A stochastic exponential Euler scheme for simulation of stiff biochemical reaction systems

In order to simulate stiff biochemical reaction systems, an explicit exponential Euler scheme is derived for multidimensional, non-commutative stochastic differential equations with a semilinear drift term. The scheme is of strong order one half and A-stable in mean square. The combination with this and the projection method shows good performance in numerical experiments dealing with an alternative formulation of the chemical Langevin equation for a human ether a-go-go related gene ion channel mode

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach

Reconstruction of biochemical reaction networks (BRN) and genetic regulatory networks (GRN) in particular is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and rational functions are typically used to model biochemical reaction networks. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data quite difficult. In this paper, we present a network reconstruction algorithm that can deal with ODE model descriptions containing polynomial and rational functions. Rather than identifying the parameters of linear or nonlinear ODEs characterised by pre-defined equation structures, our methodology allows us to determine the nonlinear ODEs structure together with their associated parameters. To solve the network reconstruction problem, we cast it as a compressive sensing (CS) problem and use sparse Bayesian learning (SBL) algorithms as a computationally efficient and robust way to obtain its solution. © 2012 IEEE.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge-Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E coli, and conclude with a discussion on the significance of this work. (C) 2004 Elsevier Ltd. All rights reserved.

Innovative reaction systems for acetal (1,1 diethoxy butane) production from renewable sources

370 p.: il., graf.

