Predicting stress and interstitial fluid pressure in tumors based on biphasic theory.

The uncontrolled proliferation of cancer cells causes the growth of the tumor mass. Consequently, the normal surrounding tissue exerts a compressive force on the tumor mass to oppose its expansion. These stresses directly promote tumor metastasis and invasion and affect drug delivery. In the past, the mechanical behavior of solid tumors has been extensively studied using linear elastic and nonlinear hyperelastic constitutive models. In this study, we develop a two-dimensional biomechanical model based on the biphasic assumption of the solid matrix and fluid phase of the tissues. Heterogeneous vasculature and nonuniform blood perfusion are also investigated by incorporating in the model a necrotic core and a well-vascularized zone. The findings of our study demonstrate a significant difference between the linear and nonlinear tissue responses to stress, while the interstitial fluid pressure (IFP) distribution is found to be independent of the constitutive model. The proposed biphasic model may be useful for elasticity imaging techniques aiming at predicting stress and IFP in tumors.

The Texas A&M University Hypervelocity Impact Laboratory: A modern aeroballistic range facility.

Novel engineering materials and structures are increasingly designed for use in severe environments involving extreme transient variations in temperature and loading rates, chemically reactive flows, and other conditions. The Texas A&M University Hypervelocity Impact Laboratory (HVIL) enables unique ultrahigh-rate materials characterization, testing, and modeling capabilities by tightly integrating expertise in high-rate materials behavior, computational and polymer chemistry, and multi-physics multiscale numerical algorithm development, validation, and implementation. The HVIL provides a high-throughput test bed for development and tailoring of novel materials and structures to mitigate hypervelocity impacts (HVIs). A conventional, 12.7 mm, smooth bore, two-stage light gas gun (2SLGG) is being used as the aeroballistic range launcher to accelerate single and simultaneously launched projectiles to velocities in the range 1.5-7.0 km/s. The aeroballistic range is combined with conventional and innovative experimental, diagnostic, and modeling capabilities to create a unique HVI and hypersonic test bed. Ultrahigh-speed imaging (10M fps), ultrahigh-speed schlieren imaging, multi-angle imaging, digital particle tracking, flash x-ray radiography, nondestructive/destructive inspection, optical and scanning electron microscopy, and other techniques are being used to characterize HVIs and study interactions between hypersonic projectiles and suspended aerosolized particles. Additionally, an overview of 65 2SLGG facilities operational worldwide since 1990 is provided, which is the most comprehensive survey published to date. The HVIL aims to (i) couple recent theoretical developments in shock physics with advances in numerical methods to perform HVI risk assessments of materials and structures, (ii) characterize environmental effects (water, ice, dust, etc.) on hypersonic vehicles, and (iii) address key high-rate materials and hypersonics research problems.

A dual mesh finite domain method for the analysis of functionally graded beams.

A method that employs a dual mesh, one for primary variables and another for dual variables, for the numerical analysis of functionally graded beams is presented. The formulation makes use of the traditional finite element interpolation of the primary variables (primal mesh) and the concept of the finite volume method to satisfy the integral form of the governing differential equations on a dual mesh. The method is used to analyze bending of straight, through-thickness functionally graded beams using the Euler-Bernoulli and the Timoshenko beam theories, in which the axial and bending deformations are coupled. Both the displacement and mixed models using the new method are developed accounting for the coupling. Numerical results are presented to illustrate the methodology and a comparison of the generalized displacements and forces/stresses computed with those of the corresponding finite element models. The influence of the coupling stiffness on the deflections is also brought out.

Linkage disequilibrium mapping for grain Fe and Zn enhancing QTLs useful for nutrient dense rice breeding.

