Simulations of Chemotaxis and Random Motility in Finite Domains

2004 ◽  
Vol 845 ◽  
Author(s):  
Ehsan Jabbarzadeh ◽  
Cameron F. Abrams
Keyword(s):  
Boundary Conditions ◽  
Cellular Response ◽  
Rational Design ◽  
Computational Simulation ◽  
Concentration Field ◽  
Chemical Species ◽  
Reaction Diffusion Equation ◽  
Cellular Transport ◽  
Pore Level ◽  
Reactive Surfaces

ABSTRACTRational design and selection of candidate porous biomaterials to serve as tissue engineering constructs rests on our ability to understand the influence of the porous microarchitecture on the transport of chemical species (e.g., nutrients and signaling compounds), fluid flow, and cellular locomotion and growth. We have begun to study the behavior of chemotactically mobile cells in response to unsteady signaling molecule concentration fields using a computational simulation-based model. The model couples fully time-dependent finite-difference solution of a reaction-diffusion equation for the concentration field of a generic chemoattractant to biased random walks representing individual moving cells. This model is a first step in building a quantitative, pore-level model of mass and cellular transport in porous tissue-engineered constructs. In these proceedings, we focus on our recent findings regarding the influence of flux-reactive boundary conditions in heterogeneous 2D domains on the chemotactic response of otherwise randomly moving cells. In particular, we find that, when cells are forced to “crawl” around obstacles in order to approach a point source of chemoattractant, the reactivity of the obstacle surface with respect to the chemoattractant strongly determines the morphology of the cells' paths of locomotion. Cells crawl along non-reactive surfaces and strongly avoid reactive surfaces, due to the nature of the chemoattractant concentration gradients near the surface. We show further that tuning the reactivity of the surfaces of two obstacles defining a gap can control the passage of cells through the gap. From our work, we infer the importance of a proper treatment of boundary conditions in any future pore-level quantitatve modeling of mass transport and cellular response in porous media.

scholarly journals Effects of Loading and Boundary Conditions on the Performance of Ultrasound Compressional Viscoelastography: A Computational Simulation Study to Guide Experimental Design

Materials ◽  
2021 ◽  
Vol 14 (10) ◽  
pp. 2590
Author(s):  
Che-Yu Lin ◽  
Ke-Vin Chang
Keyword(s):  
Boundary Conditions ◽  
Simulation Study ◽  
Viscoelastic Properties ◽  
Measurement Accuracy ◽  
Computational Simulation ◽  
Vertical Direction ◽  
Fixation Method ◽  
Element Analysis ◽  
Sample Container

Most biomaterials and tissues are viscoelastic; thus, evaluating viscoelastic properties is important for numerous biomedical applications. Compressional viscoelastography is an ultrasound imaging technique used for measuring the viscoelastic properties of biomaterials and tissues. It analyzes the creep behavior of a material under an external mechanical compression. The aim of this study is to use finite element analysis to investigate how loading conditions (the distribution of the applied compressional pressure on the surface of the sample) and boundary conditions (the fixation method used to stabilize the sample) can affect the measurement accuracy of compressional viscoelastography. The results show that loading and boundary conditions in computational simulations of compressional viscoelastography can severely affect the measurement accuracy of the viscoelastic properties of materials. The measurement can only be accurate if the compressional pressure is exerted on the entire top surface of the sample, as well as if the bottom of the sample is fixed only along the vertical direction. These findings imply that, in an experimental validation study, the phantom design should take into account that the surface area of the pressure plate must be equal to or larger than that of the top surface of the sample, and the sample should be placed directly on the testing platform without any fixation (such as a sample container). The findings indicate that when applying compressional viscoelastography to real tissues in vivo, consideration should be given to the representative loading and boundary conditions. The findings of the present simulation study will provide a reference for experimental phantom designs regarding loading and boundary conditions, as well as guidance towards validating the experimental results of compressional viscoelastography.

