the limitations of linear scenarios for reaction-diffusion systems and will help to guide projects to engineer synthetic Turing patterns.

Determination Hypoiodous Acid (HIO) By Peroxidase System Using Peroxidase Enzyme

NASA Astrophysics Data System (ADS)

Al-Baarri, A. N.; Legowo, A. M.; Widayat; Abduh, S. B. M.; Hadipernata, M.; Wisnubroto; Ardianti, D. K.; Susanto, M. N.; Yusuf, M.; Demasta, E. K.

2018-02-01

It has been understood that peroxidase enzyme including peroxidase serves as catalyzer to enzymatic reaction among hydrogen peroxide and halides, therefore this research was done for generating hypoiodous acid (HIO) from peroxidase system using peroxidase enzyme. Hydrogen peroxide, potassium iodide, and peroxidase enzyme were used to produce HIO. Determination the amount of formed HIO was done using 2,2'-azino-bis(3- ethylbenzothiazoline-6-sulphonic acid) or ABTS as substrate through the colorimetric measurement of hydrogen peroxide residue during reaction process using at 412 nm. The result indicated that residual hydrogen peroxide showed the minimum concentration after 60 minutes reaction time. Because the reaction started at the beginning time of mixing, hydrogen peroxide was unable to be eliminated totally to produce HIO. The reaction of peroxidase system was able to determine the beginning of mixing process but the reaction process could not eliminate the initial concentration of hydrogen peroxide indicating the maximum amount of production of HIO could be determined. In conclusion, the less of H2O2, higher HIO obtained and peroxidase enzymes can accelerate the formation of HIO.

Permanganate diffusion and reaction in sedimentary rocks.

PubMed

Huang, Qiuyuan; Dong, Hailiang; Towne, Rachael M; Fischer, Timothy B; Schaefer, Charles E

2014-04-01

In situ chemical oxidation using permanganate has frequently been used to treat chlorinated solvents in fractured bedrock aquifers. However, in systems where matrix back-diffusion is an important process, the ability of the oxidant to migrate and treat target contaminants within the rock matrix will likely determine the overall effectiveness of this remedial approach. In this study, a series of diffusion experiments were performed to measure the permanganate diffusion and reaction in four different types of sedimentary rocks (dark gray mudstone, light gray mudstone, red sandstone, and tan sandstone). Results showed that, within the experimental time frame (~2 months), oxidant migration into the rock was limited to distances less than 500 μm. The observed diffusivities for permanganate into the rock matrices ranged from 5.3 × 10(-13) to 1.3 × 10(-11) cm(2)/s. These values were reasonably predicted by accounting for both the rock oxidant demand and the effective diffusivity of the rock. Various Mn minerals formed as surface coatings from reduction of permanganate coupled with oxidation of total organic carbon (TOC), and the nature of the formed Mn minerals was dependent upon the rock type. Post-treatment tracer testing showed that these Mn mineral coatings had a negligible impact on diffusion through the rock. Overall, our results showed that the extent of permanganate diffusion and reaction depended on rock properties, including porosity, mineralogy, and organic carbon. These results have important implications for our understanding of long-term organic contaminant remediation in sedimentary rocks using permanganate. Copyright © 2014 Elsevier B.V. All rights reserved.

Chemical composition and heterogeneous reactivity of soot generated in the combustion of diesel and GTL (Gas-to-Liquid) fuels and amorphous carbon Printex U with NO2 and CF3COOH gases

NASA Astrophysics Data System (ADS)

Tapia, A.; Salgado, S.; Martín, P.; Villanueva, F.; García-Contreras, R.; Cabañas, B.

2018-03-01

The heterogeneous reactions of nitrogen dioxide (NO2) and trifluoroacetic acid (CF3COOH) with soot produced by diesel and GTL (gas-to-liquid) fuels were investigated using a Knudsen flow reactor with mass spectrometry as a detection system for gas phase species. Soot was generated with a 4 cylinder diesel engine working under steady-state like urban operation mode. Heterogeneous reaction of the mentioned gases with a commercial carbon, Printex U, used as reference, was also analyzed. The initial and the steady-state uptake coefficients, γ0 and γss, respectively, were measured indicating that GTL soot reacts faster than diesel soot and Printex U carbon for NO2 gas reactant. According to the number of reacted molecules on the surface, Printex U soot presents more reducing sites than diesel and GTL soot. Initial uptake coefficients for GTL and diesel soot for the reaction with CF3COOH gas reactant are very similar and no clear conclusions can be obtained related to the initial reactivity. The number of reacted molecules calculated for CF3COOH reactions shows values two orders of magnitude higher than the corresponding to NO2 reactions, indicating a greater presence of basic functionalities in the soot surfaces. More information of the surface composition has been obtained using Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) before and after the reaction of soot samples with gas reactants. As conclusion, the interface of diesel and GTL soot before reaction mainly consists of polycyclic aromatic hydrocarbons (PAHs), nitro-compounds as well as ether functionalities. After reaction with gas reactant, it was observed that PAHs and nitro-compounds remain on the soot surface and new spectral bands such as carbonyl groups (carboxylic acids, aldehydes, esters and ketones) are observed. Physical properties of soot from both fuels studied such as BET surface isotherm and SEM analysis were also developed and related to the observed reactivity.

Pore and Continuum Scale Study of the Effect of Subgrid Transport Heterogeneity on Redox Reaction Rates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yuanyuan; Liu, Chongxuan; Zhang, Changyong

2015-08-01

A micromodel system with a pore structure for heterogeneous flow and transport was used to investigate the effect of subgrid transport heterogeneity on redox reaction rates. Hematite reductive dissolution by injecting a reduced form of flavin mononucleotide (FMNH2) at variable flow rates was used as an example to probe the variations of redox reaction rates in different subgrid transport domains. Experiments, pore-scale simulations, and macroscopic modeling were performed to measure and simulate in-situ hematite reduction and to evaluate the scaling behavior of the redox reaction rates from the pore to macroscopic scales. The results indicated that the measured pore-scale ratesmore » of hematite reduction were consistent with the predictions from a pore scale reactive transport model. A general trend is that hematite reduction followed reductant transport pathways, starting from the advection-dominated pores toward the interior of diffusion-dominated domains. Two types of diffusion domains were considered in the micromodel: a micropore diffusion domain, which locates inside solid grains or aggregates where reactant transport is limited by diffusion; and a macropore diffusion domain, which locates at wedged, dead-end pore spaces created by the grain-grain contacts. The rate of hematite reduction in the advection-dominated domain was faster than those in the diffusion-controlled domains, and the rate in the macropore diffusion domain was faster than that in the micropore domain. The reduction rates in the advection and macropore diffusion domains increased with increasing flow rate, but were affected by different mechanisms. The rate increase in the advection domain was controlled by the mass action effect as a faster flow supplied more reactants, and the rate increase in the macropore domain was more affected by the rate of mass exchange with the advection domain, which increased with increasing flow rate. The hematite reduction rate in the micropore domain was, however, not affected by the flow rate because molecular diffusion limits reductant supply to the micropore domain interior. Domain-based macroscopic models were evaluated to scale redox reaction rates from the pore to macroscopic scales. A single domain model, which ignores subgrid transport heterogeneity deviated significantly from the pore-scale results. Further analysis revealed that the rate expression for hematite reduction was not scalable from the pore to porous media using the single domain model. A three-domain model, which effectively considers subgrid reactive diffusion in the micropore and macropore domains, significantly improved model description. Overall this study revealed the importance of subgrid transport heterogeneity in the manifestation of redox reaction rates in porous media and in scaling reactions from the pore to porous media. The research also supported that the domain-based scaling approach can be used to directly scale redox reactions in porous media with subgrid transport heterogeneity.« less

Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

NASA Technical Reports Server (NTRS)

Rosner, D. E.; Nagarajan, R.

1985-01-01

Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

Effective Stochastic Model for Reactive Transport

NASA Astrophysics Data System (ADS)

Tartakovsky, A. M.; Zheng, B.; Barajas-Solano, D. A.

2017-12-01

We propose an effective stochastic advection-diffusion-reaction (SADR) model. Unlike traditional advection-dispersion-reaction models, the SADR model describes mechanical and diffusive mixing as two separate processes. In the SADR model, the mechanical mixing is driven by random advective velocity with the variance given by the coefficient of mechanical dispersion. The diffusive mixing is modeled as a fickian diffusion with the effective diffusion coefficient. Both coefficients are given in terms of Peclet number (Pe) and the coefficient of molecular diffusion. We use the experimental results of to demonstrate that for transport and bimolecular reactions in porous media the SADR model is significantly more accurate than the traditional dispersion model, which overestimates the mass of the reaction product by as much as 25%.

The Development of a Compact Refrigeration System using Metal Hydrides

NASA Astrophysics Data System (ADS)

Bae, Sang-Chul; Ogawa, Masahito; Katsuta, Masafumi

The MH refrigeration systems are regarded as important and compact ones for solving energy and environmental issues. Our purposes are to develop the compact refrigeration system for the vending machine and the show case using MH, and to attain a refrigeration temperature of 243K by using a heat source of 403∼423K. The kinetics of MH hydriding and dehydriding reactions is of importance relative to their practical use as a refrigerator system. The kinetics of the reaction between hydrogen and MHHigh (Ti0.18Zr0.84Cr1.0FeO.7Mn0.3CuO.057)has been followed in this paper. A relatively rapid absorption of hydrogen takes place for values of relative composition to about 0.3∼0.4. It is evident that a hydrogen diffusion plays a minor role during this stage, as that part of the metal not covered by hydride is always in contact with hydrogen. The direct chemical reaction between the hydrogen and the exposed metal surface is therefore postulated as the rate-controlling process. The rate of the reaction then decreases, and for values of relative composition above about 0.8, the reaction becomes slow. After the metal particles have been completely covered by a hydride layer, the transport of materials through the layer by diffusion becomes rate controlling process

Laser Spot Detection Based on Reaction Diffusion.

PubMed

Vázquez-Otero, Alejandro; Khikhlukha, Danila; Solano-Altamirano, J M; Dormido, Raquel; Duro, Natividad

2016-03-01

Center-location of a laser spot is a problem of interest when the laser is used for processing and performing measurements. Measurement quality depends on correctly determining the location of the laser spot. Hence, improving and proposing algorithms for the correct location of the spots are fundamental issues in laser-based measurements. In this paper we introduce a Reaction Diffusion (RD) system as the main computational framework for robustly finding laser spot centers. The method presented is compared with a conventional approach for locating laser spots, and the experimental results indicate that RD-based computation generates reliable and precise solutions. These results confirm the flexibility of the new computational paradigm based on RD systems for addressing problems that can be reduced to a set of geometric operations.

Non-Neuronal Release of Gamma-Aminobutyric Acid by Embryonic Pluripotent Stem Cells

PubMed Central

Teng, Lin; Tang, Ya-Bin; Sun, Fan; An, Shi-Min; Zhang, Chun; Yang, Xin-Jie; Lv, Hao-Yu; Lu, Qin; Cui, Yong-Yao; Hu, Jin-Jia

2013-01-01

γ-Aminobutyric acid (GABA), the principle inhibitory transmitter in the mature central nervous system, is also involved in activities outside the nervous system. Recent studies have shown that functional GABA receptors are expressed in embryonic stem (ES) cells and these receptors control ES cell proliferation. However, it is not clear whether ES cells have their own GABAergic transmission output machinery that can fulfill GABA release or whether the cells merely process the GABA receptors by receiving and responding to the diffused GABA released elsewhere. To get further insight into this unresolved problem, we detected the repertoire of components for GABA synthesis, storage, reaction, and termination in ES and embryonal carcinoma stem cells by biological assays, and then directly quantified released GABA in the intercellular milieu from these pluripotent stem (PS) cells by an analytical chemical assay based on high-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS). We found that embryonic PS cells processed a GABAergic circuit machinery and spontaneously released GABA, which suggests the potential that embryonic PS cells could autonomously establish a GABA niche via release of the transmitter. PMID:23799822

Interdiffusion and reactions between U-Mo and Zr at 650 °C as a function of time

NASA Astrophysics Data System (ADS)

Park, Y.; Keiser, D. D.; Sohn, Y. H.

2015-01-01

Development of monolithic U-Mo alloy fuel (typically U-10 wt.%Mo) for the Reduced Enrichment for Research and Test Reactors (RERTR) program entails a use of Zr diffusion barrier to eliminate the interdiffusion-reactions between the fuel alloy and Al-alloy cladding. The application of Zr barrier to the U-Mo fuel system requires a co-rolling process that utilizes a soaking temperature of 650 °C, which represents the highest temperature the fuel system is exposed to during both fuel manufacturing and reactor application. Therefore, in this study, development of phase constituents, microstructure and diffusion kinetics of U-10 wt.%Mo and Zr was examined using solid-to-solid diffusion couples annealed at 650 °C for 240, 480 and 720 h. Phase constituents and microstructural development were analyzed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Concentration profiles were mapped as diffusion paths on the isothermal ternary phase diagram. Within the diffusion zone, single-phase layers of β-Zr and β-U were observed along with a discontinuous layer of Mo2Zr between the β-Zr and β-U layers. In the vicinity of Mo2Zr phase, islands of α-Zr phases were also found. In addition, acicular α-Zr and U6Zr3Mo phases were observed within the γ-U(Mo) terminal alloy. Growth rate of the interdiffusion-reaction zone was determined to be 7.75 (± 5.84) × 10-16 m2/s at 650 °C, however with an assumption of a certain incubation period.

Application of Bogolyubov's theory of weakly nonideal Bose gases to the A+A, A+B, B+B reaction-diffusion system

NASA Astrophysics Data System (ADS)

Konkoli, Zoran

2004-01-01

Theoretical methods for dealing with diffusion-controlled reactions inevitably rely on some kind of approximation, and to find the one that works on a particular problem is not always easy. Here the approximation used by Bogolyubov to study a weakly nonideal Bose gas, referred to as the weakly nonideal Bose gas approximation (WBGA), is applied in the analysis of three reaction-diffusion models: (i) A+A→Ø, (ii) A+B→Ø, and (iii) A+A,B+B,A+B→Ø (the ABBA model). Two types of WBGA are considered, the simpler WBGA-I and the more complicated WBGA-II. All models are defined on the lattice to facilitate comparison with computer experiment (simulation). It is found that the WBGA describes the A+B reaction well, it reproduces the correct d/4 density decay exponent. However, it fails in the case of the A+A reaction and the ABBA model. (To cure the deficiency of WBGA in dealing with the A+A model, a hybrid of the WBGA and Kirkwood superposition approximations is suggested.) It is shown that the WBGA-I is identical to the dressed-tree calculation suggested by Lee [J. Phys. A 27, 2633 (1994)], and that the dressed-tree calculation does not lead to the d/2 density decay exponent when applied to the A+A reaction, as normally believed, but it predicts the d/4 decay exponent. Last, the usage of the small n0 approximation suggested by Mattis and Glasser [Rev. Mod. Phys. 70, 979 (1998)] is questioned if used beyond the A+B reaction-diffusion model.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiegel, Aaron A.; Liu, Matthew J.; Hinsberg, William D.

Multiphase chemical reactions (gas + solid/liquid) involve a complex interplay between bulk and interface chemistry, diffusion, evaporation, and condensation. Reactions of atmospheric aerosols are an important example of this type of chemistry: the rich array of particle phase states and multiphase transformation pathways produce diverse but poorly understood interactions between chemistry and transport. Their chemistry is of intrinsic interest because of their role in controlling climate. Their characteristics also make them useful models for the study of principles of reactivity of condensed materials under confined conditions. Previously, we have reported a computational study of the oxidation chemistry of a liquidmore » aliphatic aerosol. In this study, we extend the calculations to investigate nearly the same reactions at a semisolid gas-aerosol interface. A reaction-diffusion model for heterogeneous oxidation of triacontane by hydroxyl radicals (OH) is described, and its predictions are compared to measurements of aerosol size and composition, which evolve continuously during oxidation. Our results are also explicitly compared to those obtained for the corresponding liquid system, squalane, to pinpoint salient elements controlling reactivity. The diffusive confinement of the free radical intermediates at the interface results in enhanced importance of a few specific chemical processes such as the involvement of aldehydes in fragmentation and evaporation, and a significant role of radical-radical reactions in product formation. The simulations show that under typical laboratory conditions semisolid aerosols have highly oxidized nanometer-scale interfaces that encapsulate an unreacted core and may confer distinct optical properties and enhanced hygroscopicity. This highly oxidized layer dynamically evolves with reaction, which we propose to result in plasticization. The validated model is used to predict chemistry under atmospheric conditions, where the OH radical concentration is much lower. The oxidation reactions are more strongly influenced by diffusion in the particle, resulting in a more liquid-like character.« less

Cluster geometry and survival probability in systems driven by reaction diffusion dynamics

NASA Astrophysics Data System (ADS)

Windus, Alastair; Jensen, Henrik J.

2008-11-01

We consider a reaction-diffusion model incorporating the reactions A→phi, A→2A and 2A→3A. Depending on the relative rates for sexual and asexual reproduction of the quantity A, the model exhibits either a continuous or first-order absorbing phase transition to an extinct state. A tricritical point separates the two phase lines. While we comment on this critical behaviour, the main focus of the paper is on the geometry of the population clusters that form. We observe the different cluster structures that arise at criticality for the three different types of critical behaviour and show that there exists a linear relationship for the survival probability against initial cluster size at the tricritical point only.

Summer Work Experience: Determining Methane Combustion Mechanisms and Sub-Scale Diffuser Properties for Space Transporation System Engine Testing

NASA Technical Reports Server (NTRS)

Williams, Powtawche N.