Advanced Reaction Systems for Hydrogen Production

[EN] This PhD work started in March 2010 with the support of the University of the Basque Country (UPV/EHU) under the program named “Formación de Personal Investigador” at the Chemical and Environmental Engineering Department in the Faculty of Engineering of Bilbao. The major part of the Thesis work was carried out in the mentioned department, as a member of the Sustainable Process Engineering (SuPrEn) research group. In addition, this PhD Thesis includes the research work developed during a period of 6 months at the Institut für Mikrotechnik Mainz GmbH, IMM, in Germany. During the four years of the Thesis, conventional and microreactor systems were tested for several feedstocks renewable and non-renewable, gases and liquids through several reforming processes in order to produce hydrogen. For this purpose, new catalytic formulations which showed high activity, selectivity and stability were design. As a consequence, the PhD work performed allowed the publication of seven scientific articles in peer-reviewed journals. This PhD Thesis is divided into the following six chapters described below. The opportunity of this work is established on the basis of the transition period needed for moving from a petroleum based energy system to a renewable based new one. Consequently, the present global energy scenario was detailed in Chapter 1, and the role of hydrogen as a real alternative in the future energy system was justified based on several outlooks. Therefore, renewable and non-renewable hydrogen production routes were presented, explaining the corresponding benefits and drawbacks. Then, the raw materials used in this Thesis work were described and the most important issues regarding the processes and the characteristics of the catalytic formulations were explained. The introduction chapter finishes by introducing the concepts of decentralized production and process intensification with the use of microreactors. In addition, a small description of these innovative reaction systems and the benefits that entailed their use were also mentioned. In Chapter 2 the main objectives of this Thesis work are summarized. The development of advanced reaction systems for hydrogen rich mixtures production is the main objective. In addition, the use and comparison between two different reaction systems, (fixed bed reactor (FBR) and microreactor), the processing of renewable raw materials, the development of new, active, selective and stable catalytic formulations, and the optimization of the operating conditions were also established as additional partial objectives. Methane and natural gas (NG) steam reforming experimental results obtained when operated with microreactor and FBR systems are presented in Chapter 3. For these experiments nickel-based (Ni/Al2O3 and Ni/MgO) and noble metal-based (Pd/Al2O3 and Pt/Al2O3) catalysts were prepared by wet impregnation and their catalytic activity was measured at several temperatures, from 973 to 1073 K, different S/C ratios, from 1.0 to 2.0, and atmospheric pressure. The Weight Hourly Space Velocity (WHSV) was maintained constant in order to compare the catalytic activity in both reaction systems. The results obtained showed a better performance of the catalysts operating in microreactors. The Ni/MgO catalyst reached the highest hydrogen production yield at 1073 K and steam-to-carbon ratio (S/C) of 1.5 under Steam methane Reforming (SMR) conditions. In addition, this catalyst also showed good activity and stability under NG reforming at S/C=1.0 and 2.0. The Ni/Al2O3 catalyst also showed high activity and good stability and it was the catalyst reaching the highest methane conversion (72.9 %) and H2out/CH4in ratio (2.4) under SMR conditions at 1073 K and S/C=1.0. However, this catalyst suffered from deactivation when it was tested under NG reforming conditions. Regarding the activity measurements carried out with the noble metal-based catalysts in the microreactor systems, they suffered a very quick deactivation, probably because of the effects attributed to carbon deposition, which was detected by Scanning Electron Microscope (SEM). When the FBR was used no catalytic activity was measured with the catalysts under investigation, probably because they were operated at the same WHSV than the microreactors and these WHSVs were too high for FBR system. In Chapter 4 biogas reforming processes were studied. This chapter starts with an introduction explaining the properties of the biogas and the main production routes. Then, the experimental procedure carried out is detailed giving concrete information about the experimental set-up, defining the parameters measured, specifying the characteristics of the reactors used and describing the characterization techniques utilized. Each following section describes the results obtained from activity testing with the different catalysts prepared, which is subsequently summarized: Section 4.3: Biogas reforming processes using γ-Al2O3 based catalysts The activity results obtained by several Ni-based catalysts and a bimetallic Rh-Ni catalyst supported on magnesia or alumina modified with oxides like CeO2 and ZrO2 are presented in this section. In addition, an alumina-based commercial catalyst was tested in order to compare the activity results measured. Four different biogas reforming processes were studied using a FBR: dry reforming (DR), biogas steam reforming (BSR), biogas oxidative reforming (BOR) and tri-reforming (TR). For the BSR process different steam to carbon ratios (S/C) from 1.0 to 3.0, were tested. In the case of BOR process the oxygen-to-methane (O2/CH4) ratio was varied from 0.125 to 0.50. Finally, for TR processes different S/C ratios from 1.0 to 3.0, and O2/CH4 ratios of 0.25 and 0.50 were studied. Then, the catalysts which achieved high activity and stability were impregnated in a microreactor to explore the viability of process intensification. The operation with microreactors was carried out under the best experimental conditions measured in the FBR. In addition, the physicochemical characterization of the fresh and spent catalysts was carried out by Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), N2 physisorption, H2 chemisorption, Temperature Programmed Reduction (TPR), SEM, X-ray Photoelectron Spectroscopy (XPS) and X-ray powder Diffraction (XRD). Operating with the FBR, conversions close to the ones predicted by thermodynamic calculations were obtained by most of the catalysts tested. The Rh-Ni/Ce-Al2O3 catalyst obtained the highest hydrogen production yield in DR. In BSR process, the Ni/Ce-Al2O3 catalyst achieved the best activity results operating at S/C=1.0. In the case of BOR process, the Ni/Ce-Zr-Al2O3 catalyst showed the highest reactants conversion values operating at O2/CH4=0.25. Finally, in the TR process the Rh-Ni/Ce-Al2O3 catalyst obtained the best results operating at S/C=1.0 and O2/CH4=0.25. Therefore, these three catalysts were selected to be coated onto microchannels in order to test its performance under BOR and TR processes conditions. Although the operation using microreactors was carried out under considerably higher WHSV, similar conversions and yields as the ones measured in FBR were measured. Furthermore, attending to other measurements like Turnover Frequency (TOF) and Hydrogen Productivity (PROD), the values calculated for the catalysts tested in microreactors were one order of magnitude higher. Thus, due to the low dispersion degree measured by H2-chemisorption, the Ni/Ce-Al2O3 catalyst reached the highest TOF and PROD values. Section 4.4: Biogas reforming processes using Zeolites L based catalysts In this section three type of L zeolites, with different morphology and size, were synthesized and used as catalyst support. Then, for each type of L zeolite three nickel monometallic and their homologous Rh-Ni bimetallic catalysts were prepared by the wetness impregnation method. These catalysts were tested using the FBR under DR process and different conditions of BSR (S/C ratio of 1.0 and 2.0), BOR (O2/CH4 ratio of 0.25 and 0.50) and TR processes (at S/C=1.0 and O2/CH4=0.25). The characterization of these catalysts was also carried out by using the same techniques mentioned in the previous section. Very high methane and carbon dioxide conversion values were measured for almost all the catalysts under investigation. The experimental results evidenced the better catalytic behavior of the bimetallic catalysts as compared to the monometallic ones. Comparing the catalysts behavior with regards to their morphology, for the BSR process the Disc catalysts were the most active ones at the lowest S/C ratio tested. On the contrary, the Cylindrical (30–60 nm) catalysts were more active under BOR conditions at O2/CH4=0.25 and TR processes. By the contrary, the Cylindrical (1–3 µm) catalysts showed the worst activity results for both processes. Section 4.5: Biogas reforming processes using Na+ and Cs+ doped Zeolites LTL based catalysts A method for the synthesis of Linde Type L (LTL) zeolite under microwave-assisted hydrothermal conditions and its behavior as a support for heterogeneously catalyzed hydrogen production is described in this section. Then, rhodium and nickel-based bimetallic catalysts were prepared in order to be tested by DR process and BOR process at O2/CH4=0.25. Moreover, the characterization of the catalysts under investigation was also carried out. Higher activities were achieved by the catalysts prepared from the non-doped zeolites, Rh-Ni/D and Rh-Ni/N, as compared to the ones supported on Na+ and Cs+ exchanged supports. However, the differences between them were not very significant. In addition, the Na+ and Cs+ incorporation affected mainly to the Disc catalysts. Comparing the results obtained by these catalysts with the ones studied in the section 4.4, in general worst results were achieved under DR conditions and almost the same results when operated under BOR conditions. In Chapter 5 the ethylene glycol (EG) as feed for syngas production by steam reforming (SR) and oxidative steam reforming (OSR) was studied by using microchannel reactors. The product composition was determined at a S/C of 4.0, reaction temperatures between 625°C and 725°C, atmospheric pressure and Volume Hourly Space Velocities (VHSV) between 100 and 300 NL/(gcath). This work was divided in two sections. The first one corresponds to the introduction of the main and most promising EG production routes. Then, the new experimental procedure is detailed and the information about the experimental set-up and the measured parameters is described. The characterization was carried out using the same techniques as for the previous chapter. Then, the next sections correspond to the catalytic activity and catalysts characterization results. Section 5.3: xRh-cm and xRh-np catalysts for ethylene glycol reforming Initially, catalysts with different rhodium loading, from 1.0 to 5.0 wt. %, and supported on α-Al2O3 were prepared by two different preparation methods (conventional impregnation and separate nanoparticle synthesis). Then, the catalysts were compared regarding their measured activity and selectivity, as well as the characterization results obtained before and after the activity tests carried out. The samples prepared by a conventional impregnation method showed generally higher activity compared to catalysts prepared from Rh nanoparticles. By-product formation of species such as acetaldehyde, ethane and ethylene was detected, regardless if oxygen was added to the feed or not. Among the catalysts tested, the 2.5Rh-cm catalyst was considered the best one. Section 5.4: 2.5Rh-cm catalyst support modification with CeO2 and La2O3 In this part of the Chapter 5, the catalyst showing the best performance in the previous section, the 2.5Rh-Al2O3 catalyst, was selected in order to be improved. Therefore, new Rh based catalysts were designed using α-Al2O3 and being modified this support with different contents of CeO2 or La2O3 oxides. All the catalysts containing additives showed complete conversion and selectivities close to the equilibrium in both SR and OSR processes. In addition, for these catalysts the concentrations measured for the C2H4, CH4, CH3CHO and C2H6 by-products were very low. Finally, the 2.5Rh-20Ce catalyst was selected according to its catalytic activity and characterization results in order to run a stability test, which lasted more than 115 hours under stable operation. The last chapter, Chapter 6, summarizes the main conclusions achieved throughout this Thesis work. Although very high reactant conversions and rich hydrogen mixtures were obtained using a fixed bed reaction system, the use of microreactors improves the key issues, heat and mass transfer limitations, through which the reforming reactions are intensified. Therefore, they seem to be a very interesting and promising alternative for process intensification and decentralized production for remote application.

