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A reaction-diffusion modeling of carbonation process in self-compacting concrete

COMPUTERS AND CONCRETE 2015年第5期15卷 847-864页

作者： Fu, Chuanqing Ye, Hailong Jin, Xianyu Jin, Nanguo Gong, Lingli Zhejiang Univ Coll Civil Engn & Architecture Hangzhou 310058 Zhejiang Peoples R China Zhejiang Univ Technol Coll Civil Engn & Architecture Hangzhou 310014 Zhejiang Peoples R China Zhejiang Key Lab Civil Engn Struct & Disaster Pre Hangzhou Zhejiang Peoples R China Penn State Univ Dept Civil & Environm Engn State Coll PA 16801 USA

In this paper, a reaction-diffusion model of carbonation process in self-compacting concrete (SCC) was realized with a consideration of multi-field couplings. Various effects from environmental conditions, e.g. ambient temperature, relative humidity, carbonation reaction, were incorporated into a numerical simulation proposed by ANSYS. In addition, the carbonation process of SCC was experimentally investigated and compared with a conventionally vibrated concrete (CVC). It is found that SCC has a higher carbonation resistance than CVC with a comparable compressive strength. The numerical solution analysis agrees well with the test results, indicating that the proposed model is appropriate to calculate and predict the carbonation process in SCC. The parameters sensitivity analysis also shows that the carbon dioxide diffusion coefficient and moisture field are essentially crucial to the carbonation process in SCC.

关键词： SCC carbonation process numerical simulation reaction-diffusion modeling

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modeling reaction-diffusion processes within catalyst washcoats: I. Microscale processes based on three-dimensional reconstructions

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CHEMICAL ENGINEERING SCIENCE 2016年 145卷 299-307页

作者： Karakaya, Canan Weddle, Peter J. Blasi, Justin M. Diercks, David R. Kee, Robert J. Colorado Sch Mines Dept Mech Engn Golden CO 80401 USA Colorado Sch Mines Met & Mat Engn Dept Golden CO 80401 USA

This paper develops a detailed analysis of reaction-diffusion processes within a porous rhodium-alumina catalyst washcoat. Focused-ion-beam-scanning-electron-microscope (FIB-SEM) techniques are developed and applied to reconstruct the actual catalyst-support microstructure. Three-dimensional transport processes within washcoat micro-pore structures are modeled using a dimensionless representation of reaction and diffusion rates based on the Damkohler number. Three-dimensional computational solutions for particular porous microstructures are modeled and interpreted. In a companion paper, these microstructural results are used to assist development of larger-scale models that can be incorporated into reactor-scale simulations. (C) 2016 Elsevier Ltd. All rights reserved.

关键词： Catalyst washcoat Tomography Pore microstructure FIB-SEM reaction-diffusion modeling Porous media

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SymPhas-General Purpose Software for Phase-Field, Phase-Field Crystal, and reaction-diffusion Simulations

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ADVANCED THEORY AND SIMULATIONS 2022年第1期5卷

作者： Silber, Steven A. Karttunen, Mikko Univ Western Ontario Dept Phys & Astron Ctr Adv Mat & Biomat Res 1151 Richmond St London ON N6A 3K7 Canada Univ Western Ontario Dept Chem 1151 Richmond St London ON N6A 3K7 Canada

This work develops a new open source application programming interface (API) and software package called SymPhas for simulations of phase-field, phase-field crystal, and reaction-diffusion models, supporting up to three dimensions and an arbitrary number of fields. SymPhas delivers two novel program capabilities: 1) User specification of models from the associated dynamical equations in an unconstrained form and 2) extensive support for integrating user-developed discrete-grid-based numerical solvers into the API. The capability to specify general phase-field models is primarily achieved by developing a novel symbolic algebra functionality that can formulate mathematical expressions at compile time;is able to apply rules of symbolic algebra such as distribution, factoring, and automatic simplification;and support user-driven expression tree manipulation. A modular design based on the C++ template meta-programming paradigm is applied to the symbolic algebra library and general API implementation to minimize application runtime and increase the accessibility of the API for third party development. SymPhas is written in C/C++ and emphasizes high-performance capabilities via parallelization with OpenMP and the C++ standard library. SymPhas is equipped with a forward Euler solver and a semi-implicit Fourier spectral solver. Sample implementations and simulations of several phase-field models are presented, generated using the semi-implicit Fourier spectral solver.