1998-01-01

To assess engine performance during the testing of Space Shuttle Main Engines (SSMEs), the design of an optimal altitude diffuser is studied for future Space Transportation Systems (STS). For other Space Transportation Systems, rocket propellant using kerosene is also studied. Methane and dodecane have similar reaction schemes as kerosene, and are used to simulate kerosene combustion processes at various temperatures. The equations for the methane combustion mechanism at high temperature are given, and engine combustion is simulated on the General Aerodynamic Simulation Program (GASP). The successful design of an altitude diffuser depends on the study of a sub-scaled diffuser model tested through two-dimensional (2-D) flow-techniques. Subroutines given calculate the static temperature and pressure at each Mach number within the diffuser flow. Implementing these subroutines into program code for the properties of 2-D compressible fluid flow determines all fluid characteristics, and will be used in the development of an optimal diffuser design.

Computational approach on PEB process in EUV resist: multi-scale simulation

NASA Astrophysics Data System (ADS)

Kim, Muyoung; Moon, Junghwan; Choi, Joonmyung; Lee, Byunghoon; Jeong, Changyoung; Kim, Heebom; Cho, Maenghyo

2017-03-01

For decades, downsizing has been a key issue for high performance and low cost of semiconductor, and extreme ultraviolet lithography is one of the promising candidates to achieve the goal. As a predominant process in extreme ultraviolet lithography on determining resolution and sensitivity, post exposure bake has been mainly studied by experimental groups, but development of its photoresist is at the breaking point because of the lack of unveiled mechanism during the process. Herein, we provide theoretical approach to investigate underlying mechanism on the post exposure bake process in chemically amplified resist, and it covers three important reactions during the process: acid generation by photo-acid generator dissociation, acid diffusion, and deprotection. Density functional theory calculation (quantum mechanical simulation) was conducted to quantitatively predict activation energy and probability of the chemical reactions, and they were applied to molecular dynamics simulation for constructing reliable computational model. Then, overall chemical reactions were simulated in the molecular dynamics unit cell, and final configuration of the photoresist was used to predict the line edge roughness. The presented multiscale model unifies the phenomena of both quantum and atomic scales during the post exposure bake process, and it will be helpful to understand critical factors affecting the performance of the resulting photoresist and design the next-generation material.

Formation of Amino Acid Thioesters for Prebiotic Peptide Synthesis: Catalysis By Amino Acid Products

NASA Technical Reports Server (NTRS)

Weber, Arthur L.; DeVincenzi, Donald L. (Technical Monitor)

1999-01-01

The origin of life can be described as a series of events in which a prebiotic chemical process came increasingly under the control of its catalytic products. In our search for this prebiotic process that yielded catalytic takeover products (such as polypeptides), we have been investigating a reaction system that generates peptide-forming amino acid thioesters from formaldehyde, glycolaldehyde, and ammonia in the presence of thiols. As shown below, this model process begins by aldol condensation of formaldehyde and glycolaldehyde to give trioses and releases. These sugars then undergo beta-dehydration yielding their respective alpha-ketoaldehydes. Addition of ammonia to the alpha-ketoaldehydes yields imines which can either: (a) rearrange in the presence of thesis to give amino acid thioesters or (be react with another molecule of aldehyde to give imidazoles. This 'one-pot' reaction system operates under mild aqueous conditions, and like modem amino acid biosynthesis, uses sugar intermediates which are converted to products by energy-yielding redox reactions. Recently, we discovered that amino acids, such as the alanine reaction product, catalyze the first and second steps of the process. In the presence of ammonia the process also generates other synthetically useful products, like the important biochemical -- pyruvic acid.

Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damköhler numbers

NASA Astrophysics Data System (ADS)

Bandopadhyay, Aditya; Le Borgne, Tanguy; Méheust, Yves; Dentz, Marco

2017-02-01

Mixing fronts, where fluids of different chemical compositions mix with each other, are known to represent hotspots of chemical reaction in hydrological systems. These fronts are typically subjected to velocity gradients, ranging from the pore scale due to no slip boundary conditions at fluid solid interfaces, to the catchment scale due to permeability variations and complex geometry of the Darcy velocity streamlines. A common trait of these processes is that the mixing interface is strained by shear. Depending on the Péclet number Pe , which represents the ratio of the characteristic diffusion time to the characteristic shear time, and the Damköhler number Da , 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. So far, this impact has been characterized mostly either in kinetics-limited or in mixing-limited conditions, that is, for either low or high Da. Here the coupling of shear flow and chemical reactivity is investigated for arbitrary Damköhler 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 Pe < Da , reaction kinetics and stretching effects are decoupled, a scenario which we name "weak stretching", for Pe > Da , 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.

Minimal wave speed for a class of non-cooperative reaction-diffusion systems of three equations

NASA Astrophysics Data System (ADS)

Zhang, Tianran

2017-05-01

In this paper, we study the traveling wave solutions and minimal wave speed for a class of non-cooperative reaction-diffusion systems consisting of three equations. Based on the eigenvalues, a pair of upper-lower solutions connecting only the invasion-free equilibrium are constructed and the Schauder's fixed-point theorem is applied to show the existence of traveling semi-fronts for an auxiliary system. Then the existence of traveling semi-fronts of original system is obtained by limit arguments. The traveling semi-fronts are proved to connect another equilibrium if natural birth and death rates are not considered and to be persistent if these rates are incorporated. Then non-existence of bounded traveling semi-fronts is obtained by two-sided Laplace transform. Then the above results are applied to some disease-transmission models and a predator-prey model.

Surface charge- and space-dependent transport of proteins in crowded environments of nanotailored posts.

PubMed

Choi, Chang Kyoung; Fowlkes, Jason D; Retterer, Scott T; Siuti, Piro; Iyer, Sukanya; Doktycz, Mitchel J

2010-06-22

The reaction and diffusion of molecules across barriers and through crowded environments is integral to biological system function and to separation technologies. Ordered, microfabricated post arrays are a promising route to creating synthetic barriers with controlled chemical and physical characteristics. They can be used to create crowded environments, to mimic aspects of cellular membranes, and to serve as engineered replacements of polymer-based separation media. Here, the translational diffusion of fluorescein isothiocyante and various forms of green fluorescent protein (GFP), including "supercharged" variants, are examined in a silicon-based post array environment. The technique of fluorescence recovery after photobleaching (FRAP) is combined with analytical approximations and numerical simulations to assess the relative effects of reaction and diffusion on molecular transport, respectively. FRAP experiments were conducted for 64 different cases where the molecular species, the density of the posts, and the chemical surface charge of the posts were varied. In all cases, the dense packing of the posts hindered the diffusive transport of the fluorescent species. The supercharged GFPs strongly interacted with oppositely charged surfaces. With similar molecular and surface charges, transport is primarily limited by hindered diffusion. For conventional, enhanced GFP in a positively charged surface environment, transport was limited by the coupled action of hindered diffusion and surface interaction with the posts. Quantification of the size-, space-, time-, and charge-dependent translational diffusion in the post array environments can provide insight into natural processes and guide the design and development of selective membrane systems.

Intermediate temperature proton conductors for PEM fuel cells based on phosphonic acid as protogenic group: a progress report.

PubMed

Steininger, H; Schuster, M; Kreuer, K D; Kaltbeitzel, A; Bingöl, B; Meyer, W H; Schauff, S; Brunklaus, G; Maier, J; Spiess, H W

2007-04-21

The melting behaviour and transport properties of straight chain alkanes mono- and difunctionalized with phosphonic acid groups have been investigated as a function of their length. The increase of melting temperature and decrease of proton conductivity with increasing chain length is suggested to be the consequence of an increasing ordering of the alkane segments which constrains the free aggregation of the phosphonic acid groups. However, the proton mobility is reduced to a greater extent than the proton diffusion coefficient indicating an increasing cooperativity of proton transport with increasing length of the alkane segment. The results clearly indicate that the "spacer concept", which had been proven successful in the optimization of the proton conductivity of heterocycle based systems, fails in the case of phosphonic acid functionalized polymers. Instead, a very high concentration of phosphonic acid functional groups forming "bulky" hydrogen bonded aggregates is suggested to be essential for obtaining very high proton conductivity. Aggregation is also suggested to reduce condensation reactions generally observed in phosphonic acid containing systems. On the basis of this understanding, the proton conductivities of poly(vinyl phosphonic acid) and poly(meta-phenylene phosphonic acid) are discussed. Though both polymers exhibit a substantial concentration of phosphonic acid groups, aggregation seems to be constrained to such an extent that intrinsic proton conductivity is limited to values below sigma = 10(-3) S cm(-1) at T = 150 degrees C. The results suggest that different immobilization concepts have to be developed in order to minimize the conductivity reduction compared to the very high intrinsic proton conductivity of neat phosphonic acid under quasi dry conditions. In the presence of high water activities, however, (as usually present in PEM fuel cells) the very high ion exchange capacities (IEC) possible for phosphonic acid functionalized ionomers (IEC >10 meq g(-1)) may allow for high proton conductivities in the intermediate temperature range (T approximately 120 -160 degrees C).

Low-Temperature (75 To 400°C) Oxidation Study Of Coal By Diffuse Reflectance Infrared Fourier Transform (DRIFT) Spectroscopy

NASA Astrophysics Data System (ADS)

Smyrl, Norman R.; Fuller, E. L.

1989-12-01

In situ low-temperature air oxidation studies of subbituminous coal have been performed at 77, 125, 200, 300, and 400°C by diffuse reflectance Fourier transform (DRIFT) spectroscopy. The oxidation reaction proceeds via oxygen insertion at aliphatic sites in the coal structure, which progressively produces aldo/keto groups, acid groups, and acid anhydride entities with the simultaneous consumption of hydrogen at these sites. The production of anhydrides occurs even at the lowest temperature (77?°C), but only above 200°C is there sufficient mobility of the acid functionalities for major quantities of the anhydride species to be formed. Above 400C, the anhydro groups predominate in the steady-state production of carbon dioxide and water vapor. In addition to the detailed information concerning the carbonyl species, the spectra of the oxidized coal reveal some new information regarding the aromatic C-H stretching bands, which can be studied in some detail unencumbered by interference from the aliphatic bands that have been removed in the oxidation process. Further details related to the aromatic bands are revealed by deuterium exchange of the remaining 0-H groups (primarily phenolic type 0-H) in the oxidized coal structure. This exchange removes these bands from overlap with the broad 0-H stretching band resulting from hydrogen bonding of the 0-H groups. The present study reveals further merits of in situ DRIFT analysis in extending the knowledge of coal structure and reactions. The study also indicates much potential for further work.

Convection and reaction in a diffusive boundary layer in a porous medium: nonlinear dynamics.

PubMed

Andres, Jeanne Therese H; Cardoso, Silvana S S

2012-09-01

We study numerically the nonlinear interactions between chemical reaction and convective fingering in a diffusive boundary layer in a porous medium. The reaction enhances stability by consuming a solute that is unstably distributed in a gravitational field. We show that chemical reaction profoundly changes the dynamics of the system, by introducing a steady state, shortening the evolution time, and altering the spatial patterns of velocity and concentration of solute. In the presence of weak reaction, finger growth and merger occur effectively, driving strong convective currents in a thick layer of solute. However, as the reaction becomes stronger, finger growth is inhibited, tip-splitting is enhanced and the layer of solute becomes much thinner. Convection enhances the mass flux of solute consumed by reaction in the boundary layer but has a diminishing effect as reaction strength increases. This nonlinear behavior has striking differences to the density fingering of traveling reaction fronts, for which stronger chemical kinetics result in more effective finger merger owing to an increase in the speed of the front. In a boundary layer, a strong stabilizing effect of reaction can maintain a long-term state of convection in isolated fingers of wavelength comparable to that at onset of instability.

Automatic simplification of systems of reaction-diffusion equations by a posteriori analysis.

PubMed

Maybank, Philip J; Whiteley, Jonathan P

2014-02-01

Many mathematical models in biology and physiology are represented by systems of nonlinear differential equations. In recent years these models have become increasingly complex in order to explain the enormous volume of data now available. A key role of modellers is to determine which components of the model have the greatest effect on a given observed behaviour. An approach for automatically fulfilling this role, based on a posteriori analysis, has recently been developed for nonlinear initial value ordinary differential equations [J.P. Whiteley, Model reduction using a posteriori analysis, Math. Biosci. 225 (2010) 44-52]. In this paper we extend this model reduction technique for application to both steady-state and time-dependent nonlinear reaction-diffusion systems. Exemplar problems drawn from biology are used to demonstrate the applicability of the technique. Copyright © 2014 Elsevier Inc. All rights reserved.

Semi-analytical solutions of the Schnakenberg model of a reaction-diffusion cell with feedback

NASA Astrophysics Data System (ADS)

Al Noufaey, K. S.

2018-06-01

This paper considers the application of a semi-analytical method to the Schnakenberg model of a reaction-diffusion cell. The semi-analytical method is based on the Galerkin method which approximates the original governing partial differential equations as a system of ordinary differential equations. Steady-state curves, bifurcation diagrams and the region of parameter space in which Hopf bifurcations occur are presented for semi-analytical solutions and the numerical solution. The effect of feedback control, via altering various concentrations in the boundary reservoirs in response to concentrations in the cell centre, is examined. It is shown that increasing the magnitude of feedback leads to destabilization of the system, whereas decreasing this parameter to negative values of large magnitude stabilizes the system. The semi-analytical solutions agree well with numerical solutions of the governing equations.

Geochemical roots of autotrophic carbon fixation: hydrothermal experiments in the system citric acid, H 2O-(±FeS)-(±NiS)

NASA Astrophysics Data System (ADS)

Cody, G. D.; Boctor, N. Z.; Hazen, R. M.; Brandes, J. A.; Morowitz, Harold J.; Yoder, H. S.

2001-10-01

Recent theories have proposed that life arose from primitive hydrothermal environments employing chemical reactions analogous to the reductive citrate cycle (RCC) as the primary pathway for carbon fixation. This chemistry is presumed to have developed as a natural consequence of the intrinsic geochemistry of the young, prebiotic, Earth. There has been no experimental evidence, however, demonstrating that there exists a natural pathway into such a cycle. Toward this end, the results of hydrothermal experiments involving citric acid are used as a method of deducing such a pathway. Homocatalytic reactions observed in the citric acid-H2O experiments encompass many of the reactions found in modern metabolic systems, i.e., hydration-dehydration, retro-Aldol, decarboxylation, hydrogenation, and isomerization reactions. Three principal decomposition pathways operate to degrade citric acid under thermal and aquathermal conditions. It is concluded that the acid catalyzed βγ decarboxylation pathway, leading ultimately to propene and CO2, may provide the most promise for reaction network reversal under natural hydrothermal conditions. Increased pressure is shown to accelerate the principal decarboxylation reactions under strictly hydrothermal conditions. The effect of forcing the pH via the addition of NaOH reveals that the βγ decarboxylation pathway operates even up to intermediate pH levels. The potential for network reversal (the conversion of propene and CO2 up to a tricarboxylic acid) is demonstrated via the Koch (hydrocarboxylation) reaction promoted heterocatalytically with NiS in the presence of a source of CO. Specifically, an olefin (1-nonene) is converted to a monocarboxylic acid; methacrylic acid is converted to the dicarboxylic acid, methylsuccinic acid; and the dicarboxylic acid, itaconic acid, is converted into the tricarboxylic acid, hydroaconitic acid. A number of interesting sulfur-containing products are also formed that may provide for additional reaction. The intrinsic catalytic qualities of FeS and NiS are also explored in the absence of CO. It was shown that the addition of NiS has a minimal effect in the product distribution, whereas the addition of FeS leads to the formation of hydrogenated and sulfur-containing products (thioethers). These results point to a simple hydrothermal redox pathway for citric acid synthesis that may have provided a geochemical ignition point for the reductive citrate cycle.

Volatile emissions and gas geochemistry of Hot Spring Basin, Yellowstone National Park, USA

USGS Publications Warehouse

Werner, C.; Hurwitz, S.; Evans, William C.; Lowenstern, J. B.; Bergfeld, D.; Heasler, H.; Jaworowski, C.; Hunt, A.

2008-01-01

We characterize and quantify volatile emissions at Hot Spring Basin (HSB), a large acid-sulfate region that lies just outside the northeastern edge of the 640??ka Yellowstone Caldera. Relative to other thermal areas in Yellowstone, HSB gases are rich in He and H2, and mildly enriched in CH4 and H2S. Gas compositions are consistent with boiling directly off a deep geothermal liquid at depth as it migrates toward the surface. This fluid, and the gases evolved from it, carries geochemical signatures of magmatic volatiles and water-rock reactions with multiple crustal sources, including limestones or quartz-rich sediments with low K/U (or 40*Ar/4*He). Variations in gas chemistry across the region reflect reservoir heterogeneity and variable degrees of boiling. Gas-geothermometer temperatures approach 300????C and suggest that the reservoir feeding HSB is one of the hottest at Yellowstone. Diffuse CO2 flux in the western basin of HSB, as measured by accumulation-chamber methods, is similar in magnitude to other acid-sulfate areas of Yellowstone and is well correlated to shallow soil temperatures. The extrapolation of diffuse CO2 fluxes across all the thermal/altered area suggests that 410 ?? 140??t d- 1 CO2 are emitted at HSB (vent emissions not included). Diffuse fluxes of H2S were measured in Yellowstone for the first time and likely exceed 2.4??t d- 1 at HSB. Comparing estimates of the total estimated diffuse H2S emission to the amount of sulfur as SO42- in streams indicates ~ 50% of the original H2S in the gas emission is lost into shallow groundwater, precipitated as native sulfur, or vented through fumaroles. We estimate the heat output of HSB as ~ 140-370??MW using CO2 as a tracer for steam condensate, but not including the contribution from fumaroles and hydrothermal vents. Overall, the diffuse heat and volatile fluxes of HSB are as great as some active volcanoes, but they are a small fraction (1-3% for CO2, 2-8% for heat) of that estimated for the entire Yellowstone system.

Coupling of active motion and advection shapes intracellular cargo transport.