BACKGROUND: High yielding rice varieties are usually low in grain iron (Fe) and zinc (Zn) content. These two micronutrients are involved in many enzymatic activities, lack of which cause many disorders in human body. Bio-fortification is a cheaper and easier way to improve the content of these nutrients in rice grain. RESULTS: A population panel was prepared representing all the phenotypic classes for grain Fe-Zn content from 485 germplasm lines. The panel was studied for genetic diversity, population structure and association mapping of grain Fe-Zn content in the milled rice. The population showed linkage disequilibrium showing deviation of Hardy-Weinberg's expectation for Fe-Zn content in rice. Population structure at K = 3 categorized the panel population into distinct sub-populations corroborating with their grain Fe-Zn content. STRUCTURE analysis revealed a common primary ancestor for each sub-population. Novel quantitative trait loci (QTLs) namely qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected using association mapping. Four QTLs, namely qFe3.3, qFe7.3, qFe8.1 and qFe12.2 for grain Fe content were detected to be co-localized with qZn3.1, qZn7, qZn8.3 and qZn12.3 QTLs controlling grain Zn content, respectively. Additionally, some Fe-Zn controlling QTLs were co-localized with the yield component QTLs, qTBGW, OsSPL14 and qPN. The QTLs qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qZn6, qZn7 and gRMm9-1 for grain Fe-Zn content reported in earlier studies were validated in this study. CONCLUSION: Novel QTLs, qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected for these two traits. Four Fe-Zn controlling QTLs and few yield component QTLs were detected to be co-localized. The QTLs, qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qFe3.3, qFe7.3, qZn6, qZn7, qZn2.2, qZn8.3 and qZn12.3 will be useful for biofortification of the micronutrients. Simultaneous enhancement of Fe-Zn content may be possible with yield component traits in rice.

Modeling and Analysis of Ultrasound Elastographic Axial Strains for Spine Fracture Identification.

This study reports the first use of ultrasound (US) elastography for imaging spinal fractures by assessing the mechanical response of the soft tissue at the posterior vertebra boundary to a uniaxial compression in rabbit ex vivo samples. Three-dimensional finite-element (FE) models of the vertebra-soft tissue complex in rabbit samples are generated and analyzed to evaluate the distribution of the axial normal and shear strains at the vertebra-soft tissue interface. Experiments on the same samples are performed to corroborate simulation findings. Results of this study indicate that the distribution of the axial strains manifests as distinct patterns around intact and fractured vertebrae. Numerical characteristics of the axial strain's spatial distribution are further used to construct two shape descriptors to make inferences on spinal abnormalities: 1) axial normal strain asymmetry for assessing the presence of fractures and 2) principal orientation of axial shear strain concentration regions (shear zones) for measurement of spinous process dislocation. This study demonstrates that axial normal strain and axial shear strain maps obtained via US elastography can provide a new means to detect spine fractures and abnormalities in the selected ex vivo animal models. Spinal fracture detection is important for the assessment of spinal cord injuries and stability. However, identification of spinal fractures using US is currently challenging. Our results show that features resulting from strain elastograms can serve as a useful adjunct to B-mode images in identifying spine fractures in the selected animal samples, and this information could be helpful in clinical settings.

Association mapping reveals multiple QTLs for grain protein content in rice useful for biofortification.

Rice is the staple food for majority of the global population. But, rice grain has low protein content (PC). Mapping of QTLs controlling grain PC is essential for enhancement of the trait through breeding programs. A shortlisted panel population for grain protein content was studied for genetic diversity, population structure and association mapping for grain PC. Phenotyping results showed a wide variation for grain PC. The panel population showed a moderate level of genetic diversity estimated through 98 molecular markers. AMOVA and structure analysis indicated linkage disequilibrium for grain PC and deviation of Hardy-Weinberg's expectation. The analysis showed 15% of the variation among populations and 73% among individuals in the panel population. STRUCTURE analysis categorized the panel population into three subpopulations. The analysis also revealed a common primary ancestor for each subpopulation with few admix individuals. Marker-trait association using 98 molecular markers detected 7 strongly associated QTLs for grain PC by both MLM and GLM analysis. Three novel QTLs qPC3.1, qPC5.1 and qPC9.1 were detected for controlling the grain PC. Four reported QTLs viz., qPC3, QPC8, qPC6.1 and qPC12.1 were validated for use in breeding programs. Reported QTLs, qPC6, qPC6.1 and qPC6.2 may be same QTL controlling PC in rice. A very close marker RM407 near to protein controlling QTL, qProt8 and qPC8, was detected. The study provided clue for simultaneous improvement of PC with high grain yield in rice. The strongly associated markers with grain PC, namely qPC3, qPC3.1, qPC5.1, qPC6.1, qPC8, qPC9.1 and qPC12.1, will be useful for their pyramiding for developing protein rich high yielding rice.