关键词： application programming interface generic programming phase-field modeling reaction-diffusion modeling symbolic algebra

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Cell mediated reactions create TGF-β delivery limitations in engineered cartilage

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ACTA BIOMATERIALIA 2024年 190卷 178-190页

作者： Dogru, Sedat Alba, Gabriela M. Pierce, Kirk C. Wang, Tianbai Kia, Danial Sharifi Albro, Michael B. Boston Univ Coll Engn Boston MA 02215 USA

During native cartilage development, endogenous TGF-beta activity is tightly regulated by cell-mediated chemical reactions in the extracellular milieu (e.g., matrix and receptor binding), providing spatiotemporal control in a manner that is localized and short acting. These regulatory paradigms appear to be at odds with TGF-beta delivery needs in tissue engineering (TE) where administered TGF-beta is required to transport long distances or reside in tissues for extended durations. In this study, we perform a novel examination of the influence of cell-mediated reactions on the spatiotemporal distribution of administered TGF-beta in cartilage TE applications. reaction rates of TGF-beta binding to cell-deposited ECM and TGF-beta internalization by cell receptors are experimentally characterized in bovine chondrocyte-seeded tissue constructs. TGF-beta binding to the construct ECM exhibits non-linear Brunauer-Emmett-Teller (BET) adsorption behavior, indicating that as many as seven TGF-beta molecules can aggregate at a binding site. Cell-mediated TGF-beta internalization rates exhibit a biphasic trend, following a Michaelis-Menten relation (Vmax = 2.4 molecules cell(-1) s(-1), Km = 1.7 ng mL(-1)) at low ligand doses (<= 130 ng/mL), but exhibit an unanticipated non-saturating power trend at higher doses (>= 130 ng/mL). Computational models are developed to illustrate the influence of these reactions on TGF-beta spatiotemporal delivery profiles for conventional TGF-beta administration platforms. For TGF-beta delivery via supplementation in culture medium, these reactions give rise to pronounced steady state TGF-beta spatial gradients;TGF-beta concentration decays by similar to 90 % at a depth of only 500 mu m from the media-exposed surface. For TGF-beta delivery via heparin-conjugated affinity scaffolds, cell mediated internalization reactions significantly reduce the TGF-beta scaffold retention time (160-360-fold reduction) relative to acellular heparin scaffolds. This wo

关键词： Cartilage tissue engineering TGF-(3 delivery Growth factor transport reaction-diffusion modeling

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Real-time measurement and modeling of intraparticle pH gradient formation in immobilized cephalosporin C amidase

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PROCESS BIOCHEMISTRY 2013年第4期48卷 593-604页

作者： Zahel, Thomas Boniello, Caterina Nidetzky, Bernd Graz Univ Technol Inst Biotechnol & Biochem Engn A-8010 Graz Austria Austrian Ctr Ind Biotechnol A-8010 Graz Austria

A new and generic approach of dynamic reaction-diffusion modeling was applied to analyze the catalytic performance of an industrially used cephalosporin C amidase immobilized on a series of insoluble carriers (epoxy-activated Sepabeads) that differed in particle or pore diameter. Enzymatic conversion of cephalosporin C into 7-amino cephalosporanic acid and D-alpha-amino adipic acid (DAAA) results in net proton release, and this was shown previously to bring about significant internal acidification of the enzyme immobilizates during reaction. In this study, we demonstrate first time model parameter estimation to in situ measured real-time pH data, recorded both inside the enzyme carrier as well as externally in the liquid bulk of a stirred tank reactor. An essential and novel feature of the model was applicability to intraparticle pH data derived from space-averaged opto-chemical measurements. Using model-based estimation, we determined the maximal intrinsic reaction rate of the immobilized amidase completely unmasked from diffusional and carrier acidification effects (v,, specific) as well as the effective proton diffusion coefficient (D-eff,D-H+). Neither parameter is accessible directly from the experiment. The resulting v(max),(speafic) estimates showed that carrier-bound amidase had lost between 14% and 55% of the free enzyme's activity due to immobilization, depending on the carrier type used. The(Deff.H+) estimate (P-1 x 10(-10) m(2)/s) was about one order of magnitude lower than expected for proton diffusion in such porous structures, suggesting a role for co-diffusion of the proton and the corresponding DAAA anion in decreasing the proton diffusivity. The model was validated against independent time-course data sets, and it was shown to give useful prediction of immobilized enzyme effectiveness factors for the applied range of carrier characteristics and enzyme loadings. Simulation was used to characterize the influence of geometrical features of the carrier

关键词： pH gradients reaction-diffusion modeling Immobilized cephalosporin C amidase Porous carrier optimization

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modeling of liver metastatic disease with applied drug therapy

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COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2014年第3期115卷 162-170页