PubMed

Khuc Trong, Philipp; Guck, Jochen; Goldstein, Raymond E

2012-07-13

Intracellular cargo transport can arise from passive diffusion, active motor-driven transport along cytoskeletal filament networks, and passive advection by fluid flows entrained by such cargo-motor motion. Active and advective transport are thus intrinsically coupled as related, yet different representations of the same underlying network structure. A reaction-advection-diffusion system is used here to show that this coupling affects the transport and localization of a passive tracer in a confined geometry. For sufficiently low diffusion, cargo localization to a target zone is optimized either by low reaction kinetics and decoupling of bound and unbound states, or by a mostly disordered cytoskeletal network with only weak directional bias. These generic results may help to rationalize subtle features of cytoskeletal networks, for example as observed for microtubules in fly oocytes.

Singlet oxygen production by chloroperoxidase-hydrogen peroxide-halide systems.

PubMed

Kanofsky, J R

1984-05-10

Singlet oxygen production in the chloroperoxidase-hydrogen peroxide-halide system was studied using 1268 nm chemiluminescence. With chloride or bromide ions, singlet oxygen is produced by the mechanism (formula; see text) (formula; see text) where X- is chloride or bromide ion. Under conditions where there is high enzyme activity and when Reaction B is fast relative to Reaction A, singlet oxygen is produced in near stoichiometric amounts. In contrast, when Reaction A is fast relative to Reaction B, oxidized halogen species (chlorine and hypochlorous acid for chloride ion; bromide, tribromide ion, and hypobromous acid for bromide ion) are the principle reaction products. With iodide ion, no 1268 nm chemiluminescence was detected. Past studies have shown that iodine and iodate ion are the major end products of this system.

Reaction Mechanisms and Structural and Physicochemical Properties of Caffeic Acid Grafted Chitosan Synthesized in Ascorbic Acid and Hydroxyl Peroxide Redox System.

PubMed

Liu, Jun; Pu, Huimin; Chen, Chong; Liu, Yunpeng; Bai, Ruyu; Kan, Juan; Jin, Changhai

2018-01-10

The ascorbic acid (AA) and hydroxyl peroxide (H 2 O 2 ) redox pair induced free radical grafting reaction is a promising approach to conjugate phenolic groups with chitosan (CS). In order to reveal the exact mechanisms of the AA/H 2 O 2 redox pair induced grafting reaction, free radicals generated in the AA/H 2 O 2 redox system were compared with hydroxyl radical ( • OH) produced in the Fe 2+ /H 2 O 2 redox system. Moreover, the structural and physicochemical properties of caffeic acid grafted CS (CA-g-CS) synthesized in these two redox systems were compared. Results showed that only ascorbate radical (Asc •- ) was produced in the AA/H 2 O 2 system. The reaction between Asc •- and CS produced novel carbon-centered radicals, whereas no new free radicals were detected when • OH reacted with CS. Thin layer chromatography, UV-vis, Fourier transform infrared, and nuclear magnetic resonance spectroscopic analyses all confirmed that CA was successfully grafted onto CS through Asc •- . However, CA could be hardly grafted onto CS via • OH. CA-g-CS synthesized through Asc •- exhibited lower thermal stability and crystallinity than the reaction product obtained through • OH. For the first time, our results demonstrated that the synthesis of CA-g-CS in the AA/H 2 O 2 redox system was mediated by Asc •- rather than • OH.

Flow/Soot-Formation Interactions in Nonbuoyant Laminar Diffusion Flames

NASA Technical Reports Server (NTRS)

Dai, Z.; Lin, K.-C.; Sunderland, P. B.; Xu, F.; Faeth, G. M.

2002-01-01

This is the final report of a research program considering interactions between flow and soot properties within laminar diffusion flames. Laminar diffusion flames were considered because they provide model flame systems that are far more tractable for theoretical and experimental studies than more practical turbulent diffusion flames. In particular, understanding the transport and chemical reaction processes of laminar flames is a necessary precursor to understanding these processes in practical turbulent flames and many aspects of laminar diffusion flames have direct relevance to turbulent diffusion flames through application of the widely recognized laminar flamelet concept of turbulent diffusion flames. The investigation was divided into three phases, considering the shapes of nonbuoyant round laminar jet diffusion flames in still air, the shapes of nonbuoyant round laminar jet diffusion flames in coflowing air, and the hydrodynamic suppression of soot formation in laminar diffusion flames.

A mathematical model for the generation and control of a pH gradient in an immobilized enzyme system involving acid generation.

PubMed

Chen, G; Fournier, R L; Varanasi, S

1998-02-20

An optimal pH control technique has been developed for multistep enzymatic synthesis reactions where the optimal pH differs by several units for each step. This technique separates an acidic environment from a basic environment by the hydrolysis of urea within a thin layer of immobilized urease. With this technique, a two-step enzymatic reaction can take place simultaneously, in proximity to each other, and at their respective optimal pH. Because a reaction system involving an acid generation represents a more challenging test of this pH control technique, a number of factors that affect the generation of such a pH gradient are considered in this study. The mathematical model proposed is based on several simplifying assumptions and represents a first attempt to provide an analysis of this complex problem. The results show that, by choosing appropriate parameters, the pH control technique still can generate the desired pH gradient even if there is an acid-generating reaction in the system. Copyright 1998 John Wiley & Sons, Inc.

On a nonlocal reaction-diffusion-advection system modelling the growth of phytoplankton with cell quota structure

NASA Astrophysics Data System (ADS)

Hsu, Sze-Bi; Mei, Linfeng; Wang, Feng-Bin

2015-11-01

Phytoplankton species in a water column compete for mineral nutrients and light, and the existing models usually neglect differences in the nutrient content and the amount of light absorbed of individuals. In this current paper, we examine a size-structured and nonlocal reaction-diffusion-advection system which describes the dynamics of a single phytoplankton species in a water column where the species depends simply on light for its growth. Our model is under the assumption that the amount of light absorbed by individuals is proportional to cell size, which varies for populations that reproduce by simple division into two equally-sized daughters. We first establish the existence of a critical death rate and our analysis indicates that the phytoplankton survives if and only if its death rate is less than the critical death rate. The critical death rate depends on a general reproductive rate, the characteristics of the water column (e.g., turbulent diffusion rate, sinking, depth), cell growth, cell division, and cell size.

The chemistry, physiology and pathology of pH in cancer.

PubMed

Swietach, Pawel; Vaughan-Jones, Richard D; Harris, Adrian L; Hulikova, Alzbeta

2014-03-19

Cell survival is conditional on the maintenance of a favourable acid-base balance (pH). Owing to intensive respiratory CO2 and lactic acid production, cancer cells are exposed continuously to large acid-base fluxes, which would disturb pH if uncorrected. The large cellular reservoir of H(+)-binding sites can buffer pH changes but, on its own, is inadequate to regulate intracellular pH. To stabilize intracellular pH at a favourable level, cells control trans-membrane traffic of H(+)-ions (or their chemical equivalents, e.g. ) using specialized transporter proteins sensitive to pH. In poorly perfused tumours, additional diffusion-reaction mechanisms, involving carbonic anhydrase (CA) enzymes, fine-tune control extracellular pH. The ability of H(+)-ions to change the ionization state of proteins underlies the exquisite pH sensitivity of cellular behaviour, including key processes in cancer formation and metastasis (proliferation, cell cycle, transformation, migration). Elevated metabolism, weakened cell-to-capillary diffusive coupling, and adaptations involving H(+)/H(+)-equivalent transporters and extracellular-facing CAs give cancer cells the means to manipulate micro-environmental acidity, a cancer hallmark. Through genetic instability, the cellular apparatus for regulating and sensing pH is able to adapt to extracellular acidity, driving disease progression. The therapeutic potential of disturbing this sequence by targeting H(+)/H(+)-equivalent transporters, buffering or CAs is being investigated, using monoclonal antibodies and small-molecule inhibitors.

Cure Kinetics of Benzoxazine/Cycloaliphatic Epoxy Resin by Differential Scanning Calorimetry

NASA Astrophysics Data System (ADS)

Gouni, Sreeja Reddy

Understanding the curing kinetics of a thermoset resin has a significant importance in developing and optimizing curing cycles in various industrial manufacturing processes. This can assist in improving the quality of final product and minimizing the manufacturing-associated costs. One approach towards developing such an understanding is to formulate kinetic models that can be used to optimize curing time and temperature to reach a full cure state or to determine time to apply pressure in an autoclave process. Various phenomenological reaction models have been used in the literature to successfully predict the kinetic behavior of a thermoset system. The current research work was designed to investigate the cure kinetics of Bisphenol-A based Benzoxazine (BZ-a) and Cycloaliphatic epoxy resin (CER) system under isothermal and nonisothermal conditions by Differential Scanning Calorimetry (DSC). The cure characteristics of BZ-a/CER copolymer systems with 75/25 wt% and 50/50 wt% have been studied and compared to that of pure benzoxazine under nonisothermal conditions. The DSC thermograms exhibited by these BZ-a/CER copolymer systems showed a single exothermic peak, indicating that the reactions between benzoxazine-benzoxazine monomers and benzoxazine-cycloaliphatic epoxy resin were interactive and occurred simultaneously. The Kissinger method and isoconversional methods including Ozawa-Flynn-Wall and Freidman were employed to obtain the activation energy values and determine the nature of the reaction. The cure behavior and the kinetic parameters were determined by adopting a single step autocatalytic model based on Kamal and Sourour phenomenological reaction model. The model was found to suitably describe the cure kinetics of copolymer system prior to the diffusion-control reaction. Analyzing and understanding the thermoset resin system under isothermal conditions is also important since it is the most common practice in the industry. The BZ-a/CER copolymer system with 75/25 wt% ratio which exhibited high glass transition temperature compared to polybenzoxazine was investigated under isothermal conditions. The copolymer system exhibited the maximum reaction rate at an intermediate degree of cure (20 to 40%), indicating that the reaction was autocatalytic. Similar to the nonisothermal cure kinetics, Kamal and Sourour phenomenological reaction model was adopted to determine the kinetic behavior of the system. The theoretical values based on the developed model showed a deviation from the obtained experimental values, which indicated the change in kinetics from a reaction-controlled mechanism to a diffusion-controlled mechanism with increasing reaction conversion. To substantiate the hypothesis, Fournier et al's diffusion factor was introduced into the model, resulting in an agreement between the theoretical and experimental values. The changes in cross-linking density and the glass transition temperature (Tg) with increasing epoxy concentration were investigated under Dynamic Mechanical Analyzer (DMA). The BZ-a/CER copolymer system with the epoxy content of less than 40 wt% exhibited the greatest Tg and cross-linking density compared to benzoxazine homopolymer and other ratios.

Modeling convection-diffusion-reaction systems for microfluidic molecular communications with surface-based receivers in Internet of Bio-Nano Things

PubMed Central

Akan, Ozgur B.

2018-01-01

We consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics. PMID:29415019

Modeling convection-diffusion-reaction systems for microfluidic molecular communications with surface-based receivers in Internet of Bio-Nano Things.

PubMed

Kuscu, Murat; Akan, Ozgur B

2018-01-01

We consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics.

Lipase-catalyzed synthesis of fattythioic acids from palm oil.

PubMed

Al-Mulla, Emad A Jaffar

2011-01-01

The present work focuses on the synthesis of fattythioic acids (FTAs) by a one-step lipase catalyzed reaction of palm oil with carbonothioic S,S-acid using Lipozyme. The product was characterized using Fourier transform infrared (FTIR) spectroscopy, proton nuclear magnetic resonance ((1)H NMR) technique and elemental analysis. The effects of various reaction parameters such as reaction time, temperature, amount of enzyme, molar ratio of substrates, and various organic solvents of the reaction system were investigated. The optimum conditions to produce FTAs were respectively, incubation time, 20 h, temperature, 40°C, amount of enzyme, 0.05 g and molar ratio of carbonothioic S,S-acid to palm oil, 5.0:1.0. Hexane was the best solvent for this reaction. The conversion of the products at optimum conditions was around 91%.

Modeling the transport of chemical warfare agents and simulants in polymeric substrates for reactive decontamination

NASA Astrophysics Data System (ADS)

Pearl, Thomas; Mantooth, Brent; Varady, Mark; Willis, Matthew

2014-03-01

Chemical warfare agent simulants are often used for environmental testing in place of highly toxic agents. This work sets the foundation for modeling decontamination of absorbing polymeric materials with the focus on determining relationships between agents and simulants. The correlations of agents to simulants must consider the three way interactions in the chemical-material-decontaminant system where transport and reaction occur in polymer materials. To this end, diffusion modeling of the subsurface transport of simulants and live chemical warfare agents was conducted for various polymer systems (e.g., paint coatings) with and without reaction pathways with applied decontamination. The models utilized 1D and 2D finite difference diffusion and reaction models to simulate absorption and reaction in the polymers, and subsequent flux of the chemicals out of the polymers. Experimental data including vapor flux measurements and dynamic contact angle measurements were used to determine model input parameters. Through modeling, an understanding of the relationship of simulant to live chemical warfare agent was established, focusing on vapor emission of agents and simulants from materials.

Modified Fe3O4- hydroxyapatite nanocomposites as heterogeneous catalysts in three UV, Vis and Fenton like degradation systems

NASA Astrophysics Data System (ADS)

Valizadeh, S.; Rasoulifard, M. H.; Dorraji, M. S. Seyed

2014-11-01

The magnetite-hydroxyapatite (M-HAP) nanocomposites were prepared by a chemical co- precipitation procedure and characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), scanning electron microscopy (SEM) and diffuse reflectance spectra (DRS). The ability of the synthesized catalyst for photocatalytic degradation of Acid Blue 25 (AB25), as an organic dye, under UV irradiation was studied. The catalyst was modified employing transition metals (Mn, Fe, Co, Ni, Cu and Zn) trying to improve the catalytic performance of HAP in absence of UV irradiation and in the presence of hydrogen peroxide i.e. a Fenton like reaction. The best results obtained for Cu and Co modified M-HAPs and the effect of operational parameters such pH, amount of catalyst and hydrogen peroxide concentration was studied. In order to investigate the performance of HAP based photocatalyst in visible light region, M-HAP was modified with silver ions. At the end, Langmuir-Hinshelwood kinetic expression used to evaluate and compare the catalytic systems. The strongest degradation activity was observed for Ag-M-HAP/Vis system because of Ag3PO4 formation. Apparent reaction rate constant (Kapp) by Ag-M-HAP/Vis was 63, 36 and 19 times faster than Cu-M-HAP(II)/H2O2, Co-M-HAP(II)/H2O2 and M-HAP (I)/UV systems, respectively.

Multi-layer light-weight protective coating and method for application

NASA Technical Reports Server (NTRS)

Wiedemann, Karl E. (Inventor); Clark, Ronald K. (Inventor); Taylor, Patrick J. (Inventor)

1992-01-01

A thin, light-weight, multi-layer coating is provided for protecting metals and their alloys from environmental attack at high temperatures. A reaction barrier is applied to the metal substrate and a diffusion barrier is then applied to the reaction barrier. A sealant layer may also be applied to the diffusion barrier if desired. The reaction barrier is either non-reactive or passivating with respect to the metal substrate and the diffusion barrier. The diffusion barrier is either non-reactive or passivating with respect to the reaction barrier and the sealant layer. The sealant layer is immiscible with the diffusion barrier and has a softening point below the expected use temperature of the metal.

Preferential amino acid sequences in alumina-catalyzed peptide bond formation.

PubMed

Bujdák, J; Rode, B M

2002-05-21

The catalytic effect of activated alumina on amino acid condensation was investigated. The readiness of amino acids to form peptide sequences was estimated on the basis of the yield of dipeptides and was found to decrease in the order glycine (Gly), alanine (Ala), leucine (Leu), valine (Val), proline (Pro). For example, approximately 15% Gly was converted to the dipeptide (Gly(2)), 5% to cyclic anhydride (cyc(Gly(2))) and small amounts of tri- (Gly(3)) and tetrapeptide (Gly(4)) were formed after 28 days. On the other hand, only trace amounts of Pro(2) were formed from proline under the same conditions. Preferential formation of certain sequences was observed in the mixed reaction systems containing two amino acids. For example, almost ten times more Gly-Val than Val-Gly was formed in the Gly+Val reaction system. The preferred sequences can be explained on the basis of an inductive effect that side groups have on the nucleophilicity and electrophilicity, respectively, of the amino and carboxyl groups. A comparison with published data of amino acid reactions in other reaction systems revealed that the main trends of preferential sequence formation were the same as those described for the salt-induced peptide formation (SIPF) reaction. The results of this work and other previously published papers show that alumina and related mineral surfaces might have played a crucial role in the prebiotic formation of the first peptides on the primitive earth.

General theory for integrated analysis of growth, gene, and protein expression in biofilms.

PubMed

Zhang, Tianyu; Pabst, Breana; Klapper, Isaac; Stewart, Philip S

2013-01-01

A theory for analysis and prediction of spatial and temporal patterns of gene and protein expression within microbial biofilms is derived. The theory integrates phenomena of solute reaction and diffusion, microbial growth, mRNA or protein synthesis, biomass advection, and gene transcript or protein turnover. Case studies illustrate the capacity of the theory to simulate heterogeneous spatial patterns and predict microbial activities in biofilms that are qualitatively different from those of planktonic cells. Specific scenarios analyzed include an inducible GFP or fluorescent protein reporter, a denitrification gene repressed by oxygen, an acid stress response gene, and a quorum sensing circuit. It is shown that the patterns of activity revealed by inducible stable fluorescent proteins or reporter unstable proteins overestimate the region of activity. This is due to advective spreading and finite protein turnover rates. In the cases of a gene induced by either limitation for a metabolic substrate or accumulation of a metabolic product, maximal expression is predicted in an internal stratum of the biofilm. A quorum sensing system that includes an oxygen-responsive negative regulator exhibits behavior that is distinct from any stage of a batch planktonic culture. Though here the analyses have been limited to simultaneous interactions of up to two substrates and two genes, the framework applies to arbitrarily large networks of genes and metabolites. Extension of reaction-diffusion modeling in biofilms to the analysis of individual genes and gene networks is an important advance that dovetails with the growing toolkit of molecular and genetic experimental techniques.