Numerical Investigation of Inlet Turbulence Intensity Effect on a Bluff-Body Stabilized Flame at Near Flame Blow-Off Conditions

2020 ◽  
Author(s):  
Amir Ali Montakhab ◽  
Benjamin Akih Kumgeh
Keyword(s):  
Boundary Conditions ◽  
Numerical Investigation ◽  
Turbulence Intensity ◽  
Bluff Body ◽  
Chemical Species ◽  
Simulation Method ◽  
Intensity Effect ◽  
Flame Instability ◽  
Eddy Simulation ◽  
Lean Conditions

Abstract This paper investigates the effects of the inlet turbulence intensity (ITI) on the dynamics of a bluff-body stabilized flame operating very close to its blow-off condition. This work is motivated by the understanding that more stringent regulations on combustion-generated emission have forced the industry to design combustion systems that operate at very fuel-lean conditions. Combustion at very lean conditions, however, induces flame instability that can ultimately lead to flame extinction. The dynamics of the flame at lean conditions can therefore be very sensitive to boundary conditions. Here, a numerical investigation is conducted using Large Eddy Simulation method to understand the flame sensitivity to inlet turbulence intensity. Combustion is accounted for through the transport of chemical species. The sensitivity to inlet turbulence is assessed by carrying out simulations in which the inlet turbulence is varied in increments of 5%. It is observed that while the inlet intensity of 5% causes blow-off, further increased to 10% preserves a healthy flame on account of greater heat release arising from greater and balanced entrainment of combustible mixtures into the flame zone just behind the bluff-body. This balanced stabilization is again lost as the inlet turbulence intensity is further increased to 15%. Since experimental data pertaining to the topic of this paper are rare, the reasonableness of the combination of models is first checked by validating Volvo propane bluff-body flame, whereby reasonable agreement is observed. This study will advance our understanding of the sensitivity of bluff-body flames to boundary conditions specifically to the inlet turbulent boundary condition at near critical blow-off flame conditions.

scholarly journals Insight of thermally stratified Jeffrey fluid flow inside porous medium subject to chemical species and melting heat transfer

2019 ◽  
Vol 11 (9) ◽  
pp. 168781401987618
Author(s):  
Mubashar Javed ◽  
Muhammad Farooq ◽  
Aisha Anjum ◽  
Shakeel Ahmad
Keyword(s):  
Heat Transfer ◽  
Velocity Field ◽  
Thermal Stratification ◽  
Heterogeneous Reaction ◽  
Concentration Field ◽  
Chemical Species ◽  
Internal Heat ◽  
Nonlinear Problems ◽  
Deborah Number ◽  
Jeffrey Fluid

This article concentrates on two-dimensional magnetohydrodynamic stagnation flow of Jeffrey liquid on a nonlinearly stretching sheet which possesses variable thickness. Simultaneous impact of melting as well as thermal stratification is specifically investigated in this study due to their tremendous involvement in plenty of natural and industrial processes. Internal heat generation and presence of chemical species are considered to ponder at heat transfer properties. Series solution has been obtained by solving the developed nonlinear problems. Physical behavior of various controlling parameters such as velocity, thermal, and concentration fields are investigated. It has been found that temperature field decays due to higher intensity of thermal stratification parameter, but thickness of thermal boundary layer boosts up. Larger Deborah number results in incremented velocity field. For uplifted wall thickness parameter, velocity field depreciates. Concentration field declines for enhanced parameters of homogeneous as well as heterogeneous reaction. Moreover, velocity is decreasing function of porosity parameter.

scholarly journals Engineering DNA recognition and allosteric response properties of TetR family proteins by using a module-swapping strategy

2019 ◽  
Vol 47 (16) ◽  
pp. 8913-8925 ◽  
Author(s):  
Rey P Dimas ◽  
Benjamin R Jordan ◽  
Xian-Li Jiang ◽  
Catherine Martini ◽  
Joseph S Glavy ◽  
...  
Keyword(s):  
Dna Binding ◽  
Ligand Binding ◽  
Cellular Response ◽  
Rational Design ◽  
Dna Recognition ◽  
Response Properties ◽  
Effective Components ◽  
Uniprot Accession ◽  
Engineering Strategy ◽  
Molecular Signal