作者： Filipovic, Nenad Djukic, Tijana Saveljic, Igor Milenkovic, Petar Jovicic, Gordana Djuric, Marija Univ Kragujevac Fac Engn Kragujevac 34000 Serbia BioIRC R&D Bioengn Ctr Kragujevac 34000 Serbia Harvard Univ Boston MA 02115 USA Inst Oncol & Radiol Serbia Belgrade 11000 Serbia Univ Belgrade Sch Med Inst Anat Lab Anthropol Belgrade 11000 Serbia

Colorectal carcinoma is acknowledged as the second leading cause of total cancer-related death in the European Region. The majority of deaths related to colorectal carcinoma are connected with liver metastatic disease. Approximately, in 25% of all patients, liver metastatic disease is diagnosed at the same time as the primary diagnosis, while up to a quarter of others would develop liver metastases in the course of the illness. In this study, we developed reaction-diffusion model and analyzed the effect of drug therapy on liver metastatic disease for a specific patient. Tumor volumes in specific time points were obtained using CT scan images. The nonlinear function for cell proliferation rate as well as data about clinically applied drug therapy was included in the model. Fitting procedure was used for parameter estimation. Good agreement of numerical and experimental results shows the feasibility and efficacy of the proposed system. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

关键词： Colorectal carcinoma Liver metastases reaction-diffusion modeling Chemotherapy Cancer cell proliferation rate

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Data Processing in Cellular Microphysiometry

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IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING 2016年第11期63卷 2368-2375页

作者： Wiest, Joachim Namias, Aldric Pfister, Cornelia Wolf, Peter Demmel, Franz Brischwein, Martin Cellasys GmbH R&D D-80802 Munich Germany Tech Univ Munich Heinz Nixdorf Lehrstuhl Med Elektron Munich Germany HP Med Tech GmbH Oberschleissheim Germany

Goal: This contribution points out the need for well-defined and documented data processing protocols in microphysiometry, an evolving field of label-free cell assays. The sensitivity of the obtained cell metabolic rates toward different routines of raw data processing is evaluated. Methods: A standard microphysiometric experiment structured in discrete measurement intervals was performed on a platform with a pH-and O-2-sensor readout. It is evaluated using three different data evaluation protocols, based on A) fast Fourier transformation of such dynamics, B) linear regression (LIN) of pH(t) and O-2 (t) dynamics, and C) numerical simulation (SIM) with a subsequent fitting of dynamics for parameter estimation. Results: We propose a sequence of well documented steps for an organized processing of raw sensor data. Figures of merit for the quality of raw data and the performance of data processing are provided. To estimate metabolic rates, a reaction-diffusion modeling approach is recommended if the necessary model input parameters such as the distribution of the active biomass, sensor response time, and material properties are available. Conclusion: The information about cellular metabolic activity contained by measured sensor data dynamics is superimposed by manifold sources of error. Careful consideration of data processing is necessary to eliminate these errors as much as possible and to avoid an incorrect interpretation of data.

关键词： Biomedical transducers data processing Fourier transforms metabolism microphysiometry micro-sensors oxygen pH reaction-diffusion modeling

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A quantitative study of the structure-activity relationship in hierarchical zeolites using liquid-phase reactions

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AICHE JOURNAL 2019年第3期65卷 1067-1075页

作者： Xu, Dandan Abdelrahman, Omar Ahn, Sang Hyun Guefrachi, Yasmine Kuznetsov, Anatoliy Ren, Limin Hwang, Sonjong Khaleel, Maryam Al Hassan, Saeed Liu, Dongxia Hong, Suk Bong Dauenhauer, Paul Tsapatsis, Michael Univ Minnesota Dept Chem Engn & Mat Sci Minneapolis MN 55414 USA Pohang Univ Sci & Technol Div Environm Sci & Engn Pohang 37673 South Korea CALTECH Div Chem & Chem Engn Pasadena CA 91125 USA Khalifa Univ Sci & Technol Petr Inst Dept Chem Engn Abu Dhabi U Arab Emirates Univ Maryland Dept Chem & Biomol Engn College Pk MD 20740 USA Johns Hopkins Univ Dept Chem & Biomol Engn Baltimore MD 21218 USA Johns Hopkins Univ Inst NanoBioTechnol Baltimore MD 21218 USA