Impact Parameter Dependence of Double Neutron/Proton Ratio of Nucleon Emissions in Isotopic Reaction Systems

Within the transport model IBUU04, we investigate the double neutron/proton ratio of free nucleons taken from two reaction systems using two Sn isotopes at the beam energy of 50MeV/nucleon and with the impact parameters 2 fm, 4 fm and 8 fm, respectively. It is found that the double neutron/proton ratio from peripheral collisions is more sensitive to the density dependence of the symmetry energy than those from mid-central and central collisions.

Double neutron/proton ratio of nucleon emissions in isotopic reaction systems as a robust probe of nuclear symmetry energy

The double neutron/proton ratio of nucleon emissions taken from two reaction systems using four isotopes of the same element, namely, the neutron/proton ratio in the neutron-rich system over that in the more symmetric system, has the advantage of reducing systematically the influence of the Coulomb force and the normally poor efficiencies of detecting low energy neutrons. The double ratio thus suffers less systematic errors. Within the IBUU04 transport model the double neutron/proton ratio is shown to have about the same sensitivity to the density dependence of nuclear symmetry energy as the single neutron/proton ratio in the neutron-rich system involved. The double neutron/proton ratio is therefore more useful for further constraining the symmetry energy of neutron-rich matter.

Studies on nonlinear dynamics of certain reaction systems

The nonlinear dynamics of certain important reaction systems are discussed and analysed in this thesis. The interest in the theoretical and the experimental studies of chemical reactions showing oscillatory dynamics and associated properties is increasing very rapidly. An attempt is made to study some nonlinear phenomena exhibited by the well known chemical oscillator, the BelousovZhabotinskii reaction whose mathematical properties are much in common with the properties of biological oscillators. While extremely complex, this reaction is still much simpler than biological systems at least from the modelling point of view. A suitable model [19] for the system is analysed and the researcher has studied the limit cycle behaviour of the system, for different values of the stoichiometric parameter f, by keeping the value of the reaction rate (k6) fixed at k6 = l. The more complicated three-variable model is stiff in nature.

The underlying pathway structure of biochemical reaction networks

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge–Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work.