Abstract The development of synthetic biological systems requires modular biomolecular components to flexibly alter response pathways. In previous studies, we have established a module-swapping design principle to engineer allosteric response and DNA recognition properties among regulators in the LacI family, in which the engineered regulators served as effective components for implementing new cellular behavior. Here we introduced this protein engineering strategy to two regulators in the TetR family: TetR (UniProt Accession ID: P04483) and MphR (Q9EVJ6). The TetR DNA-binding module and the MphR ligand-binding module were used to create the TetR-MphR. This resulting hybrid regulator possesses DNA-binding properties of TetR and ligand response properties of MphR, which is able to control gene expression in response to a molecular signal in cells. Furthermore, we studied molecular interactions between the TetR DNA-binding module and MphR ligand-binding module by using mutant analysis. Together, we demonstrated that TetR family regulators contain discrete and functional modules that can be used to build biological components with novel properties. This work highlights the utility of rational design as a means of creating modular parts for cell engineering and introduces new possibilities in rewiring cellular response pathways.

scholarly journals A Numerical Method for Time-Fractional Reaction-Diffusion and Integro Reaction-Diffusion Equation Based on Quasi-Wavelet

Complexity ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Sachin Kumar ◽  
Jinde Cao ◽  
Xiaodi Li
Keyword(s):  
Diffusion Equation ◽  
Boundary Conditions ◽  
Numerical Method ◽  
Numerical Solutions ◽  
Exact Analytical Solution ◽  
Research Work ◽  
Reaction Diffusion ◽  
Dirichlet Boundary Conditions ◽  
Reaction Diffusion Equation ◽  
Fractional Reaction

In this research work, we focused on finding the numerical solution of time-fractional reaction-diffusion and another class of integro-differential equation known as the integro reaction-diffusion equation. For this, we developed a numerical scheme with the help of quasi-wavelets. The fractional term in the time direction is approximated by using the Crank–Nicolson scheme. The spatial term and the integral term present in integro reaction-diffusion are discretized and approximated with the help of quasi-wavelets. We study this model with Dirichlet boundary conditions. The discretization of these initial and boundary conditions is done with a different approach by the quasi-wavelet-based numerical method. The validity of this proposed method is tested by taking some numerical examples having an exact analytical solution. The accuracy of this method can be seen by error tables which we have drawn between the exact solution and the approximate solution. The effectiveness and validity can be seen by the graphs of the exact and numerical solutions. We conclude that this method has the desired accuracy and has a distinctive local property.

Smoke and Heat Propagation Modeling in Transportation Interchange Stations Using LES and RANS Methods

2013 ◽  
Author(s):  
Claudio Zanzi ◽  
Alberto Mozas ◽  
Julio Hernández ◽  
Antonio García-Hortelano ◽  
Javier Aldecoa
Keyword(s):  
Boundary Conditions ◽  
Turbulence Modeling ◽  
Numerical Study ◽  
Combustion Process ◽  
Chemical Species ◽  
Computer Code ◽  
Heat Propagation ◽  
Safety Level ◽  
Cpu Time ◽  
Bus Station

A numerical study of smoke and heat transport from fires occurring in a large interchange bus station is presented. The ultimate goal of this type of study is to increase the fire safety level of the station by improving the design of fire protection systems and evacuation procedures. The phenomena involved in the fire are highly transient and three dimensional, and their modeling requires large computational resources. In the present work, we introduce several simplifications in the numerical model, mainly related to turbulence modeling and the boundary conditions used to reproduce the effects of the combustion process, which allow us capturing the essential features of the fire while keeping the memory requirements and the CPU time at a reasonable level. In particular, we are interested in describing in a realistic way the spread of smoke and heat in a typical fire scenario in the lobby of an interchange bus station. The numerical analysis is carried out with the aid of a general-purpose computer code, using two different approaches for turbulence modeling (RANS and LES) and several discretization schemes. The fire effects are reproduced in a simple way, describing the fire focus as a source of mass, heat and chemical species. Boundary conditions are imposed at the fire focus, by setting the inlet velocity, temperature and gas composition (combustion products) at a section of appropriate area. The values of these quantities are chosen to be consistent with the prescribed heat release rate, type of fuel (heptane) and fire spread area. A comparison of the results obtained with the different methods, along with the CPU time consumption and dependence on the computational mesh, is presented. The capabilities and limitations of unsteady RANS and LES methods to reproduce the main features of the smoke and heat propagation patterns are analyzed.