Acid–base bifunctional shell cross-linked micelle nanoreactor for one-pot tandem reaction

DOE PAGES

Lee, Li -Chen; Lu, Jie; Weck, Marcus; ...

2015-12-29

In shell cross-linked micelles (SCMs) containing acid sites in the shell and base sites in the core are prepared from amphiphilic poly(2-oxazoline) triblock copolymers. These materials are utilized as two-chamber nanoreactors for a prototypical acid-base bifunctional tandem deacetalization-nitroaldol reaction. Furthermore, the acid and base sites are localized in different regions of the micelle, allowing the two steps in the reaction sequence to largely proceed in separate compartments, akin to the compartmentalization that occurs in biological systems.

Pattern formations and optimal packing.

PubMed

Mityushev, Vladimir

2016-04-01

Patterns of different symmetries may arise after solution to reaction-diffusion equations. Hexagonal arrays, layers and their perturbations are observed in different models after numerical solution to the corresponding initial-boundary value problems. We demonstrate an intimate connection between pattern formations and optimal random packing on the plane. The main study is based on the following two points. First, the diffusive flux in reaction-diffusion systems is approximated by piecewise linear functions in the framework of structural approximations. This leads to a discrete network approximation of the considered continuous problem. Second, the discrete energy minimization yields optimal random packing of the domains (disks) in the representative cell. Therefore, the general problem of pattern formations based on the reaction-diffusion equations is reduced to the geometric problem of random packing. It is demonstrated that all random packings can be divided onto classes associated with classes of isomorphic graphs obtained from the Delaunay triangulation. The unique optimal solution is constructed in each class of the random packings. If the number of disks per representative cell is finite, the number of classes of isomorphic graphs, hence, the number of optimal packings is also finite. Copyright © 2016 Elsevier Inc. All rights reserved.

Analytical solution of reaction-diffusion equations for calcium wave propagation in a starburst amacrine cell.

PubMed

Poznanski, R R

2010-09-01

A reaction-diffusion model is presented to encapsulate calcium-induced calcium release (CICR) as a potential mechanism for somatofugal bias of dendritic calcium movement in starburst amacrine cells. Calcium dynamics involves a simple calcium extrusion (pump) and a buffering mechanism of calcium binding proteins homogeneously distributed over the plasma membrane of the endoplasmic reticulum within starburst amacrine cells. The system of reaction-diffusion equations in the excess buffer (or low calcium concentration) approximation are reformulated as a nonlinear Volterra integral equation which is solved analytically via a regular perturbation series expansion in response to calcium feedback from a continuously and uniformly distributed calcium sources. Calculation of luminal calcium diffusion in the absence of buffering enables a wave to travel at distances of 120 μm from the soma to distal tips of a starburst amacrine cell dendrite in 100 msec, yet in the presence of discretely distributed calcium-binding proteins it is unknown whether the propagating calcium wave-front in the somatofugal direction is further impeded by endogenous buffers. If so, this would indicate CICR to be an unlikely mechanism of retinal direction selectivity in starburst amacrine cells.

Something new in the field of PLA/GA bioresorbable polymers?

PubMed

Vert, M; Schwach, G; Engel, R; Coudane, J

1998-04-30

Polymers issued from glycolic acid and lactic acids (PLAGA) are now used worldwide as bioresorbable devices in surgery and in pharmacology. Their abiotic hydrolytic degradation has been shown to depend on diffusion-reaction phenomena and to proceed homogeneously or heterogeneously, depending on many factors. Two initiators are presently used industrially to make PLAGA polymers by ring opening polymerisation of lactide and/or glycolide in the bulk, namely Sn octanoate and zinc metal. In this contribution, attention is paid to the differences generated by the use of these two initiator systems in the case of the polymerisation of DL-lactide. Various poly(DL-lactide)s were prepared and characterised by size-exclusion chromatography (SEC), differential scanning calorimetry (DSC) and nuclear magnetic resonance spectroscopy (NMR). These polymers were allowed to age in pH=7.4 isoosmolar phosphate buffer at 37 degrees C. Under these conditions, polymers prepared by the two initiator systems showed dramatic differences when the fates of parallel sided specimens of rather large dimensions were considered. These differences were related to the esterification of some of the OH chain ends by octanoic acid and to the presence of rather hydrophobic low molecular weight by-products which were insoluble in the solvent generally used to purify the crude PLAGA polymers. These new findings should be of great interest in the case of PLAGA based matrices aimed at drug delivery.

Propagating gene expression fronts in a one-dimensional coupled system of artificial cells

NASA Astrophysics Data System (ADS)

Tayar, Alexandra M.; Karzbrun, Eyal; Noireaux, Vincent; Bar-Ziv, Roy H.

2015-12-01

Living systems employ front propagation and spatiotemporal patterns encoded in biochemical reactions for communication, self-organization and computation. Emulating such dynamics in minimal systems is important for understanding physical principles in living cells and in vitro. Here, we report a one-dimensional array of DNA compartments in a silicon chip as a coupled system of artificial cells, offering the means to implement reaction-diffusion dynamics by integrated genetic circuits and chip geometry. Using a bistable circuit we programmed a front of protein synthesis propagating in the array as a cascade of signal amplification and short-range diffusion. The front velocity is maximal at a saddle-node bifurcation from a bistable regime with travelling fronts to a monostable regime that is spatially homogeneous. Near the bifurcation the system exhibits large variability between compartments, providing a possible mechanism for population diversity. This demonstrates that on-chip integrated gene circuits are dynamical systems driving spatiotemporal patterns, cellular variability and symmetry breaking.

Dynamical spike solutions in a nonlocal model of pattern formation

NASA Astrophysics Data System (ADS)

Marciniak-Czochra, Anna; Härting, Steffen; Karch, Grzegorz; Suzuki, Kanako

2018-05-01

Coupling a reaction-diffusion equation with ordinary differential equa- tions (ODE) may lead to diffusion-driven instability (DDI) which, in contrast to the classical reaction-diffusion models, causes destabilization of both, constant solutions and Turing patterns. Using a shadow-type limit of a reaction-diffusion-ODE model, we show that in such cases the instability driven by nonlocal terms (a counterpart of DDI) may lead to formation of unbounded spike patterns.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duncan, Andrew, E-mail: a.duncan@imperial.ac.uk; Erban, Radek, E-mail: erban@maths.ox.ac.uk; Zygalakis, Konstantinos, E-mail: k.zygalakis@ed.ac.uk

Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the “fast” reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when onemore » or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.« less

In General, the Total Voltammetric Current from a Mixture of Redox-Active Substances will Not be the Sum of the Currents that Each Substance would Produce Independently at the Same Concentration as in the Mixture

NASA Technical Reports Server (NTRS)

Leventis, Nicholas; Oh, Woon Su; Gao, Xue-Rong; Rawashdeh, Abdel Monem M.

2003-01-01

At the potential range where both decamethylferrocene (dMeFc) and ferrocene (Fc) are oxidized with rates controlled by linear diffusion, electrogenerated Fc(+) radicals diffusing outwards from the electrode react quantitatively (K23 C=5.8 x 10(exp 8) with dMeFc diffusing towards the electrode and produce Fc and dMeFc. That reaction replaces dMeFc with Fc, whose diffusion coefficient is higher than that of dMeFc(+), and the total mass-transfer limited current from the mixture is increased by approximately 10%. Analogous observations are made when mass-transfer is controlled by convective-diffusion as in RDE voltammetry. Similar results have been obtained with another, and for all practical purposes randomly selected pair of redox-active substances, [Co(bipy)3](2+) and N - methylphenothiazine (MePTZ); reaction of MePTZ(+) with [Co(bipy)3](2+) replaces the latter with MePTZ, which diffuses faster and the current increases by approximately 20%. The experimental voltammograms have been simulated numerically and the role of (a) the rate constant of the homogeneous reaction; (b) the relative concentrations; and, (c) the diffusion coefficients of all species involved have been studied in detail. Importantly, it was also identified that within any given redox system the dependence of the mass-transfer limited current on the bulk concentrations of the redox-active species is expected to be non-linear. These findings are discussed in terms of their electroanalytical implications.

Trainable Nonlinear Reaction Diffusion: A Flexible Framework for Fast and Effective Image Restoration.

PubMed

Chen, Yunjin; Pock, Thomas

2017-06-01

Image restoration is a long-standing problem in low-level computer vision with many interesting applications. We describe a flexible learning framework based on the concept of nonlinear reaction diffusion models for various image restoration problems. By embodying recent improvements in nonlinear diffusion models, we propose a dynamic nonlinear reaction diffusion model with time-dependent parameters (i.e., linear filters and influence functions). In contrast to previous nonlinear diffusion models, all the parameters, including the filters and the influence functions, are simultaneously learned from training data through a loss based approach. We call this approach TNRD-Trainable Nonlinear Reaction Diffusion. The TNRD approach is applicable for a variety of image restoration tasks by incorporating appropriate reaction force. We demonstrate its capabilities with three representative applications, Gaussian image denoising, single image super resolution and JPEG deblocking. Experiments show that our trained nonlinear diffusion models largely benefit from the training of the parameters and finally lead to the best reported performance on common test datasets for the tested applications. Our trained models preserve the structural simplicity of diffusion models and take only a small number of diffusion steps, thus are highly efficient. Moreover, they are also well-suited for parallel computation on GPUs, which makes the inference procedure extremely fast.

Systems analysis of electricity production from coal using fuel cells

NASA Technical Reports Server (NTRS)

Fleming, D. K.

1983-01-01

Gasifiers, heat transfer, gas stability, quench, water-gas shift reaction, reforming-methanation, other catalytic reactions, compressors and expanders, acid-gas removal, the fuel cell, and catalytic combustors are described. System pressure drops, efficiency of rotating power equipment, heat exchangers, chemical reactions, steam systems, and the fuel cell subsystems are discussed.

Lithium manganese oxide spinel electrodes

NASA Astrophysics Data System (ADS)

Darling, Robert Mason

Batteries based oil intercalation eletrodes are currently being considered for a variety of applications including automobiles. This thesis is concerned with the simulation and experimental investigation of one such system: spinel LiyMn2O4. A mathematical model simulating the behavior of an electrochemical cell containing all intercalation electrode is developed and applied to Li yMn2O4 based systems. The influence of the exchange current density oil the propagation of the reaction through the depth of the electrode is examined theoretically. Galvanostatic cycling and relaxation phenomena on open circuit are simulated for different particle-size distributions. The electrode with uniformly sized particles shows the best performance when the current is on, and relaxes towards equilibrium most quickly. The impedance of a porous electrode containing a particle-size distribution at low frequencies is investigated with all analytic solution and a simplified version of the mathematical model. The presence of the particle-size distribution leads to an apparent diffusion coefficient which has all incorrect concentration dependence. A Li/1 M LiClO4 in propylene carbonate (PC)/ LiyMn 2O4 cell is used to investigate the influence of side reactions oil the current-potential behavior of intercalation electrodes. Slow cyclic voltammograms and self-discharge data are combined to estimate the reversible potential of the host material and the kinetic parameters for the side reaction. This information is then used, together with estimates of the solid-state diffusion coefficient and main-reaction exchange current density, in a mathematical model of the system. Predictions from the model compare favorably with continuous cycling results and galvanostatic experiments with periodic current interruptions. The variation with respect to composition of' the diffusion coefficient of lithium in LiyMn2O4 is estimated from incomplete galvanostatic discharges following open-circult periods. The results compared favorably with those available in the literature. Dynamic Monte Carlo simulations were conducted to investigate the concentration dependence of the diffusion coefficient fundamentally. The dynamic Monte Carlo predictions compare favorably with the experimental data.

The Scales Of Chemical Transport During Dehydration Reactions: The Roles Of Diffusion And Fluid Expulsion

NASA Astrophysics Data System (ADS)

Bedford, J. D.; Wheeler, J.; Fusseis, F.; Leclere, H.; Faulkner, D.

2016-12-01

The growth of new minerals in response to disequilibrium is the most fundamental metamorphic process. However, the kinetics controls on metamorphic reactions, including the transport of chemical components to growing minerals, are poorly understood as direct observation has been impossible both in nature and experiments. Dehydration reactions are common during prograde metamorphism and require both the expulsion of H2O and the transport of solid chemical components to the product mineral(s) in order for reaction to proceed. The expulsion of H2O is particularly important in understanding when fluid overpressures might develop, which can in turn lead to sudden failure (earthquakes) if the fluid is unable to drain. Using time-resolved (4D) synchrotron X-ray microtomography we have imaged a complete dehydration reaction and show how chemical transport of both the solid and fluid phases evolves during reaction. The reaction analysed is the dehydration of gypsum to form bassanite and H2O - an analogue for silicate dehydration but with much faster and controllable reaction rate. Like most dehydration reactions, the breakdown of gypsum is associated with a solid volume reduction which generates pore space. This new porosity wraps around growing bassanite grains, producing fluid-filled moats, across which transport of dissolved solutes to the growing grains occurs via diffusion. As moats grow in width, diffusion and hence reaction rate slow down. Each new grain-moat pair evolves in relative isolation from each other indicating that the chemical transport of solid components occurs over relatively short distances. This is despite the overall pore network becoming connected during the early stages of reaction, thus allowing efficient expulsion of excess H2O. A dehydrating system can therefore act as an open system with respect to the fluid phase and in contrast be restricted to the grain-scale with respect to the dissolved chemicals. This is in accord with observations that many rocks appear to have preserved their chemistry during dehydration (apart from the loss of H2O).

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting.

PubMed

Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

2014-06-01

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity.

The effect of carbon surface chemical composition on the adsorption of acetanilide.

PubMed

Terzyk, Artur P

2004-04-01

The study of acetanilide adsorption-desorption performed at three temperatures (300, 310, and 320 K) and at two pH levels (7.0 and 1.5) on the series of D43/1 carbons (initial and modified with HNO3, fuming H2SO4, and gaseous NH3) is reported. Sorption data are additionally supplemented with the results of thermal analysis and calorimetric and kinetic measurements. It is shown that, generally, acetanilide adsorption at the neutral pH level is reversible (only on the more acidic carbons and at the lowest temperature does hysteresis occur due to the formation of hydrogen bonds with surface OH groups), and it decreases for the chemically modified carbons. In contrast, at the acidic pH level acetanilide adsorption is irreversible. A mechanism of irreversibility is proposed and it is shown that hysteresis is caused by the chemical reaction between the nucleophile (carbon) and the protonized acetanilide molecules. For all studied carbons, at the acidic pH level, adsorption increases and this is caused by the weakly basic character of acetanilide molecule. Adsorption results are described applying adsorbability and Dubinin-Astakhov, quasi-Freundlich and solution analogue of the Toth adsorption isotherm equations. Using the kinetic data, the effective diffusion coefficients and the energy of diffusion are calculated. It is shown that the diffusion is mainly a surface process, and the contribution of the pore diffusion increases with the rise in temperature. By applying different correlations between the parameters obtained from the theoretical description of experimental data and those characterizing the chemical composition of the studied carbons, the role of the latter in the adsorption and kinetics of acetanilide adsorption is determined.

Microchemical Pen: An Open Microreactor for Region-Selective Surface Modification.

PubMed

Mao, Sifeng; Sato, Chiho; Suzuki, Yuma; Yang, Jianmin; Zeng, Hulie; Nakajima, Hizuru; Yang, Ming; Lin, Jin-Ming; Uchiyama, Katsumi

2016-10-18

Various micro surface-modification approaches including photolithography, dip-pen lithography and ink-jet systems have been developed and used to extend the functionalities of solid surfaces. While those approaches work in the "open space", push-pull systems which work in solutions have recently drawn considerable attention. However, the confining flows performed by push-pull systems have realized only the dispense process, while microscale, region-selective chemical reactions have remained unattainable. This study reports a microchemical pen that enables region-selective chemical reactions for the micro surface modification/patterning. The chemical pen is based on the principle of microfluidic laminar flows and the resulting mixing of reagents by the mutual diffusion. The tiny diffusion layer performs as the working region. This report represents the first demonstration of an open microreactor in which two different reagents react on a real solid sample. The multifunctional characteristics of the microchemical pen are confirmed by different types of reactions in many research areas, including inorganic chemistry, polymer science, electrochemistry and biological sample treatment. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Connecting localized DNA strand displacement reactions

NASA Astrophysics Data System (ADS)

Mullor Ruiz, Ismael; Arbona, Jean-Michel; Lad, Amitkumar; Mendoza, Oscar; Aimé, Jean-Pierre; Elezgaray, Juan

2015-07-01

Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions.Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions. Electronic supplementary information (ESI) available. See DOI: 10.1039/C5NR02434J

Phase Equilibria of the Sn-Ni-Si Ternary System and Interfacial Reactions in Sn-(Cu)/Ni-Si Couples

NASA Astrophysics Data System (ADS)

Fang, Gu; Chen, Chih-chi

2015-07-01

Interfacial reactions in Sn/Ni-4.5 wt.%Si and Sn-Cu/Ni-4.5 wt.%Si couples at 250°C, and Sn-Ni-Si ternary phase equilibria at 250°C were investigated in this study. Ni-Si alloys, which are nonmagnetic, can be regarded as a diffusion barrier layer material in flip chip packaging. Solder/Ni-4.5 wt.%Si interfacial reactions are crucial to the reliability of soldered joints. Phase equilibria information is essential for development of solder/Ni-Si materials. No ternary compound is present in the Sn-Ni-Si ternary system at 250°C. Extended solubility of Si in the phases Ni3Sn2 and Ni3Sn is 3.8 and 6.1 at.%, respectively. As more Si dissolves in these phases their lattice constants decrease. No noticeable ternary solubility is observed for the other intermetallics. Interfacial reactions in solder/Ni-4.5 wt.%Si are similar to those for solder/Ni. Si does not alter the reaction phases. No Si solubility in the reaction phases was detected, although rates of growth of the reaction phases were reduced. Because the alloy Ni-4.5 wt.%Si reacts more slowly with solders than pure Ni, the Ni-4.5 wt.%Si alloy could be a potential new diffusion barrier layer material for flip chip packaging.