Marker Assisted Breeding to Develop Multiple Stress Tolerant Varieties for Flood and Drought Prone Areas.

BACKGROUND: Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of qDTY1.1, qDTY2.1, qDTY3.1 and Sub1. Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal. RESULTS: Grain yield advantage of the NILs with qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 and qDTY2.1 + qDTY3.1 + Sub1 ranged from 76 to 2479 kg ha- 1 and 396 to 2376 kg ha- 1 under non-stress (NS) respectively and 292 to 1118 kg ha- 1 and 284 to 2086 kg ha- 1 under reproductive drought stress (RS), respectively. The NIL, IR96322-34-223-B-1-1-1-1 having qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 has been released as variety CR dhan 801 in India. IR 96321-1447-651-B-1-1-2 having qDTY1.1 + qDTY3.1 + Sub 1 and IR 94391-131-358-19-B-1-1-1 having qDTY3.1 + Sub1 have been released as varieties Bahuguni dhan-1' and 'Bahuguni dhan-2' respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322-34-223-B-1-1-1-1, IR 96321-1447-651-B-1-1-2 and IR 94391-131-358-19-B-1-1-1 respectively on 6 K SNP Infinium chip. CONCLUSION: The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha- 1 under reproductive stage drought stress and 0.1 to 1.0 t ha- 1 under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.

An Analytical Poroelastic Model of a Nonhomogeneous Medium Under Creep Compression for Ultrasound Poroelastography Applications-Part II.

An analytical theory for the unconfined creep behavior of a cylindrical inclusion (simulating a soft tissue tumor) embedded in a cylindrical background sample (simulating normal tissue) is presented and analyzed in this paper. Both the inclusion and the background are considered as fluid-filled, porous materials, each of them being characterized by a set of mechanical parameters. Specifically, in this derivation, the inclusion is assumed to have significantly higher interstitial permeability than the background. The formulations of the effective Poisson's ratio (EPR) and fluid pressure in the inclusion and in the background are derived for the case of a sample subjected to a creep compression. The developed analytical expressions are validated using finite element models (FEM). Statistical comparison between the results obtained from the developed model and the results from FEM demonstrates accuracy of the proposed theoretical model higher than 99.4%. The model presented in this paper complements the one reported in the companion paper (Part I), which refers to the case of an inclusion having less interstitial permeability than the background.

An Analytical Poroelastic Model of a Nonhomogeneous Medium Under Creep Compression for Ultrasound Poroelastography Applications-Part I.

An analytical theory for the unconfined creep behavior of a cylindrical inclusion (simulating a soft tissue tumor) embedded in a cylindrical background sample (simulating normal tissue) is presented and analyzed in this paper. Both the inclusion and the background are considered as fluid-filled, porous materials, each of them being characterized by a set of mechanical properties. Specifically, in this paper, the inclusion is considered to be less permeable than the background. The cylindrical sample is compressed using a constant pressure within two frictionless plates and is allowed to expand in an unconfined way along the radial direction. Analytical expressions for the effective Poisson's ratio (EPR) and fluid pressure inside and outside the inclusion are derived and analyzed. The theoretical results are validated using finite element models (FEMs). Statistical analysis shows excellent agreement between the results obtained from the developed model and the results from FEM. Thus, the developed theoretical model can be used in medical imaging modalities such as ultrasound poroelastography to extract the mechanical parameters of tissues and/or to better understand the impact of different mechanical parameters on the estimated displacements, strains, stresses, and fluid pressure inside a tumor and in the surrounding tissue.

A model-based approach to investigate the effect of elevated interstitial fluid pressure on strain elastography.