Volumetric Flow at the Supraceliac and Infrarenal Levels in Patients With Abdominal Aortic Aneurysm: Waveforms and Allometric Scaling Relationships

2009 ◽  
Author(s):  
Andrea S. Les ◽  
Janice J. Yeung ◽  
Phillip M. Young ◽  
Robert J. Herfkens ◽  
Ronald L. Dalman ◽  
...  
Keyword(s):  
Blood Flow ◽  
Abdominal Aortic Aneurysm ◽  
Aortic Aneurysm ◽  
Boundary Conditions ◽  
Computational Simulation ◽  
Critical Role ◽  
Healthy Person ◽  
Patient Specific ◽  
Hemodynamic Forces ◽  
Abdominal Aortic

Hemodynamic forces are thought to play a critical role in abdominal aortic aneurysm (AAA) formation and growth, as well as in the migration and failure of aortic stent grafts. Computational simulation of blood flow enables the study of such hemodynamic forces; however, these simulations require accurate geometries and boundary conditions, usually in the form of flow and pressure data at specific locations. Although hundreds of computed tomography (CT) and magnetic resonance (MR) imaging studies of AAA geometry are performed daily in the clinical setting, flow information is difficult to obtain: It is not possible to reliably measure flow using CT, and while phase-contrast MRI (PC-MRI) can measure velocities, it is rarely used clinically for AAA patients. As a result, many AAA blood flow simulations use highly resolved patient-specific geometries, but may utilize literature-derived flows for inlet boundary conditions from a single, unrelated, sometimes healthy person of dissimilar body mass.

scholarly journals Rational Design of an Ion-Imprinted Polymer for Aqueous Methylmercury Sorption

Nanomaterials ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2541
Author(s):  
Ruddy L. M. Mesa ◽  
Javier E. L. Villa ◽  
Sabir Khan ◽  
Rafaella R. Alves Peixoto ◽  
Marcelo A. Morgano ◽  
...  
Keyword(s):  
Density Functional ◽  
Rational Design ◽  
Tap Water ◽  
Computational Simulation ◽  
Health Concern ◽  
Mercury Species ◽  
Ion Imprinted Polymer ◽  
Imprinted Polymer ◽  
Surface Areas ◽  
Ion Imprinted

Methylmercury (MeHg+) is a mercury species that is very toxic for humans, and its monitoring and sorption from environmental samples of water are a public health concern. In this work, a combination of theory and experiment was used to rationally synthesize an ion-imprinted polymer (IIP) with the aim of the extraction of MeHg+ from samples of water. Interactions among MeHg+ and possible reaction components in the pre-polymerization stage were studied by computational simulation using density functional theory. Accordingly, 2-mercaptobenzimidazole (MBI) and 2-mercaptobenzothiazole (MBT), acrylic acid (AA) and ethanol were predicted as excellent sulfhydryl ligands, a functional monomer and porogenic solvent, respectively. Characterization studies by scanning electron microscopy (SEM) and Brunauer–Emmett–Teller (BET) revealed the obtention of porous materials with specific surface areas of 11 m2 g−1 (IIP–MBI–AA) and 5.3 m2 g−1 (IIP–MBT–AA). Under optimized conditions, the maximum adsorption capacities were 157 µg g−1 (for IIP–MBI–AA) and 457 µg g−1 (for IIP–MBT–AA). The IIP–MBT–AA was selected for further experiments and application, and the selectivity coefficients were MeHg+/Hg2+ (0.86), MeHg+/Cd2+ (260), MeHg+/Pb2+ (288) and MeHg+/Zn2+ (1510), highlighting the material’s high affinity for MeHg+. The IIP was successfully applied to the sorption of MeHg+ in river and tap water samples at environmentally relevant concentrations.

Sign in / Sign up

Export Citation Format

Share Document