Development of the Monolith Froth Reactor for Catalytic Wet Oxidation of CELSS Model Wastes

NASA Technical Reports Server (NTRS)

Fisher, John W.; Abraham, Martin

1993-01-01

The aqueous phase oxidation of acetic acid, used as a model compound for the treatment of CELSS (Controlled Ecological Life Support System) waste, was carried out in the monolith froth reactor which utilizes two-phase flow in the monolith channels. The catalytic oxidation of acetic acid was carried out over a Pt/Al2O3 catalyst at temperatures and pressures below the critical point of water. The effect of externally controllable parameters (temperature, liquid flow rate, distributor plate orifice size, pitch, and catalyst distance from the distributor plate) on the rate of acetic acid oxidation was investigated. Results indicate reaction rate increased with increasing temperature and exhibited a maximum with respect to liquid flow rate. The apparent activation energy calculated from reaction rate data was 99.7 kJ/mol. This value is similar to values reported for the oxidation of acetic acid in other systems and is comparable to intrinsic values calculated for oxidation reactions. The kinetic data were modeled using simple power law kinetics. The effect of "froth" feed system characteristics was also investigated. Results indicate that the reaction rate exhibits a maximum with respect to distributor plate orifice size, pitch, and catalyst distance from the distributor plate. Fundamental results obtained were used to extrapolate where the complete removal of acetic acid would be obtained and for the design and operation of a full scale CELSS treatment system.

Significance of vapor phase chemical reactions on CVD rates predicted by chemically frozen and local thermochemical equilibrium boundary layer theories

NASA Technical Reports Server (NTRS)

Gokoglu, Suleyman A.

1988-01-01

This paper investigates the role played by vapor-phase chemical reactions on CVD rates by comparing the results of two extreme theories developed to predict CVD mass transport rates in the absence of interfacial kinetic barrier: one based on chemically frozen boundary layer and the other based on local thermochemical equilibrium. Both theories consider laminar convective-diffusion boundary layers at high Reynolds numbers and include thermal (Soret) diffusion and variable property effects. As an example, Na2SO4 deposition was studied. It was found that gas phase reactions have no important role on Na2SO4 deposition rates and on the predictions of the theories. The implications of the predictions of the two theories to other CVD systems are discussed.

Switching catalysis from hydrolysis to perhydrolysis in P. fluorescens esterase

PubMed Central

Yin, De Lu (Tyler); Bernhardt, Peter; Morley, Krista L.; Jiang, Yun; Cheeseman, Jeremy D.; Purpero, Vincent; Schrag, Joseph D.; Kazlauskas, Romas J.

2010-01-01

Many serine hydrolases catalyze perhydrolysis – the reversible formation of per-acids from carboxylic acids and hydrogen peroxide. Recently we showed that a single amino acid substitution in the alcohol binding pocket - L29P - in Pseudomonas fluorescens (SIK WI) aryl esterase (PFE) increased the specificity constant of PFE for peracetic acid formation >100-fold [Bernhardt et al. Angew. Chem. Intl. Ed. 2005, 44, 2742]. In this paper, we extend this work to address the three following questions. First, what is the molecular basis of the increase in perhydrolysis activity? We previously proposed that the L29P substitution creates a hydrogen bond between the enzyme and hydrogen peroxide in the transition state. Here we report two x-ray structures of L29P PFE that support this proposal. Both structures show a main chain carbonyl oxygen closer to the active-site serine as expected. One structure further shows acetate in the active site in an orientation consistent with reaction by an acyl-enzyme mechanism. We also detected an acyl-enzyme intermediate in the hydrolysis of ε-caprolactone by mass spectrometry. Second, can we further increase perhydrolysis activity? We discovered that the reverse reaction – hydrolysis of peracetic acid to acetic acid and hydrogen peroxide – occurs at nearly the diffusion limited rate. Since the reverse reaction cannot increase further, neither can the forward reaction. Consistent with this prediction, two variants with additional amino acid substitutions showed two fold higher kcat, but Km also increased so the specificity constant, kcat/Km, remained similar. Third, how does the L29P substitution change the esterase activity? Ester hydrolysis decreased for most esters (75-fold for ethyl acetate), but not for methyl esters. In contrast, L29P PFE catalyzed hydrolysis of ε-caprolactone five times more efficiently than wild-type PFE. Molecular modeling suggests that moving the carbonyl group closer to the active site blocks access for larger alcohol moieties, but binds ε-caprolactone more tightly. These results are consistent with the natural function of perhydrolases being either hydrolysis of peroxycarboxylic acids or hydrolysis of lactones. PMID:20112920

Removal of PCB and Other Halogenated Organic Contaminants found in Ex Situ Structures

NASA Technical Reports Server (NTRS)

Quinn, Jacqueline (Inventor); Clausen, Christian (Inventor); Geiger, Cherie L. (Inventor); Coon, Christina (Inventor); Berger, Cristina M. (Inventor); Filipek, Laura B. (Inventor); Milum, Kristen M. (Inventor)

2007-01-01

Emulsified systems or a surfactant-stabilized, biodegradable water-in-solvent emulsion with bimetallic particles contained with the emulsion droplets are useful at removing PCBs from ex situ structures. The hydrophobic emulsion system draws PCBs through the solvent/surfactant membrane. Once inside the membrane, the PCBs diffuse into the bimetallic particles and undergo degradation. The PCBs continue to enter, diffuse, degrade, and biphenyl will exit the particle maintaining a concentration gradient across the membrane and maintaining a driving force of the reaction.

Removal of PCB and other halogenated organic contaminants found in ex situ structures

NASA Technical Reports Server (NTRS)

Quinn, Jacqueline (Inventor); Clausen, Christian (Inventor); Geiger, Cherie L. (Inventor); Coon, Christina (Inventor); Berger, Cristina M. (Inventor); Filipek, Laura B. (Inventor); Milum, Kristen M. (Inventor)

2007-01-01

Emulsified systems of a surfactant-stabilized, biodegradable water-in-solvent emulsion with bimetallic particles contained with the emulsion droplets are useful at removing PCBs from ex situ structures. The hydrophobic emulsion system draws PCBs through the solvent/surfactant membrane. Once inside the membrane, the PCBs diffuse into the bimetallic particles and undergo degradation. The PCBs continue to enter, diffuse, degrade, and biphenyl will exit the particle maintaining a concentration gradient across the membrane and maintaining a driving force of the reaction.

Removal of PCB and other halogenated organic contaminants found in ex situ structures

NASA Technical Reports Server (NTRS)

Clausen, Christian A. (Inventor); Milum, Kristen M. (Inventor); Quinn, Jacqueline W. (Inventor); Berger, Cristina M. (Inventor); Geiger, Cherie L. (Inventor); Filipek, Laura B. (Inventor); Coon, Christina (Inventor)

2009-01-01

Emulsified systems of a surfactant-stabilized, biodegradable water-in-solvent emulsion with bimetallic particles contained with the emulsion droplets are useful at removing PCBs from ex situ structures. The hydrophobic emulsion system draws PCBs through the solvent/surfactant membrane. Once inside the membrane, the PCBs diffuse into the bimetallic particles and undergo degradation. The PCBs continue to enter, diffuse, degrade, and biphenyl will exit the particle maintaining a concentration gradient across the membrane and maintaining a driving force of the reaction.

Effect of isospin diffusion on the production of neutron-rich nuclei in multinucleon transfer reactions

NASA Astrophysics Data System (ADS)

Niu, Fei; Chen, Peng-Hui; Guo, Ya-Fei; Ma, Chun-Wang; Feng, Zhao-Qing

2018-03-01

The isospin dissipation dynamics in multinucleon transfer reactions has been investigated within the dinuclear system model. Production cross sections of neutron-rich isotopes around projectile-like and target-like fragments are estimated in collisions of Ni,6458+208Pb and 78.86,91Kr +198Pt near Coulomb barrier energies. The isospin diffusion in the nucleon transfer process is coupled to the dissipation of relative motion energy and angular momentum of colliding system. The available data of projectile-like fragments via multinucleon transfer reactions are nicely reproduced. It is found that the light projectile-like fragments are produced in the neutron-rich region because of the isospin equilibrium in two colliding nuclei. However, the heavy target-like fragments tend to be formed on the neutron-poor side above the β -stability line. The neutron-rich projectiles move the maximal yields of heavy nuclei to the neutron-rich domain and are available for producing the heavy exotic isotopes, in particular around the neutron shell closure of N =126 .

Ultrafast photodimerization dynamics in α-cyano-4-hydroxycinnamic and sinapinic acid crystals

NASA Astrophysics Data System (ADS)

Hoyer, Theo; Tuszynski, Wilfried; Lienau, Christoph

2007-07-01

We report a sub-picosecond time-resolved fluorescence spectroscopic study of different cinnamic acid crystals, model systems for solid-state photodimerization reactions. For α-cyano-4-hydroxycinnamic acid (α-CHC), we identify the emission spectra of both monomers and dimers, allowing us to directly probe the photoinduced dynamics of both species. The dimerization occurs on a timescale of 10 ps and results in a long-lived dimer product, stable for hours. For sinapinic acid, we find an extremely fast, sub-picosecond dimerization reaction and a short-lived dimer. This first sub-picosecond time-resolved dimerization study in cinnamic acid crystals provides a new basis for relating their structural properties and microscopic reaction dynamics.

Time-delayed feedback control of breathing localized structures in a three-component reaction-diffusion system.

PubMed

Gurevich, Svetlana V

2014-10-28

The dynamics of a single breathing localized structure in a three-component reaction-diffusion system subjected to time-delayed feedback is investigated. It is shown that variation of the delay time and the feedback strength can lead either to stabilization of the breathing or to delay-induced periodic or quasi-periodic oscillations of the localized structure. A bifurcation analysis of the system in question is provided and an order parameter equation is derived that describes the dynamics of the localized structure in the vicinity of the Andronov-Hopf bifurcation. With the aid of this equation, the boundaries of the stabilization domains as well as the dependence of the oscillation radius on delay parameters can be explicitly derived, providing a robust mechanism to control the behaviour of the breathing localized structure in a straightforward manner. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Plasma chemistry and organic synthesis

NASA Technical Reports Server (NTRS)

Tezuka, M.

1980-01-01

The characteristic features of chemical reactions using low temperature plasmas are described and differentiated from those seen in other reaction systems. A number of examples of applications of plasma chemistry to synthetic reactions are mentioned. The production of amino acids by discharge reactions in hydrocarbon-ammonia-water systems is discussed, and its implications for the origins of life are mentioned.

Kinetic Aspects of Leaching Zinc from Waste Galvanizing Zinc by Using Hydrochloric Acid Solutions

NASA Astrophysics Data System (ADS)

Sminčáková, Emília; Trpčevská, Jarmila; Pirošková, Jana

2017-10-01

In this work, the results of acid leaching of flux skimmings coming from two plants are presented. Sample A contained two phases, Zn(OH)Cl and NH4Cl. In sample B, the presence of three phases, Zn5(OH)8Cl2·H2O, (NH4)2(ZnCl4) and ZnCl2(NH3)2, was proved. The aqueous solution of hydrochloric acid and distilled water was used as the leaching medium. The effects of the leaching time, temperature and concentration of the leaching medium on the zinc extraction were investigated. The apparent activation energy, E a = 4.61 kJ mol-1, and apparent reaction order n = 0.18 for sample A, and the values E a = 6.28 kJ mol-1 and n = 0.33 for sample B were experimentally determined. Zinc leaching in acid medium is a diffusion-controlled process.

Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests

PubMed Central

Mauk, Michael G.; Song, Jinzhao; Liu, Changchun; Bau, Haim H.

2018-01-01

Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges (‘chips’) that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed. PMID:29495424

Investigation on uric acid biosensor model for enzyme layer thickness for the application of arthritis disease diagnosis.

PubMed

Parthasarathy, P; Vivekanandan, S

2018-12-01

Uric acid biosensors for arthritis disease has been developed for the specific selection of uricase enzyme film thickness coated over the TiO 2 -CeO 2 nano-composite matrix is modelled mathematically. This model is purely based on R-diffusion conditions with irreversible first-order catalytic reactions. By arithmetical method, the impact of the thickness of enzyme layer on the current response of the biosensor was explored. This article displays a structure for choice of the enzyme layer thickness, guaranteeing the adequately stable sensitivity of a biosensor in a required extent of the maximal enzymatic rate. The numerical outcomes showed subjective and sensible quantitative information for oxidation current due to uric acid also shows the maximum change in the biosensor current response due to the change in membrane thickness, which will be more suitable for uric acid biosensor for the application of arthritis disease diagnosis.

Reaction Gradients Viewed Inside Single Photoactive Particles

NASA Astrophysics Data System (ADS)

Alpert, P.; Corral Arroyo, P.; Dou, J.; Kreiger, U.; Luo, B.; Peter, T.; Ammann, M.

2017-12-01

In terms of chemical selectivity and spatial resolution, a technique known as scanning transmission X-ray microscopy coupled to near-edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS) is unmatched and will remain so for years into the future. We present a recent development coupling STXM/NEXAFS to a custom-built photochemical environmental reactor in which aerosol particles reside allowing for in situ chemical imaging. A laboratory investigation of metal-organic complex photochemistry was conducted. Transition metals are of great importance to atmospheric chemistry and aerosol photochemical aging due to their ability to catalyze oxidation reactions. Aerosol particles composed of mixtures of citric acid and iron citrate were probed for their organic carbon composition and iron oxidation state under atmospherically relevant conditions. At 40% relative humidity, oxygen diffusion and reaction was severely limited. Fe was reoxidized in the first 200 nm of the particle surface leaving reduced iron in the core. Similar gradients were observed at 60% RH, however waiting approximately 2 hours in the dark resulted in a recovery of the initial Fe(III) concentration. We draw two main conclusions from our findings. Frist, the oxidation gradients must have been the result of anoxic conditions at the interior of aerosol particles. This was predicted using a newly developed model for molecular diffusion through multiple layers with a reaction framework describing the photochemical processing of the metal organic matrix. Second, the lifetime of organic radicals in an anoxic diffusion limited organic matrix must be considerably long ( hours) to completely reoxidize iron as they wait for molecular oxygen. Long radical lifetimes in viscous organic aerosol in turn, could create high radical concentrations or favor radical-radical reactions in particles typically not considered when oxygen is plentiful. Our results impact predictions of aerosol physiochemical properties, e.g. aerosol toxicity, hygroscopicity, lifetime and light scattering properties over time which may be limited and evolve at different rates at the surface or core of particles.

Numerical solution of the unsteady diffusion-convection-reaction equation based on improved spectral Galerkin method

NASA Astrophysics Data System (ADS)

Zhong, Jiaqi; Zeng, Cheng; Yuan, Yupeng; Zhang, Yuzhe; Zhang, Ye

2018-04-01

The aim of this paper is to present an explicit numerical algorithm based on improved spectral Galerkin method for solving the unsteady diffusion-convection-reaction equation. The principal characteristics of this approach give the explicit eigenvalues and eigenvectors based on the time-space separation method and boundary condition analysis. With the help of Fourier series and Galerkin truncation, we can obtain the finite-dimensional ordinary differential equations which facilitate the system analysis and controller design. By comparing with the finite element method, the numerical solutions are demonstrated via two examples. It is shown that the proposed method is effective.

Delay-induced Turing-like waves for one-species reaction-diffusion model on a network

NASA Astrophysics Data System (ADS)

Petit, Julien; Carletti, Timoteo; Asllani, Malbor; Fanelli, Duccio

2015-09-01

A one-species time-delay reaction-diffusion system defined on a complex network is studied. Traveling waves are predicted to occur following a symmetry-breaking instability of a homogeneous stationary stable solution, subject to an external nonhomogeneous perturbation. These are generalized Turing-like waves that materialize in a single-species populations dynamics model, as the unexpected byproduct of the imposed delay in the diffusion part. Sufficient conditions for the onset of the instability are mathematically provided by performing a linear stability analysis adapted to time-delayed differential equations. The method here developed exploits the properties of the Lambert W-function. The prediction of the theory are confirmed by direct numerical simulation carried out for a modified version of the classical Fisher model, defined on a Watts-Strogatz network and with the inclusion of the delay.

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

PubMed Central

Hallock, Michael J.; Stone, John E.; Roberts, Elijah; Fry, Corey; Luthey-Schulten, Zaida

2014-01-01

Simulation of in vivo cellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel e ciency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system in E. coli. Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems. PMID:24882911

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations.

PubMed

Hallock, Michael J; Stone, John E; Roberts, Elijah; Fry, Corey; Luthey-Schulten, Zaida

2014-05-01

Simulation of in vivo cellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel e ciency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system in E. coli . Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems.

A novel in situ permeation system and its utility in cancer tissue ablation

PubMed Central

WATANABE, MASAMI

2015-01-01

Focal ablation therapy is an emerging treatment modality for localized cancer lesions. It is an attractive strategy for inhibiting tumor progression and preventing morbidity associated with open surgery. As for intratissue drug delivery systems for use in local therapy, the convection-enhanced delivery (CED) of liquid drugs has been utilized, particularly for the treatment of malignant brain tumors. Although the conventional CED system is useful for providing drug/vehicle-based local therapy, there are several reported disadvantages in terms of the ability to control the extent of drug diffusion. We herein developed and validated a novel in situ permeation (ISP)-MW-1 system for achieving intratissue drug diffusion. The ISP system includes a perfusion catheter connected to an injector and aspirator, which enables intratissue perfusion of the solute diluted in the vehicle in the tip-inserted cavity. We subsequently evaluated the utility of the ISP-MW-1 system for in situ permeation in a subcutaneous tumor model in hamsters. Dehydrated ethanol, saline and 50% acetic acid were evaluated as the vehicle, and methylene blue was used as a dissolved substance for evaluating the diffusion of the agent. As a result, almost all of the tumor tissue within the capsule (tumor size: ~3 cm) was permeated with the dehydrated ethanol and 50% acetic acid and partially with the saline. We further demonstrated that ISP treatment with 50% acetic acid completely ablated the subcutaneous tumors in all of the treated hamsters (n=3). Therefore, the ISP-MW-1 system is a promising approach for controlling the intratissue diffusion of therapeutic agents and for providing local ablation therapy for cancer lesions. We believe that this system may be applicable to a broad range of medicinal and industrial fields, such as regenerative medicine, drug delivery systems, biochemistry and material technologies as well as cancer therapy. PMID:26134633

Discovery of Amadori-Type Conjugates in a Peptide Maillard Reaction and Their Corresponding Influence on the Formation of Pyrazines.