Finite element (FE) modeling provides a useful tool to understand the mechanical behavior of complex tissues, such as cancers, in a variety of testing conditions. Although a number of numerical and analytical models for cancerous tumors are retrievable in the literature, none of these models is capable of completely describing the behavior of a cancer embedded in a normal tissue in the conditions typical for an ultrasound elastography experiment. In this paper, we first design and implement a realistic FE model of the mechanical behavior of a cancer embedded in a normal tissue under ultrasound elastography testing conditions. In addition to the commonly used tissue mechanical properties, for the cancer, elevated interstitial fluid pressure (IFP) is incorporated in the model. IFP is a parameter of great clinical significance, but it is not typically considered in elastographic models of tumors. The developed model is then used to thoroughly study the effect of IFP on the axial, lateral and volumetric strains inside the tumor. The results of this study demonstrate that the presence of the IFP affects both the temporal and spatial distributions of the axial, lateral, volumetric strains and related elastographic parameters. Thus, these results lead to two important considerations: (1) that a correct interpretation of experimental elastographic data need a clear understanding of the effect of the IFP on the obtained elastograms and (2) that this IFP-dependent alteration of the elastographic parameters may provide an opportunity to non-invasively gain localized information about this clinically relevant parameter.

A Model-Based Approach to Investigate the Effect of a Long Bone Fracture on Ultrasound Strain Elastography.

The mechanical behavior of long bones and fractures has been under investigation for many decades due to its complexity and clinical relevance. In this paper, we report a new subject-specific methodology to predict and analyze the mechanical behavior of the soft tissue at a bone interface with the intent of identifying the presence and location of bone abnormalities with high accuracy, spatial resolution, and contrast. The proposed methodology was tested on both intact and fractured rabbit femur samples with finite element-based 3-D simulations, created from actual femur computed tomography data, and ultrasound elastography experiments. The results included in this study demonstrate that elastographic strains at the bone/soft tissue interface can be used to differentiate fractured femurs from the intact ones on a distribution level. These results also demonstrate that coronal plane axial shear strain creates a unique contrast mechanism that can be used to reliably detect fractures (both complete and incomplete) in long bones. Kruskal-Wallis test further demonstrates that the contrast measure for the fracture group (simulation: 2.1286±0.2206; experiment: 2.7034 ± 1.0672) is significantly different from that for the intact group (simulation: 0 ± 0; experiment: 1.1540±0.6909) when using coronal plane axial shear strain elastography ( < 0.01). We conclude that: 1) elastography techniques can be used to accurately identify the presence and location of fractures in a long bone and 2) the proposed model-based approach can be used to predict and analyze strains at a bone fracture site and to better interpret experimental elastographic data.

An analytical poroelastic model for ultrasound elastography imaging of tumors.

The mechanical behavior of biological tissues has been studied using a number of mechanical models. Due to the relatively high fluid content and mobility, many biological tissues have been modeled as poroelastic materials. Diseases such as cancers are known to alter the poroelastic response of a tissue. Tissue poroelastic properties such as compressibility, interstitial permeability and fluid pressure also play a key role for the assessment of cancer treatments and for improved therapies. At the present time, however, a limited number of poroelastic models for soft tissues are retrievable in the literature, and the ones available are not directly applicable to tumors as they typically refer to uniform tissues. In this paper, we report the analytical poroelastic model for a non-uniform tissue under stress relaxation. Displacement, strain and fluid pressure fields in a cylindrical poroelastic sample containing a cylindrical inclusion during stress relaxation are computed. Finite element simulations are then used to validate the proposed theoretical model. Statistical analysis demonstrates that the proposed analytical model matches the finite element results with less than 0.5% error. The availability of the analytical model and solutions presented in this paper may be useful to estimate diagnostically relevant poroelastic parameters such as interstitial permeability and fluid pressure, and, in general, for a better interpretation of clinically-relevant ultrasound elastography results.

Effect of bone-soft tissue friction on ultrasound axial shear strain elastography.