Micro/meso/macroporous (hierarchical) zeolites show remarkable catalytic performance for reactions involving bulky reactants. However, quantitative assessment of the microstructural characteristics contributing to the observed performance remains elusive. Here, structure-activity relationships are established for a set of micro/mesoporous self-pillared pentasil (SPP) zeolites using two parallel liquid-phase reactions (benzyl alcohol alkylation and self-etherification) based on analysis of mass transport and reaction kinetics. A reaction-diffusion mathematical model is developed that quantitatively assigns the catalytic contributions of the external surface and micropores of SPP zeolites for these reactions. In addition, the effect of the zeolite external surface structure on the corresponding catalytic activity is quantitatively assessed by comparing SPP zeolites (with MFI structure) with MCM-22 (with MWW structure). This work demonstrates that reaction-diffusion modeling allows quantitative description of the catalytic performance of hierarchical zeolites and provides a model reaction to assess nm-sized characteristic diffusion lengths in MFI. (c) 2018 American Institute of Chemical Engineers

关键词： hierarchical zeolites liquid-phase alkylation and etherification kinetics reaction-diffusion modeling surface topology

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Predictive simulation of non-steady-state transport of gases through rubbery polymer membranes

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POLYMER 2018年 134卷 125-142页

作者： Soniat, Marielle Tesfaye, Meron Brooks, Daniel Merinov, Boris Goddard, William A., III Weber, Adam Z. Houle, Frances A. Lawrence Berkeley Natl Lab Joint Ctr Artificial Photosynthesis Berkeley CA 94720 USA Lawrence Berkeley Natl Lab Chem Sci Div Berkeley CA 94720 USA Lawrence Berkeley Natl Lab Energy Storage & Distributed Resources Div Berkeley CA 94720 USA Univ Calif Berkeley Dept Chem & Biomol Engn Berkeley CA 94720 USA CALTECH Beckman Inst Mat & Proc Simulat Ctr MSC Pasadena CA 91125 USA

A multiscale, physically-based, reaction-diffusion kinetics model is developed for non-steady-state transport of simple gases through a rubbery polymer. Experimental data from the literature, new measurements of non-steady-state permeation and a molecular dynamics simulation of a gas-polymer sticking probability for a typical system are used to construct and validate the model framework. Using no adjustable parameters, the model successfully reproduces time-dependent experimental data for two distinct systems: (1) O-2 quenching of a phosphorescent dye embedded in poly(n-butyl(amino) thionylphosphazene), and (2) O-2, N-2, CH4 and CO2 transport through poly(dimethyl siloxane). The calculations show that in the pre-steady-state regime, permeation is only correctly described if the sorbed gas concentration in the polymer is dynamically determined by the rise in pressure. The framework is used to predict selectivity targets for two applications involving rubbery membranes: CO2 capture from air and blocking of methane cross-over in an aged solar fuels device. (C) 2017 Elsevier Ltd. All rights reserved.

关键词： Rubbery polymers reaction-diffusion modeling Gas transport

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Mass transfer modeling of solid tumor growth for therapy evaluation and prognosis

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INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER 2020年 117卷 104781-104781页

作者： Caccavale, Paolo De Bonis, Maria Valeria Marino, Graziella Ruocco, Gianpaolo Univ Basilicata Coll Engn Modeling & Prototyping Lab ModProLab V Ateneo Lucano I-85100 Potenza Italy Univ Basilicata iBMB Srls Initiat Biomat Behav V Ateneo Lucano I-85100 Potenza Italy IRCSS Referral Canc Ctr Basilicata CROB Operat Unit Oncol Surg V Padre Pio 1 I-85028 Rionero In Vulture Italy

Simulation of tumor evolution at the macroscopic, tissue scale can be applied to cancer treatment optimization. This paper aims to gain deeper insight into the dynamics of tumor growth at this scale and to develop predictive, quantitative mathematical models which can be used as a decision tool supporting oncologists and surgeons. This preliminary model describes tumor progression as mass transfer governed by partial differential equations, incorporating a multi-species logistic growth/decay law to account for the production of necrosis and the interaction with therapy. The set of governing equations is integrated by a commercial platform of Finite Element Method. After a validation study with literature data on a hepatocellular carcinoma, a sensitivity analysis was conducted by including the driving source terms (growth rates, drug efficiency and its delivery/availability). Results suggest that, in the first two months of therapy, tumor volume progress is related nonlinearly so that a mere 10% of stronger/weaker cancer malignancy lead to doubling/halving the tumor volume, the increment of drug efficiency by 25% lead to a 60% decrease of the volume, while a smaller efficiency by 25% lead to a sudden runaway of the disease. Finally, the optimal administration pattern for chemoembolization was found with a 4-points therapy delivery on the same side with respect to the Region of Interest.

关键词： Mass transfer Computational oncology reaction-diffusion modeling Partial differential equations Hepato-cellular carcinoma

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