PubMed

Zou, Tingting; Liu, Jianbin; Song, Huanlu; Liu, Ye

2018-06-01

Knowledge of the role of peptides in the Maillard reaction is rather limited. In this study, peptide Maillard reaction model systems were established. Volatile and nonvolatile MRPs (Maillard reaction products) were investigated by GC-O-MS and LC-MS. Carbohydrate module labeling (CAMOLA) experiments were performed to elucidate the carbon skeleton of these compounds. Results showed that the peptide reaction system generated more pyrazines than the free amino acid group. Several new Amadori-type conjugates were identified as novel Maillard reaction products that could greatly influence the formation of pyrazines. Our work suggested anew mechanism involving these Amadori-type conjugates and subsequent investigation revealed that the conjugates could be important intermediate products in the reaction between dicarbonyl and dipeptide. Our findings demonstrate anew pyrazine generation mechanism in the dipeptide Maillard reaction. We found that a dipeptide Maillard reaction system generated more pyrazines than a reaction system composed of free amino acids. New cross-linked peptide-sugar compounds were identified and found to impact the formation of pyrazines. The results of this study may help in the preparation of thermal reaction flavors using enzymatically hydrolyzed vegetable/animal proteins, which contain a considerable amount of peptides, as one of the major reactants. © 2018 Institute of Food Technologists®.

Biotransformation of β-keto nitriles to chiral (S)-β-amino acids using nitrilase and ω-transaminase.

PubMed

Mathew, Sam; Nadarajan, Saravanan Prabhu; Sundaramoorthy, Uthayasuriya; Jeon, Hyunwoo; Chung, Taeowan; Yun, Hyungdon

2017-04-01

To enzymatically synthesize enantiomerically pure β-amino acids from β-keto nitriles using nitrilase and ω-transaminase. An enzyme cascade system was designed where in β-keto nitriles are initially hydrolyzed to β-keto acids using nitrilase from Bradyrhizobium japonicum and subsequently β-keto acids were converted to β-amino acids using ω-transaminases. Five different ω-transaminases were tested for this cascade reaction, To enhance the yields of β-amino acids, the concentrations of nitrilase and amino donor were optimized. Using this enzymatic reaction, enantiomerically pure (S)-β-amino acids (ee > 99%) were generated. As nitrilase is the bottleneck in this reaction, molecular docking analysis was carried out to depict the poor affinity of nitrilase towards β-keto acids. A novel enzymatic route to generate enantiomerically pure aromatic (S)-β-amino acids from β-keto nitriles is demonstrated for the first time.

Reaction Rate of Ti0.18Zr0.84Cr1.0Fe0.7Mn0.3Cu0.057 to Use for the Heat Driven Type Compact Metal Hydride Refrigerator

NASA Astrophysics Data System (ADS)

Bae, Sang-Chul; Katsuta, Masafumi

Our final goal of this study is to develop the heat driven type compact metal hydride (MH) refrigeration system for the vending machine and the show case, and to attain a refrigeration temperature of 243 K by using a heat source of about 423K. The reaction rate of the MH to use for the heat source, MH used for heat source is studied firstly because the MH refrigeration system consists of two MHs, one is used for the heat source and the other is used for the cooling load extracting. As for the reaction rate in the hydriding process, initially, a rapid surface reaction, governed by the relation 1-(1-F )1/3=kht . After the MH surface has been covered by hydride, the reaction becomes diffusion controlled with the relation 1-3(1-F ' )2/3+2(1-F ' )=k'ht . The reaction rates, kh and k'h , are exponentially proportional to the pressure difference and increase with temperature. And, as for the dehydriding process, it is found out that the rate-controlling step is uniquely diffusion reaction. The dehydriding reaction rate is exponentially proportional to the pressure difference and the initial reacted fraction, and increases with temperature. Finally, on the basis of these experimental results, the brand new rate correlations are reasonably derived. The predicted results for this correlation are in successfully agreement with the experimental ones.

Synchronization of Reaction-Diffusion Neural Networks With Dirichlet Boundary Conditions and Infinite Delays.

PubMed

Sheng, Yin; Zhang, Hao; Zeng, Zhigang

2017-10-01

This paper is concerned with synchronization for a class of reaction-diffusion neural networks with Dirichlet boundary conditions and infinite discrete time-varying delays. By utilizing theories of partial differential equations, Green's formula, inequality techniques, and the concept of comparison, algebraic criteria are presented to guarantee master-slave synchronization of the underlying reaction-diffusion neural networks via a designed controller. Additionally, sufficient conditions on exponential synchronization of reaction-diffusion neural networks with finite time-varying delays are established. The proposed criteria herein enhance and generalize some published ones. Three numerical examples are presented to substantiate the validity and merits of the obtained theoretical results.

Kinetics of dissolution of sapphire in melts in the CaO-Al2O3-SiO2 system

NASA Astrophysics Data System (ADS)

Shaw, Cliff S. J.; Klausen, Kim B.; Mao, Huahai

2018-05-01

The dissolution rate of sapphire in melts in the CAS system of varying silica activity, viscosity and degree of alumina saturation has been determined at 1600 °C and 1.5 GPa. After an initiation period of up to 1800 s, dissolution is controlled by diffusion of cations through the boundary layer adjacent to the dissolving sapphire. The dissolution rate decreases with increasing silica activity, viscosity and molar Al2O3/CaO. The calculated diffusion matrix for each solvent melt shows that CAS 1 and 9 which have molar Al2O3/CaO of 0.33 and 0.6 and dissolution rate constants of 0.65 × 10-6 and 0.59 × 10-6 m/s0.5 have similar directions and magnitudes of diffusive coupling: DCaO-Al2O3 and DAl2O3-CaO are both negative are approximately equal. The solvent with the fastest dissolution rate: CAS 4, which has a rate constant of 1.5 × 10-6 m/s0.5 and Al2O3/CaO of 0.31 has positive DCaO-Al2O3 and negative DAl2O3-CaO and the absolute values vary by a factor of 4. Although many studies show that aluminium is added to the melts via the reaction: Si4+ =Al3+ + 0.5Ca2+ the compositional profiles show that this reaction is not the only one involved in accommodating the aluminium added during sapphire dissolution. Rather, aluminium is incorporated as both tetrahedrally coordinated Al charge balanced by Ca and as aluminium not charge balanced by Ca (termed Alxs). This reaction: AlIV -Ca =Alxs +CaNBO where CaNBO is a non-bridging oxygen associated with calcium, may involve the formation of aluminium triclusters. The shape of the compositional profiles and oxide-oxide composition paths is controlled by the aluminium addition reaction. When Alxs exceeds 2%, CaO diffusion becomes increasingly anomalous and since the bond strength of Alxs correlates with CaO/CaO + Al2O3, the presence of more than 2% Alxs leads to significantly slower dissolution than when Alxs is absent or at low concentration. Thus, dissolution is controlled by diffusion of cations through the boundary layer, but this diffusion is itself controlled by the structural modifications required by the addition of new components to the melt. Comparison of quartz dissolution rates in similar melts shows that dissolution is much faster for quartz than for sapphire and that dissolution rates show the same correlation with silica activity and viscosity. We suggest that diffusive fluxes are related to changes in melt structure and the nature of the reaction that incorporates the added component. For the slow eigendirection, SiO2 addition occurs by a single reaction whereas Al2O3 addition requires a more complex two part reaction in which Al is accommodated by charge balance with Ca until Al is in excess of that which can be charge balanced. The Alxs incorporation reaction, is slower than the Si incorporation reaction which inhibits sapphire dissolution relative to quartz in melts of the same composition.

Reactive solid surface morphology variation via ionic diffusion.

PubMed

Sun, Zhenchao; Zhou, Qiang; Fan, Liang-Shih

2012-08-14

In gas-solid reactions, one of the most important factors that determine the overall reaction rate is the solid morphology, which can be characterized by a combination of smooth, convex and concave structures. Generally, the solid surface structure varies in the course of reactions, which is classically noted as being attributed to one or more of the following three mechanisms: mechanical interaction, molar volume change, and sintering. Here we show that if a gas-solid reaction involves the outward ionic diffusion of a solid-phase reactant then this outward ionic diffusion could eventually smooth the surface with an initial concave and/or convex structure. Specifically, the concave surface is filled via a larger outward diffusing surface pointing to the concave valley, whereas the height of the convex surface decreases via a lower outward diffusion flux in the vertical direction. A quantitative 2-D continuum diffusion model is established to analyze these two morphological variation processes, which shows consistent results with the experiments. This surface morphology variation by solid-phase ionic diffusion serves to provide a fourth mechanism that supplements the traditionally acknowledged solid morphology variation or, in general, porosity variation mechanisms in gas-solid reactions.

Activity of Co-N multi walled carbon nanotubes electrocatalysts for oxygen reduction reaction in acid conditions

NASA Astrophysics Data System (ADS)

Osmieri, Luigi; Monteverde Videla, Alessandro H. A.; Specchia, Stefania

2015-03-01

Two catalysts are synthesized by wet impregnation of multi walled carbon nanotubes (MWCNT) with a complex formed between Co(II) ions and the nitrogen-containing molecule 2,4,6-tris(2-pyridyl)-1,3,5-triazine (TPTZ), followed by one or two identical heat treatments in N2 atmosphere at 800 °C for 3 h. Catalysts are fully characterized by FESEM, EDX, BET, XRD, FTIR, TGA, XPS analyses, and electrochemical techniques. The electrocatalytic activity towards oxygen reduction reaction (ORR) of the catalysts in acid conditions is assessed by means of a rotating disk electrode (RDE) apparatus and a specific type of cell equipped with a gas diffusion working electrode (GDE). In both testing approaches, the catalyst heat-treated twice (Co-N/MWCNT-2) exhibits higher electroactivity than the catalyst heat-treated once (Co-N/MWCNT-1). Chronoamperometries both in RDE and GDE cell are also performed, showing less electroactivity decay and better current performance for the catalyst heat-treated twice.

[Function of alveoles as a result of evolutionary development of respiratory system in mammals].

PubMed

Ivanov, K P

2013-01-01

Reaction of hemoglobin oxygenation is known to occur for 40 femtoseconds (40 x 10(-15) s). However, the process of oxygen diffusion to hemoglobin under physiologic conditions decelerated this reaction approximately billion times. In mammalian lungs, blood is moving at a high rate and in a relatively high amount. The human lung mass is as low as 600 g, but the complete cardiac output approaches 6 1/min. In rat, from 20 to 40 ml of blood is passed for q min through the lung whose mass is about 1.5 g. Such blood flow rate is possible, as in lungs of high animals there exists a dense network of relatively large microvessels with diameter from 20 to 40 microm and more. In spite of a large volume and a high blood flow rate hampering oxygen diffusion, the complete blood oxygenation occurs in lung alveoli. This is due to peculiar mechanisms that facilitate markedly the oxygen diffusion and that developed in alveoli of mammals in the course of many million years of evolution of their respiratory system. Thus, alveolus is not a bubble with air, but a complex tool of fight with inertness of diffusion. It is interesting that in lungs of the low vertebrates, neither such system of blood vessels nor alveoli exist, and their blood flow rate is much lower than in mammals.

Chemical morphogenesis: recent experimental advances in reaction–diffusion system design and control

PubMed Central

Szalai, István; Cuiñas, Daniel; Takács, Nándor; Horváth, Judit; De Kepper, Patrick

2012-01-01

In his seminal 1952 paper, Alan Turing predicted that diffusion could spontaneously drive an initially uniform solution of reacting chemicals to develop stable spatially periodic concentration patterns. It took nearly 40 years before the first two unquestionable experimental demonstrations of such reaction–diffusion patterns could be made in isothermal single phase reaction systems. The number of these examples stagnated for nearly 20 years. We recently proposed a design method that made their number increase to six in less than 3 years. In this report, we formally justify our original semi-empirical method and support the approach with numerical simulations based on a simple but realistic kinetic model. To retain a number of basic properties of real spatial reactors but keep calculations to a minimal complexity, we introduce a new way to collapse the confined spatial direction of these reactors. Contrary to similar reduced descriptions, we take into account the effect of the geometric size in the confinement direction and the influence of the differences in the diffusion coefficient on exchange rates of species with their feed environment. We experimentally support the method by the observation of stationary patterns in red-ox reactions not based on oxihalogen chemistry. Emphasis is also brought on how one of these new systems can process different initial conditions and memorize them in the form of localized patterns of different geometries. PMID:23919126

Propagation failures, breathing pulses, and backfiring in an excitable reaction-diffusion system.

PubMed

Manz, Niklas; Steinbock, Oliver

2006-09-01

We report results from experiments with a pseudo-one-dimensional Belousov-Zhabotinsky reaction that employs 1,4-cyclohexanedione as its organic substrate. This excitable system shows traveling oxidation pulses and pulse trains that can undergo complex sequences of propagation failures. Moreover, we present examples for (i) breathing pulses that undergo periodic changes in speed and size and (ii) backfiring pulses that near their back repeatedly generate new pulses propagating in opposite direction.

Anomalous dielectric relaxation with linear reaction dynamics in space-dependent force fields.

PubMed

Hong, Tao; Tang, Zhengming; Zhu, Huacheng

2016-12-28

The anomalous dielectric relaxation of disordered reaction with linear reaction dynamics is studied via the continuous time random walk model in the presence of space-dependent electric field. Two kinds of modified reaction-subdiffusion equations are derived for different linear reaction processes by the master equation, including the instantaneous annihilation reaction and the noninstantaneous annihilation reaction. If a constant proportion of walkers is added or removed instantaneously at the end of each step, there will be a modified reaction-subdiffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps, there will be a standard linear reaction kinetics term but a fractional order temporal derivative operating on an anomalous diffusion term. The dielectric polarization is analyzed based on the Legendre polynomials and the dielectric properties of both reactions can be expressed by the effective rotational diffusion function and component concentration function, which is similar to the standard reaction-diffusion process. The results show that the effective permittivity can be used to describe the dielectric properties in these reactions if the chemical reaction time is much longer than the relaxation time.

Shared features of S100B immunohistochemistry and cytochrome oxidase histochemistry in the ventroposterior thalamus and lateral habenula in neonatal rats.

PubMed

Muneoka, Katsumasa; Funahashi, Hisayuki; Ogawa, Tetsuo; Whitaker-Azmitia, Patricia M; Shioda, Seiji

2012-10-01

The ventroposterior thalamus and the habenular nuclei of the epithalamus are relevant to the monoaminergic system functionally and anatomically. The glia-derived S100B protein plays a critical role in the development of the nervous system including the monoaminergic systems. In this study, we performed an immunohistochemical study of glia-related proteins including S100B, serotonin transporter, and microtubule-associated protein 2, as well as cytochrome oxidase histochemistry in neonatal rats. Results showed the same findings for S100B immunohistochemistry between the ventroposterior thalamus and the lateral habenula at postnatal day 7: intense staining in cell bodies of astrocytes, diffusely spread immunoproduct in the intercellular space, and S100B-free areas as well as a strong reaction to cytochrome oxidase histochemistry. Further common features were the scarcity of glial fibrillary acidic protein-positive astrocytes and the few apoptotic cells observed. The results of the cytochrome oxidase reaction suggested that S100B is released actively into intercellular areas in restricted brain regions showing high neuronal activity at postnatal day 7. Pathology of the ventroposterior thalamus and the habenula is suggested in mental disorders, and S100B might be a key factor for investigations in these areas. Copyright © 2012 ISDN. Published by Elsevier Ltd. All rights reserved.

Further Studies on the Lyo and Desmo Components of Several Hydrolytic Enzymes and Their Histochemical Significance

PubMed Central

Hannibal, Mark J.; Nachlas, Marvin M.

1959-01-01

This report describes additional studies of the lyo and desmo components of esterase, alkaline phosphatase, acid phosphatase, leucine aminopeptidase, and β-glucuronidase. The techniques used have already been reported (7). Enzyme diffusion occurs to different degrees in different fixatives, and varies somewhat with each enzyme. Loss of enzymatic activity during fixation occurs as a result of both inactivation due to the chemical reaction of the fixative with the enzymic protein, and diffusion of the lyo component into the fixative. The amount of diffusion into formalin can be reduced by the addition of salts, sucrose, or methocel. The pH of the aqueous medium significantly influences the removal of the lyo fraction from the tissue section. A striking similarity can be noted in the proportions of each fraction of enzyme present in the kidney of the rat, dog, and man. The procedure of fixation and paraffin embedding of tissue blocks does not wholly prevent the diffusion of the lyo component from the tissue sections when they are subsequently immersed in the aqueous incubation medium. PMID:13654449

Mathematical model for the growth of phases in binary multiphase systems upon isothermic annealing

NASA Astrophysics Data System (ADS)

Molokhina, L. A.; Rogalin, V. E.; Filin, S. A.; Kaplunov, I. A.

2017-09-01

A phenomenological mathematical model of the formation and growth of phases in a binary multiphase system with allowance for factors influencing the process of diffusion in a binary system is presented. It is shown that phases can grow for a certain time at different ratios between diffusion parameters according to a parabolic law that depends on the duration of isothermic annealing. They then slow their growth after successor phases appear at their interface with one component and can completely disappear from a diffusion layer or begin to grow again, but only at a rate slower than during their initial formation. The dependence of the thickness of each phase layer in a multiphase diffusion zone on the duration of isothermic annealing and the ratio between the diffusion parameters in neighboring phases is obtained. It is established that a certain ratio between the phase growth and rates of dissolution with allowance for the coefficients of diffusion in each phase and the periods of incubation can result in the complete disappearance of one phase as early as the onset of the growth of phase nuclei and be interpreted as a process of reaction diffusion.