Bone-soft tissue friction is an important factor affecting several musculoskeletal disorders, frictional syndromes and the ability of a bone fracture to heal. However, this parameter is difficult to determine using non-invasive imaging modalities, especially in clinical settings. Ultrasound axial shear strain elastography is a non-invasive imaging modality that has been used in the recent past to estimate the bonding between different tissue layers. As most elastography methods, axial shear strain elastography is primarily used in soft tissues. More recently, this technique has been proposed to assess the bone-soft tissue interface. In this paper, we investigate the effect of a variation in bone-soft tissue friction coefficient in the resulting axial shear strain elastograms. Finite element poroelastic models of bone specimens exhibiting different bone-soft tissue friction coefficients were created and mechanically analyzed. These models were then imported to an ultrasound elastography simulation module to assess the presence of axial shear strain patterns. In vitro experiments were performed to corroborate selected simulation results. The results of this study show that the normalized axial shear strain estimated at the bone-soft tissue interface is statistically correlated to the bone-soft tissue coefficient of friction. This information may prove useful to better interpret ultrasound elastography results obtained in bone-related applications and, possibly, monitor bone healing.

Effect of Interstitial Fluid Pressure on Ultrasound Axial Strain and Axial Shear Strain Elastography.

Ultrasound elastography is an imaging modality that has been used to diagnose tumors of the breast, thyroid, and prostate. Both axial strain elastography and axial shear strain elastography (ASSE) have shown significant potentials to differentiate between benign and malignant tumors. Elevated interstitial fluid pressure (IFP) is a characteristic of many malignant tumors and a major barrier in targeted drug delivery therapies. This parameter, however, has not received significant attention in ultrasound elastography and, in general, in most diagnostic imaging modalities yet. In this paper, we investigate the effect of an underlying IFP contrast on ultrasound axial strain and axial shear strain imaging using finite element analysis. Our results show that an underlying contrast in IFP creates a new contrast mechanism in both the axial strain and axial shear strain elastographic images. This information might be important for a better interpretation of elastographic images of tumors.

Modeling of a biological material nacre: Waviness stiffness model.

Nacre is a tough yet stiff natural composite composed of microscopic mineral polygonal tablets bonded by a tough biopolymer. The high stiffness of nacre is known to be due to its high mineral content. However, the remarkable toughness of nacre is explained by its ability to deform past a yield point and develop large inelastic strain over a large volume around defects and cracks. The high strain is mainly due to sliding and waviness of the tablets. Mimicking nacre's remarkable properties, to date, is still a challenge due in part to fabrication challenges as well as a lack of models that can predict its properties or properties of a bulk material given specific constituent materials and material structure. Previous attempts to create analytical models for nacre include tablet sliding but don't account for the waviness of the tablets. In this work, a mathematical model is proposed to account for the waviness of the tablet. Using this model, a better prediction of the elastic modulus is obtained that agrees with experimental values found in the literature. In addition, the waviness angle can be predicted which is within the recommended range. Having a good representative model aids in designing a bio-mimicked nacre.

Distinctions between dynamic characteristics of the single EG5 motor protein along neural vs. cancerous microtubules.

The kinesin 5 motor contributes critically to mitosis, and is often upregulated in cancer. In vitro motility studies of kinesin 5 moving along bovine brain microtubules indicate that the motors have limited processivity. Cancer cells have abnormal mitotic behavior, so one might wonder whether the functional properties of kinesin 5 change in such a background. Because there could be multiple unknown changes in cancerous vs normal cells, we chose to address this question in a controlled in vitro environment. Specifically, through a series of parallel experiments along bovine brain vs. breast cancer microtubules, we quantified the in vitro motility characteristics of single Eg5 molecular motors along these two types of microtubules, combining the utilization of an optical trapping technique with a study of motion in the unloaded regime. The obtained values indicate that Eg5 processivity is 40% less along MCF7 microtubules, compared to that measured on bovine brain MTs. Interestingly, not all single-molecule properties are altered, as the velocity of the single motor doesn't show any significant changes on either track, though the binding time along MCF7 microtubules is almost 25% shorter. The current results, in conjunction with our previously reported outcomes of the evaluation of the Eg5's characteristics under external load, show that in transition from no-load to high-load regime, the Eg5 binding time has less sensitivity on MCF7 as compared to bovine brain MTs. This finding is intriguing, as it suggests that, potentially, groups of Eg5 motors function more effectively in the cancer background of a large ensemble, possibly contributing to faster mitosis in cancer cells.

From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network.

Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, "From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance" was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into seven popular locally adapted rice varieties, namely, ADT 45, CR 1009, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. Genotypic background selection is being done after BC2F2 stage using an in-house designed 50K SNP chip on a set of twenty lines for each combination, identified with phenotypic similarity in the field to the recipient parent. Near-isogenic lines with more than 90% similarity to the recipient parent are now in advanced generation field trials. These climate smart varieties are expected to improve rice productivity in the adverse ecologies and contribute to the farmer's livelihood.

Effect of permeability on the performance of elastographic imaging techniques.

Elastography is a well-established imaging modality. While a number of studies aimed at evaluating the performance of elastographic techniques are retrievable in the literature, very little information is available on the effects that the presence of an underlying permeability contrast in the tissue may have on the resulting elastograms. Permeability is a fundamental tissue parameter, which characterizes the ease with which fluid can move within a tissue. This parameter plays a central role both biomechanically in the description of the temporal behavior of fluid-filled tissues and clinically in the development of a number of diagnostic and therapeutic modalities. In this paper, we present a simulation study that investigates selected elastographic image quality factors in nonhomogeneous materials, modeled as poroelastic media with different geometries and permeability contrasts. The results of this study indicate that the presence of an underlying permeability contrast may create a new contrast mechanism in the spatial and temporal distributions of the axial strains and the effective Poisson's ratios experienced by the tissue and as imaged by the corresponding elastograms. The effect of permeability on the elastographic image quality factors analyzed in this study was found to be a nonsymmetric function of the underlying mechanical contrast between background and target, the geometry of the material and the boundary conditions.

Finite element model for nutrient distribution analysis of a hollow fiber membrane bioreactor.

Hollow fiber membrane bioreactors (HFMB) are extensively used for the development of tissue substitutes for bones and cartilages. In an HFMB, the nutrient transport is dependent on the material properties of the porous scaffold and fiber membrane and also on the fluid flow through the hollow fiber. The difficulty in obtaining real-time data along with the presence of large number of variables in experimental studies have lead to increased application of computational models for the performance analysis of bioreactors. A major difficulty in the computational analysis of HFMB is the modeling of the interactions at the fluid and porous scaffold interfaces, which has often been neglected or incorporated using specific boundary conditions. In this study, a new FEM is developed to analyze the fluid flow in the fluid-porous region with the interface coupled directly into the FEM. Distribution of nutrients in the bioreactor is studied by coupling mass transport equations to the fluid-porous finite element framework. The new model is implemented to study the influence of permeability, cell density, and flow rate on the nutrient concentration distribution in the HFMB. The developed computational framework is an ideal tool to study fluid flow through porous-open channels and can also be used for the design of bioreactors for optimal tissue growth.

Molecular dynamics analysis on buckling of defective carbon nanotubes.

Owing to their remarkable mechanical properties, carbon nanotubes have been employed in many diverse areas of applications. However, similar to any of the many man-made materials used today, carbon nanotubes (CNTs) are also susceptible to various kinds of defects. Understanding the effect of defects on the mechanical properties and behavior of CNTs is essential in the design of nanotube-based devices and composites. It has been found in various past studies that these defects can considerably affect the tensile strength and fracture of CNTs. Comprehensive studies on the effect of defects on the buckling and vibration of nanotubes is however lacking in the literature. In this paper, the effects of various configurations of atomic vacancy defects, on axial buckling of single-walled carbon nanotubes (SWCNTs), in different thermal environments, is investigated using molecular dynamics simulations (MDS), based on a COMPASS force field. Our findings revealed that even a single missing atom can cause a significant reduction in the critical buckling strain and load of SWCNTs. In general, increasing the number of missing atoms, asymmetry of vacancy configurations and asymmetric distribution of vacancy clusters seemed to lead to higher deterioration in buckling properties. Further, SWCNTs with a single vacancy cluster, compared to SWCNTs with two or more vacancy clusters having the same number of missing atoms, appeared to cause higher deterioration of buckling properties. However, exceptions from the above mentioned trends could be expected due to chemical instabilities of defects. Temperature appeared to have less effect on defective CNTs compared to pristine CNTs.