Organosulfate Formation through the Heterogeneous Reaction of Sulfur Dioxide with Unsaturated Compounds

NASA Astrophysics Data System (ADS)

George, C.; Passananti, M.; Kong, L.; Shang, J.; Perrier, S.; Jianmin, C.; Donaldson, D. J.

2016-12-01

The atmospheric formation of organosulfur derivatives through reaction with SO2 is generally mediated by oxidants such as O3, OH; recently we have proposed a direct reaction between SO2 and unsaturated compounds as another possible pathway for organosulfate formation in the troposphere. For the first time it was shown recently that a heterogeneous reaction between SO2 and oleic acid (OA; an unsaturated fatty acid) takes place and leads efficiently to the formation of organosulfur products. Here, we demonstrate that this reaction proceeds on various unsaturated compounds, and may therefore have a general environmental impact. We used different experimental strategies i.e., a coated flow tube (CFT), an aerosol flow tube (AFT) and a DRIFT (diffuse reflectance infrared Fourier transform) cell. The reaction products were analyzed by means of liquid chromatography coupled to a high resolution mass spectrometer (LC-HR-MS). We report indeed that SO2 reacts with large variety of C=C unsaturations and that even in the presence of ozone, SO2 reacts with OA leading to organosulfur products. A strong enhancement in product formation is observed under actinic illumination, increases the atmospheric significance of this chemical pathway. This is probably due to the chromophoric nature of the SO2 adduct with C=C bonds, and means that the contribution of this direct addition of SO2 could be in excess of 5%. The detection in atmospheric aerosols of organosulfur compounds with the same chemical formulae as the products identified here seems to confirm the importance of this reaction in the atmosphere.

Surface diffusion of cyclic hydrocarbons on nickel

NASA Astrophysics Data System (ADS)

Silverwood, I. P.; Armstrong, J.

2018-08-01

Surface diffusion of adsorbates is difficult to measure on realistic systems, yet it is of fundamental interest in catalysis and coating reactions. quasielastic neutron scattering (QENS) was used to investigate the diffusion of cyclohexane and benzene adsorbed on a nickel metal sponge catalyst. Molecular dynamics simulations of benzene on a model (111) nickel surface showed localised motion with diffusion by intermittent jumps. The experimental data was therefore fitted to the Singwi-Sjölander model and activation energies for diffusion of 4.0 kJ mol-1 for benzene and 4.3 kJ mol-1 for cyclohexane were calculated for the two dimensional model. Limited motion out-of plane was seen in the dynamics simulations and is discussed, although the resolution of the scattering experiment is insufficient to quantify this. Good agreement is seen between the use of a perfect crystal as a model for a disordered system over short time scales, suggesting that simple models are adequate to describe diffusion over polycrystalline metal surfaces on the timescale of QENS measurement.

Solving regularly and singularly perturbed reaction-diffusion equations in three space dimensions

NASA Astrophysics Data System (ADS)

Moore, Peter K.

2007-06-01

In [P.K. Moore, Effects of basis selection and h-refinement on error estimator reliability and solution efficiency for higher-order methods in three space dimensions, Int. J. Numer. Anal. Mod. 3 (2006) 21-51] a fixed, high-order h-refinement finite element algorithm, Href, was introduced for solving reaction-diffusion equations in three space dimensions. In this paper Href is coupled with continuation creating an automatic method for solving regularly and singularly perturbed reaction-diffusion equations. The simple quasilinear Newton solver of Moore, (2006) is replaced by the nonlinear solver NITSOL [M. Pernice, H.F. Walker, NITSOL: a Newton iterative solver for nonlinear systems, SIAM J. Sci. Comput. 19 (1998) 302-318]. Good initial guesses for the nonlinear solver are obtained using continuation in the small parameter ɛ. Two strategies allow adaptive selection of ɛ. The first depends on the rate of convergence of the nonlinear solver and the second implements backtracking in ɛ. Finally a simple method is used to select the initial ɛ. Several examples illustrate the effectiveness of the algorithm.

A Design Principle for an Autonomous Post-translational Pattern Formation.

PubMed

Sugai, Shuhei S; Ode, Koji L; Ueda, Hiroki R

2017-04-25

Previous autonomous pattern-formation models often assumed complex molecular and cellular networks. This theoretical study, however, shows that a system composed of one substrate with multisite phosphorylation and a pair of kinase and phosphatase can generate autonomous spatial information, including complex stripe patterns. All (de-)phosphorylation reactions are described with a generic Michaelis-Menten scheme, and all species freely diffuse without pre-existing gradients. Computational simulation upon >23,000,000 randomly generated parameter sets revealed the design motifs of cyclic reaction and enzyme sequestration by slow-diffusing substrates. These motifs constitute short-range positive and long-range negative feedback loops to induce Turing instability. The width and height of spatial patterns can be controlled independently by distinct reaction-diffusion processes. Therefore, multisite reversible post-translational modification can be a ubiquitous source for various patterns without requiring other complex regulations such as autocatalytic regulation of enzymes and is applicable to molecular mechanisms for inducing subcellular localization of proteins driven by post-translational modifications. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Kinetics of gas phase formic acid decomposition on platinum single crystal and polycrystalline surfaces

NASA Astrophysics Data System (ADS)

Detwiler, Michael D.; Milligan, Cory A.; Zemlyanov, Dmitry Y.; Delgass, W. Nicholas; Ribeiro, Fabio H.

2016-06-01

Formic acid dehydrogenation turnover rates (TORs) were measured on Pt(111), Pt(100), and polycrystalline Pt foil surfaces at a total pressure of 800 Torr between 413 and 513 K in a batch reactor connected to an ultra-high vacuum (UHV) system. The TORs, apparent activation energies, and reaction orders are not sensitive to the structure of the Pt surface, within the precision of the measurements. CO introduced into the batch reactor depressed the formic acid dehydrogenation TOR and increased the reaction's apparent activation energies on Pt(111) and Pt(100), consistent with behavior predicted by the Temkin equation. Two reaction mechanisms were explored which explain the formic acid decomposition mechanism on Pt, both of which include dissociative adsorption of formic acid, rate limiting formate decomposition, and quasi-equilibrated hydrogen recombination and CO adsorption. No evidence was found that catalytic supports used in previous studies altered the reaction kinetics or mechanism.

Nanowire membrane-based nanothermite: towards processable and tunable interfacial diffusion for solid state reactions.

PubMed

Yang, Yong; Wang, Peng-peng; Zhang, Zhi-cheng; Liu, Hui-ling; Zhang, Jingchao; Zhuang, Jing; Wang, Xun

2013-01-01

Interfacial diffusion is of great importance in determining the performance of solid-state reactions. For nanometer sized particles, some solid-state reactions can be triggered accidently by mechanical stress owing to their large surface-to-volume ratio compared with the bulk ones. Therefore, a great challenge is the control of interfacial diffusion for solid state reactions, especially for energetic materials. Here we demonstrate, through the example of nanowire-based thermite membrane, that the thermite solid-state reaction can be easily tuned via the introduction of low-surface-energy coating layer. Moreover, this silicon-coated thermite membrane exhibit controlled wetting behavior ranging from superhydrophilic to superhydrophobic and, simultaneously, to significantly reduce the friction sensitivity of thermite membrane. This effect enables to increase interfacial resistance by increasing the amount of coating material. Indeed, our results described here make it possible to tune the solid-state reactions through the manipulation of interfacial diffusion between the reactants.

Nanowire Membrane-based Nanothermite: towards Processable and Tunable Interfacial Diffusion for Solid State Reactions

NASA Astrophysics Data System (ADS)

Yang, Yong; Wang, Peng-Peng; Zhang, Zhi-Cheng; Liu, Hui-Ling; Zhang, Jingchao; Zhuang, Jing; Wang, Xun

2013-04-01

Interfacial diffusion is of great importance in determining the performance of solid-state reactions. For nanometer sized particles, some solid-state reactions can be triggered accidently by mechanical stress owing to their large surface-to-volume ratio compared with the bulk ones. Therefore, a great challenge is the control of interfacial diffusion for solid state reactions, especially for energetic materials. Here we demonstrate, through the example of nanowire-based thermite membrane, that the thermite solid-state reaction can be easily tuned via the introduction of low-surface-energy coating layer. Moreover, this silicon-coated thermite membrane exhibit controlled wetting behavior ranging from superhydrophilic to superhydrophobic and, simultaneously, to significantly reduce the friction sensitivity of thermite membrane. This effect enables to increase interfacial resistance by increasing the amount of coating material. Indeed, our results described here make it possible to tune the solid-state reactions through the manipulation of interfacial diffusion between the reactants.

Conceptual model analysis of interaction at a concrete-Boom Clay interface

NASA Astrophysics Data System (ADS)

Liu, Sanheng; Jacques, Diederik; Govaerts, Joan; Wang, Lian

In many concepts for deep disposal of high-level radioactive waste, cementitious materials are used in the engineered barriers. For example, in Belgium the engineered barrier system is based on a considerable amount of cementitious materials as buffer and backfill in the so-called supercontainer embedded in the hosting geological formation. A potential hosting formation is Boom Clay. Insight in the interaction between the high-pH pore water of the cementitious materials and neutral-pH Boom Clay pore water is required. Two problems are quite common for modeling of such a system. The first one is the computational cost due to the long timescale model assessments envisaged for the deep disposal system. Also a very fine grid (in sub-millimeter), especially at interfaces has to be used in order to accurately predict the evolution of the system. The second one is whether to use equilibrium or kinetic reaction models. The objectives of this paper are twofold. First, we develop an efficient coupled reactive transport code for this diffusion-dominated system by making full use of multi-processors/cores computers. Second, we investigate how sensitive the system is to chemical reaction models especially when pore clogging due to mineral precipitation is considered within the cementitious system. To do this, we selected two portlandite dissolution models, i.e., equilibrium (fastest) and diffusion-controlled model with precipitation of a calcite layer around portlandite particles (diffusion-controlled dissolution). The results show that with shrinking core model portlandite dissolution and calcite precipitation are much slower than with the equilibrium model. Also diffusion-controlled dissolution smooths out dissolution fronts compared to the equilibrium model. However, only a slight difference with respect to the clogging time can be found even though we use a very small diffusion coefficient (10-20 m2/s) in the precipitated calcite layer.

The Controversial Role of Inter-diffusion in Glass Alteration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gin, Stephane; Neill, Lindsay; Fournier, M.

2016-11-15

Current kinetic models for nuclear waste glasses (e.g. GM2001, GRAAL) are based on a set of mechanisms that have been generally agreed upon within the international waste glass community. These mechanisms are: hydration of the glass, ion exchange reactions (the two processes are referred as inter-diffusion), hydrolysis of the silicate network, and condensation/precipitation of partly or completely hydrolyzed species that produces a porous and amorphous layer and crystalline phases on surface of the altered glass. Recently, a new idea with origins in the mineral dissolution community has been proposed that excludes inter-diffusion process as a potential rate-limiting mechanism. To understandmore » how the so-called interfacial dissolution/precipitation model can change the current understanding of glass behavior, a key experiment used to account for this model was replicated to further revisit the interpretation. This experiment was performed at 50°C, with SON68 glass, in static mode, deionized water and S/V ratio of 10 m-1 for 6 months. It turn out that glass alters in an intermediate kinetic regime between the forward and the residual rate. According to previous and new solid characterizations, it is concluded that neither a simple inter-diffusion model nor the interfacial dissolution precipitation model can account for the observed elemental profiles within the alteration layer. More generally, far and close-to-saturation conditions must be distinguished and literature provides evidences that inter-diffusion takes place in slightly acidic conditions and far from saturation. However, closer to saturation, when a sufficiently dense layer is formed, a new approach is proposed requiring a full description of chemical reactions taking place within the alteration layer and involving water molecules as it is thought that water accessibility to the pristine glass is the rate-limiting process.« less

Oscillation of a polymer gel entrained with a periodic force.

PubMed

Shiota, Takaya; Ikura, Yumihiko S; Nakata, Satoshi

2013-02-21

The oscillation of a polymer gel induced by the Belousov-Zhabotinsky (BZ) reaction was investigated under an external force composed of a square wave. The oscillation of the BZ reaction entrained to the periodic force and the features of this entrainment changed depending on the period and duty cycle of the square wave. The experimental results suggest that the change in the volume of the gel also gave feedback to the BZ reaction. The mechanism of entrainment is discussed in relation to the compression of the gel and the reaction-diffusion system in the BZ reaction.

Communication: Coordinate-dependent diffusivity from single molecule trajectories

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Makarov, Dmitrii E.

2017-11-01

Single-molecule observations of biomolecular folding are commonly interpreted using the model of one-dimensional diffusion along a reaction coordinate, with a coordinate-independent diffusion coefficient. Recent analysis, however, suggests that more general models are required to account for single-molecule measurements performed with high temporal resolution. Here, we consider one such generalization: a model where the diffusion coefficient can be an arbitrary function of the reaction coordinate. Assuming Brownian dynamics along this coordinate, we derive an exact expression for the coordinate-dependent diffusivity in terms of the splitting probability within an arbitrarily chosen interval and the mean transition path time between the interval boundaries. This formula can be used to estimate the effective diffusion coefficient along a reaction coordinate directly from single-molecule trajectories.

Smoldyn on graphics processing units: massively parallel Brownian dynamics simulations.

PubMed

Dematté, Lorenzo

2012-01-01

Space is a very important aspect in the simulation of biochemical systems; recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and detailed models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localized fluctuations, transportation phenomena, and diffusion. A common drawback of spatial models lies in their complexity: models can become very large, and their simulation could be time consuming, especially if we want to capture the systems behavior in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to scale up the size of models we are able to simulate, moving from sequential to parallel simulation algorithms. In this paper, we analyze Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of Graphics Processing Units (GPUs). The implementation executes the most computational demanding steps (computation of diffusion, unimolecular, and bimolecular reaction, as well as the most common cases of molecule-surface interaction) on the GPU, computing them in parallel on each molecule of the system. The implementation offers good speed-ups and real time, high quality graphics output

A thermodynamic framework for thermo-chemo-elastic interactions in chemically active materials

NASA Astrophysics Data System (ADS)

Zhang, XiaoLong; Zhong, Zheng

2017-08-01

In this paper, a general thermodynamic framework is developed to describe the thermo-chemo-mechanical interactions in elastic solids undergoing mechanical deformation, imbibition of diffusive chemical species, chemical reactions and heat exchanges. Fully coupled constitutive relations and evolving laws for irreversible fluxes are provided based on entropy imbalance and stoichiometry that governs reactions. The framework manifests itself with a special feature that the change of Helmholtz free energy is attributed to separate contributions of the diffusion-swelling process and chemical reaction-dilation process. Both the extent of reaction and the concentrations of diffusive species are taken as independent state variables, which describe the reaction-activated responses with underlying variation of microstructures and properties of a material in an explicit way. A specialized isothermal formulation for isotropic materials is proposed that can properly account for volumetric constraints from material incompressibility under chemo-mechanical loadings, in which inhomogeneous deformation is associated with reaction and diffusion under various kinetic time scales. This framework can be easily applied to model the transient volumetric swelling of a solid caused by imbibition of external chemical species and simultaneous chemical dilation arising from reactions between the diffusing species and the solid.

Liquid-phase oxidation of cyclohexanone over cerium oxide catalyst

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, H.C.; Weng, H.S.

Catalytic oxidation of cyclohexanone in the liquid phase with glacial acetic acid as the solvent over cerium oxide was studied between 5 and 15 atm and 98 and 118 {degrees} C in a batch reactor. The products were adipic acid, glutaric acid, succinic acid, caprolactone, carbon oxides, etc. The reaction undergoes a short induction period prior to a rapid reaction regime. In both regimes, the reaction is independent of oxygen pressure when the system pressure is above 10 atm. The induction period is inversely proportional to both of the catalyst weight and cyclohexanone concentration.During the rapid reaction regime, the reactionmore » rate was found to be proportional to the 0.5 power of the catalyst weight and to the 1.5 power of the cyclohexanone concentration. Reaction mechanisms and rate expressions are proposed. The carbon oxides produced in this study were much lower than those previously reported. The cerium oxide catalyst is stable during the reaction.« less

Periodic stripe formation by a Turing-mechanism operating at growth zones in the mammalian palate

PubMed Central

Economou, Andrew D.; Ohazama, Atsushi; Porntaveetus, Thantrira; Sharpe, Paul T.; Kondo, Shigeru; Basson, M. Albert; Gritli-Linde, Amel; Cobourne, Martyn T.; Green, Jeremy B.A.

2012-01-01

We present direct evidence of an activator-inhibitor system in the generation of the regularly spaced transverse ridges of the palate. We show that new ridges, or rugae, marked by stripes of Sonic hedgehog (Shh) expression, appear at two growth zones where the space between previously laid-down rugae increases. However, inter-rugal growth is not absolutely required: new stripes still appear when growth is inhibited. Furthermore, when a ruga is excised new Shh expression appears, not at the cut edge but as bifurcating stripes branching from the neighbouring Shh stripe, diagnostic of a Turing-type reaction-diffusion mechanism. Genetic and inhibitor experiments identify Fibroblast Growth Factor (FGF) and Shh as an activator-inhibitor pair in this system. These findings demonstrate a reaction-diffusion mechanism likely to be widely relevant in vertebrate development. PMID:22344222

Enzymes containing porous polymersomes as nano reaction vessels for cascade reactions.

PubMed

Kuiper, Suzanne M; Nallani, Madhavan; Vriezema, Dennis M; Cornelissen, Jeroen J L M; van Hest, Jan C M; Nolte, Roeland J M; Rowan, Alan E

2008-12-07

Polystyrene(40)-b-poly(isocyanoalanine(2-thiophen-3-yl-ethyl)amide)(50) (PS-PIAT) polymersomes have the unique property of being sufficiently porous to allow diffusion of small (organic) substrates while retaining large biomolecules such as enzymes inside. Herein we report on the encapsulation and protection of glucose oxidase (GOx) and horse radish peroxidase (HRP) in PS-PIAT polymersomes and the successful employment of these functionalised nanoreactors in a cascade reaction. The demonstrated concept allows for further application in other enzymatic cascade reactions, bio-organic hybrid systems and biosensing devices.

Systematic derivation of reaction-diffusion equations with distributed delays and relations to fractional reaction-diffusion equations and hyperbolic transport equations: application to the theory of Neolithic transition.

PubMed

Vlad, Marcel Ovidiu; Ross, John

2002-12-01

We introduce a general method for the systematic derivation of nonlinear reaction-diffusion equations with distributed delays. We study the interactions among different types of moving individuals (atoms, molecules, quasiparticles, biological organisms, etc). The motion of each species is described by the continuous time random walk theory, analyzed in the literature for transport problems, whereas the interactions among the species are described by a set of transformation rates, which are nonlinear functions of the local concentrations of the different types of individuals. We use the time interval between two jumps (the transition time) as an additional state variable and obtain a set of evolution equations, which are local in time. In order to make a connection with the transport models used in the literature, we make transformations which eliminate the transition time and derive a set of nonlocal equations which are nonlinear generalizations of the so-called generalized master equations. The method leads under different specified conditions to various types of nonlocal transport equations including a nonlinear generalization of fractional diffusion equations, hyperbolic reaction-diffusion equations, and delay-differential reaction-diffusion equations. Thus in the analysis of a given problem we can fit to the data the type of reaction-diffusion equation and the corresponding physical and kinetic parameters. The method is illustrated, as a test case, by the study of the neolithic transition. We introduce a set of assumptions which makes it possible to describe the transition from hunting and gathering to agriculture economics by a differential delay reaction-diffusion equation for the population density. We derive a delay evolution equation for the rate of advance of agriculture, which illustrates an application of our analysis.

Reaction paths in the system Al 2O 3-hBN-Y

NASA Astrophysics Data System (ADS)

Reichert, K.; Oreshina, O.; Cremer, R.; Neuschütz, D.

2001-07-01

As part of the investigations on the suitability of a new concept for a tailored fiber-matrix interface in sapphire fiber reinforced NiAl matrix composites for application as a high-temperature structural material, the interfacial reactions in the system alumina-hexagonal boron nitride-yttrium (Al 2O 3-hBN-Y) have been examined in the temperature range of 1100-1300°C. For this, alumina substrates were coated with hBN by means of CVD and subsequently with sputter deposited yttrium. Afterwards the samples were annealed for up to 16 h under inert atmosphere. Grazing incidence X-ray diffraction (GIXRD) served to analyze the phases formed by diffusion processes in the reaction zone. The peak intensities in these diffraction patterns were used to evaluate the sequence of phases formed due to diffusion and reaction. After the initial formation of YN and YB 2, the phases Y 2O 3, Al 2Y, and YB 4 were observed. Even longer annealing times or higher temperatures, respectively, led to the formation of the ternary oxides YAlO 3 and Y 3Al 5O 12 as well as metallic aluminum.

Chlorination of lanthanum oxide.

PubMed

Gaviría, Juan P; Navarro, Lucas G; Bohé, Ana E

2012-03-08

The reactive system La(2)O(3)(s)-Cl(2)(g) was studied in the temperature range 260-950 °C. The reaction course was followed by thermogravimetry, and the solids involved were characterized by X-ray diffraction, scanning electron microscopy, and energy dispersive spectroscopy. The results showed that the reaction leads to the formation of solid LaOCl, and for temperatures above 850 °C, the lanthanum oxychloride is chlorinated, producing LaCl(3)(l). The formation of the oxychloride progresses through a nucleation and growth mechanism, and the kinetic analysis showed that at temperatures below 325 °C the system is under chemical control. The influence of diffusive processes on the kinetics of production of LaOCl was evaluated by studying the effect of the reactive gas flow rate, the mass of the sample, and the chlorine diffusion through the boundary layer surrounding the solid sample. The conversion curves were analyzed and fitted according to the Johnson-Mehl-Avrami description, and the reaction order with respect to the chlorine partial pressure was obtained by varying this partial pressure between 10 and 70 kPa. The rate equation was obtained, which includes the influence of the temperature, chlorine partial pressure, and reaction degree.

Development of the Monolith Froth Reactor for Catalytic Wet Oxidation of CELSS Model Wastes

NASA Technical Reports Server (NTRS)

Abraham, Martin; Fisher, John W.

1995-01-01

The aqueous phase oxidation of acetic acid, used as a model compound for the treatment of CELSS (Controlled Ecological Life Support System) waste, was carried out in the monolith froth reactor which utilizes two-phase flow in the monolith channels. The catalytic oxidation of acetic acid was carried out over a Pt/Al2O3 catalyst, prepared at The University of Tulsa, at temperatures and pressures below the critical point of water. The effect of externally controllable parameters (temperature, liquid flow rate, distributor plate orifice size, pitch, and catalyst distance from the distributor plate) on the rate of acetic acid oxidation was investigated. Results indicate reaction rate increased with increasing temperature and exhibited a maximum with respect to liquid flow rate. The apparent activation energy calculated from reaction rate data was 99.7 kJ/mol. This value is similar to values reported for the oxidation of acetic acid in other systems and is comparable to intrinsic values calculated for oxidation reactions. The kinetic data were modeled using simple power law kinetics. The effect of "froth" feed system characteristics was also investigated. Results indicate that the reaction rate exhibits a maximum with respect to distributor plate orifice size, pitch, and catalyst distance from the distributor plate. Fundamental results obtained were used to extrapolate where the complete removal of acetic acid would be obtained and for the design and operation of a full scale CELSS treatment system.

A "desperation-reaction" model of medical diffusion.

PubMed Central

Warner, K E

1975-01-01

Knowledge about the adoption and diffusion of innovations is briefly reviewed. A model is then proposed to explain how certain innovations, intended to address dire medical problems, might diffuse in a manner not previously reported, with extensive diffusion occurring during what would be a period of small-scale experimentation and limited adoption in the conventional innovation-diffusion environment. The model is illustrated with findings from a case study of the diffusion of drug therapies for four types of leukemia. Possible implications of "desperation-reaction" diffusion are suggested. PMID:1065622

[Study of Reaction Dynamics between Bovine Serum Albumin and Folic Acid by Stopped-Flow/Fluorescence].

PubMed

Ye, San-xian; Luo, Yun-jing; Qiao, Shu-liang; Li, Li; Liu, Cai-hong; Shi, Jian-long; An, Xue-jing

2016-01-01

As a kind of coenzyme of one-carbon enzymes in vivo, folic acid belongs to B vitamins, which can interact with other vitamins and has great significance for converting among amino acids, dividing growth of cells and protein synthesis reactions. Half-life, concentration and reaction rate constant of drugs are important parameters in pharmacokinetic study. In this paper, by utilizing fluorescence spectrophotometer and stopped-flow spectrum analyzer, reaction kinetic parameters between bovine serum albumin(BSA) and folic acid in a bionic system have been investigated, which provide references for parameters of drug metabolism related to folic acid. By using Stern-Volmer equation dealing with fluorescence quenching experiments data, we concluded that under 25, 30, and 37 degrees C, the static quenching constants of folic acid to intrinsic fluorescence from bovine serum albumin were 2.455 x 10(10), 4.900 x 10(10) and 6.427 x 10(10) L x mol(-1) x s(-1) respectively; The results of kinetic reaction rate have shown that the reaction rate of BSA and folic acid are greater than 100 mol x L(-1) x s(-1) at different temperatures, pH and buffering media, illustrating that the quenching mechanism between BSA and folic acid is to form composite static quenching process. Reaction concentration of bovine serum albumin and its initial concentration were equal to the secondary reaction formula, and the correlation coefficient was 0.998 7, while the half-life (t1/2) was 0.059 s at physiological temperature. With the increase of folic acid concentration, the apparent rate constant of this reaction had a linear increasing trend, the BSA fluorescence quenching rate constant catalyzed by folic acid was 3.174 x 10(5) mol x L(-1) x s(-1). Furthermore, with different buffer, the apparent rate constant and reaction rate constant of BSA interacting with folic acid were detected to explore the influence on the reaction under physiological medium, which is of great significance to determine the clinical regimen, forecast the efficacy and toxicity of drugs and rational drug.

Metals Analyzer. User’s Manual

DTIC Science & Technology

1996-06-01

larger port diameters than the three reagent ports: matrix, psa acid and rinse acid (to minimize reagent diffusion into the cell solution). The... ferule repositioned (can be optionally replaced if unsuccessful in achieving a seal). The system must be completely watertight before proceeding to the...and concentrations (extrememly acidic and/or hazardous material), use of protective eyewear and safety gloves is recommended during the reagent

Minoxidil Skin Delivery from Nanoemulsion Formulations Containing Eucalyptol or Oleic Acid: Enhanced Diffusivity and Follicular Targeting

PubMed Central

Abd, Eman; Benson, Heather A. E.; Roberts, Michael S.; Grice, Jeffrey E.

2018-01-01

In this work, we examined enhanced skin delivery of minoxidil applied in nanoemulsions incorporating skin penetration enhancers. Aliquots of fully characterized oil-in-water nanoemulsions (1 mL), containing minoxidil (2%) and the skin penetration enhancer oleic acid or eucalyptol as oil phases, were applied to full-thickness excised human skin in Franz diffusion cells, while aqueous solutions (1 mL) containing minoxidil were used as controls. Minoxidil in the stratum corneum (SC), hair follicles, deeper skin layers, and flux through the skin over 24 h was determined, as well as minoxidil solubility in the formulations and in the SC. The nanoemulsions significantly enhanced the permeation of minoxidil through skin compared with control solutions. The eucalyptol formulations (NE) promoted minoxidil retention in the SC and deeper skin layers more than did the oleic acid formulations, while the oleic acid formulations (NO) gave the greatest hair follicle penetration. Minoxidil maximum flux enhancement was associated with increases in both minoxidil SC solubility and skin diffusivity in both nanoemulsion systems. The mechanism of enhancement appeared to be driven largely by increased diffusivity, rather than increased partitioning into the stratum corneum, supporting the concept of enhanced fluidity and disruption of stratum corneum lipids. PMID:29370122

Semi-empirical equation of limiting current for cobalt electrodeposition in the presence of magnetic field and additive electrolyte

NASA Astrophysics Data System (ADS)

Sudibyo, Aziz, N.

2016-02-01

One of the available methods to solve a roughening in cobalt electrodeposition is magneto electrodeposition (MED) in the presence of additive electrolyte. Semi-empirical equation of limiting current under a magnetic field for cobalt MED in the presence of boric acid as an additive electrolyte was successfully developed. This semi empirical equation shows the effects of the electrode area (A), the concentration of the electro active species (C), the diffusion coefficient of the electro active species (D), the kinematic viscosity of the electrolyte (v), magnetic strength (B) and the number of electrons involved in the redox process (n). The presence of boric acid led to decrease in the limiting current, but the acid was found useful as a buffer to avoid the local pH rise caused by parallel hydrogen evolution reaction (HER).

Dynamic coupling between coordinates in a model for biomolecular isomerization

NASA Astrophysics Data System (ADS)

Ma, Ao; Nag, Ambarish; Dinner, Aaron R.

2006-04-01

To understand a complex reaction, it is necessary to project the dynamics of the system onto a low-dimensional subspace of physically meaningful coordinates. We recently introduced an automatic method for identifying coordinates that relate closely to stable-state commitment probabilities and successfully applied it to a model for biomolecular isomerization, the C7eq→αR transition of the alanine dipeptide [A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005)]. Here, we explore approximate means for estimating diffusion tensors for systems subject to restraints in one and two dimensions and then use the results together with an extension of Kramers theory for unimolecular reaction rates [A. Berezhkovskii and A. Szabo, J. Chem. Phys. 122, 014503 (2005)] to show explicitly that both the potential of mean force and the diffusion tensor are essential for describing the dynamics of the alanine dipeptide quantitatively. In particular, the signficance of off-diagonal elements of the diffusion tensor suggests that the coordinates of interest are coupled by the hydrodynamic-like response of the bath of remaining degrees of freedom.

Multi-scale continuum modeling of biological processes: from molecular electro-diffusion to sub-cellular signaling transduction

NASA Astrophysics Data System (ADS)

Cheng, Y.; Kekenes-Huskey, P.; Hake, J. E.; Holst, M. J.; McCammon, J. A.; Michailova, A. P.

2012-01-01

This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.

Simulation studies of chemical erosion on carbon based materials at elevated temperatures

NASA Astrophysics Data System (ADS)

Kenmotsu, T.; Kawamura, T.; Li, Zhijie; Ono, T.; Yamamura, Y.

1999-06-01

We simulated the fluence dependence of methane reaction yield in carbon with hydrogen bombardment using the ACAT-DIFFUSE code. The ACAT-DIFFUSE code is a simulation code based on a Monte Carlo method with a binary collision approximation and on solving diffusion equations. The chemical reaction model in carbon was studied by Roth or other researchers. Roth's model is suitable for the steady state methane reaction. But this model cannot estimate the fluence dependence of the methane reaction. Then, we derived an empirical formula based on Roth's model for methane reaction. In this empirical formula, we assumed the reaction region where chemical sputtering due to methane formation takes place. The reaction region corresponds to the peak range of incident hydrogen distribution in the target material. We adopted this empirical formula to the ACAT-DIFFUSE code. The simulation results indicate the similar fluence dependence compared with the experiment result. But, the fluence to achieve the steady state are different between experiment and simulation results.

Diffusion modulation of DNA by toehold exchange

NASA Astrophysics Data System (ADS)

Rodjanapanyakul, Thanapop; Takabatake, Fumi; Abe, Keita; Kawamata, Ibuki; Nomura, Shinichiro M.; Murata, Satoshi

2018-05-01

We propose a method to control the diffusion speed of DNA molecules with a target sequence in a polymer solution. The interaction between solute DNA and diffusion-suppressing DNA that has been anchored to a polymer matrix is modulated by the concentration of the third DNA molecule called the competitor by a mechanism called toehold exchange. Experimental results show that the sequence-specific modulation of the diffusion coefficient is successfully achieved. The diffusion coefficient can be modulated up to sixfold by changing the concentration of the competitor. The specificity of the modulation is also verified under the coexistence of a set of DNA with noninteracting base sequences. With this mechanism, we are able to control the diffusion coefficient of individual DNA species by the concentration of another DNA species. This methodology introduces a programmability to a DNA-based reaction-diffusion system.

Furfural formation from the pre-hydrolysis liquor of a hardwood kraft-based dissolving pulp production process.

PubMed

Liu, Haitang; Hu, Huiren; Jahan, M Sarwar; Ni, Yonghao

2013-03-01

This study aimed to produce furfural from the PHL. Results showed best furfural yield of 32.8% and the furfural selectivity of 37.7% in the monophase system (170 °C, 100 min), while they were 60.1% and 69.8%, respectively in the biphase system. The lower furfural selectivity in the monophase system was explained by more side reactions, such as fragmentation, condensation reactions, resinification and others. Model compounds such as: xylose, furfural, syringaldehyde, were used to confirm/identify these side reactions. The addition of dilute sulfuric acid/acetic acid in the system under the same conditions decreased the recovery of furfural. The addition of syringaldehyde into the PHL also led to a decrease in the furfural yield, supporting the conclusion that lignin structures in the PHL may also be involved in the side reactions, thus decreasing the furfural yield. Copyright © 2012 Elsevier Ltd. All rights reserved.

Sequential injection titration method using second-order signals: determination of acidity in plant oils and biodiesel samples.

PubMed

del Río, Vanessa; Larrechi, M Soledad; Callao, M Pilar

2010-06-15

A new concept of flow titration is proposed and demonstrated for the determination of total acidity in plant oils and biodiesel. We use sequential injection analysis (SIA) with a diode array spectrophotometric detector linked to chemometric tools such as multivariate curve resolution-alternating least squares (MCR-ALS). This system is based on the evolution of the basic specie of an acid-base indicator, alizarine, when it comes into contact with a sample that contains free fatty acids. The gradual pH change in the reactor coil due to diffusion and reaction phenomenona allows the sequential appearance of both species of the indicator in the detector coil, recording a data matrix for each sample. The SIA-MCR-ALS method helps to reduce the amounts of sample, the reagents and the time consumed. Each determination consumes 0.413ml of sample, 0.250ml of indicator and 3ml of carrier (ethanol) and generates 3.333ml of waste. The frequency of the analysis is high (12 samples h(-1) including all steps, i.e., cleaning, preparing and analysing). The utilized reagents are of common use in the laboratory and it is not necessary to use the reagents of perfect known concentration. The method was applied to determine acidity in plant oil and biodiesel samples. Results obtained by the proposed method compare well with those obtained by the official European Community method that is time consuming and uses large amounts of organic solvents.

Survivability and Abiotic Reactions of Selected Amino Acids in Different Hydrothermal System Simulators

NASA Astrophysics Data System (ADS)

Chandru, Kuhan; Imai, Eiichi; Kaneko, Takeo; Obayashi, Yumiko; Kobayashi, Kensei

2013-04-01

We tested the stability and reaction of several amino acids using hydrothermal system simulators: an autoclave and two kinds of flow reactors at 200-250 °C. This study generally showed that there is a variation in the individual amino acids survivability in the simulators. This is mainly attributed to the following factors; heat time, cold quenching exposure, metal ions and also silica. We observed that, in a rapid heating flow reactor, high aggregation and/or condensation of amino acids could occur even during a heat exposure of 2 min. We also monitored their stability in a reflow-type of simulator for 120 min at 20 min intervals. The non-hydrolyzed and hydrolyzed samples for this system showed a similar degradation only in the absence of metal ions.