Sharif Digital Repository

The present study investigates the diversification and dynamic behavior of a multi-population microfluidic microbial fuel cell (MFC) as a biosensor. The cost effective microfluidic MFC coupled to a comprehensive model, presents a novel platform for monitoring chemical and biological phenomena. The importance of competition among different microbial groups, hierarchical biochemical processes, bacterial chemotaxis and different mechanisms of electron transfer were significant considerations in the present model. The validation of the model using experimental data from a microfluidic MFC shows an appropriate match with the hierarchal biodegradation processes of a complex substrate as well as... 

Traditional load-control musculoskeletal and finite element (FE) models of the spine fail to accurately predict in vivo intervertebral joint loads due mainly to the simplifications and assumptions when estimating redundant trunk muscle forces. An alternative powerful protocol that bypasses the calculation of muscle forces is to drive the detailed FE models by image-based in vivo displacements. Development of subject-specific models, however, both involves the risk of extensive radiation exposures while imaging in supine and upright postures and is time consuming in terms of the reconstruction of the vertebrae, discs, ligaments, and facets geometries. This study therefore aimed to introduce a... 

Laccase production by indigenous fungus, Phanerochaete chrysosporium, requires solving optimal problems to determine the maximum production of the enzyme within a definite time period and conditions specified in the solid-state fermentation process. For this purpose, parallel to response surface methodology, an analytical approach has been proposed based on the advanced concepts of Poisson geometry and Lie groups, which lead to a system of the Hamiltonian equations. Despite the dating of the Hamiltonian approach to solving biological problems, the novelty of this paper is based on the expression of a Hamiltonian system in notions of Poisson geometry, Lie algebras and symmetry groups and... 

In this work, a mathematical model was developed to simulate the urinary concentration mechanism. A 3-D geometry was derived based on the detail physiological pictures of rat kidney. The approximate region of each tubule was obtained from the volume distribution of structures based on Walter Pfaller's monograph and Layton's region-based model. Mass and momentum balances were applied to solve for the change in solutes concentration and osmolality. The osmolality of short and long descending nephrons at the end of the outer medulla was obtained to be 530 mOsmol/kgH2O and 802 mOsmol/kgH2O, respectively, which were in acceptable agreement with experimental data. The fluid osmolality of the short... 

The Calcium ion Ca2+ plays a critical role as an initiator and preserving agent of the cross-bridge cycle in the force generation of skeletal muscle. A new multi-scale chemo-mechanical model is presented in order to analyze the role of Ca2+ in muscle fatigue and to predict fatigue behavior. To this end, a cross-bridge kinematic model was incorporated in a continuum based mechanical model, considering a thermodynamic compatible framework. The contractile velocity and the generated active force were directly related to the force-bearing states that were considered for the cross-bridge cycle. In order to determine the values of the model parameters, the output results of an isometric simulation... 

Therapeutic fragmented antibodies show a poor pharmacokinetic profile that leads to frequent high-dose administration. In the current study, for the first time, a novel proline, alanine, serine (PAS) repeat sequence called PAS#208 was designed to extend the plasma half-life of a nanosized anti-vascular endothelial growth factor-A single-domain antibody. Polyacrylamide gel electrophoresis, circular dichroism, dynamic light scattering, and electrophoretic light scattering were used to assess the physicochemical properties of the newly designed PAS sequence. The effect of PAS#208 on the biologic activity of a single-domain antibody was studied using an in vitro proliferation assay. The... 

The effect of the variation in the femoral groove geometry on patellofemoral joint stability was studied using a two dimensional transverse plane model with deformable articular surfaces. The femoral and patellar bony structures were modelled as rigid bodies with their profiles expressed by splines. The articular cartilage was discretized into compression springs, distributed along the femoral and patellar profiles, based on the rigid-body spring model. The medial and lateral retinacula were modelled as linear tensile springs, and the quadriceps muscles and patellar tendon as strings with known tension. The anatomical data were obtained from the transverse plane magnetic resonance images of... 

Spine musculoskeletal (MS) models make simplifying assumptions on the intervertebral joint degrees-of-freedom (rotational and/or translational), representation (spherical or beam-like joints), and properties (linear or nonlinear). They also generally neglect the realistic structure of the joints with disc nuclei/annuli, facets, and ligaments. We aim to develop a novel MS model where trunk muscles are incorporated into a detailed finite element (FE) model of the ligamentous T12-S1 spine thus constructing a gold standard coupled MS-FE model. Model predictions are compared under some tasks with those of our earlier spherical joints, beam joints, and hybrid (uncoupled) MS-FE models. The coupled... 

Passive finite element (FE) models of the spine are commonly used to simulate intact and various pre- and postoperative pathological conditions. Being devoid of muscles, these traditional models are driven by simplistic loading scenarios, e.g., a constant moment and compressive follower load (FL) that do not properly mimic the complex in vivo loading condition under muscle exertions. We aim to develop novel passive FE models that are driven by more realistic yet simple loading scenarios, i.e., in vivo vertebral rotations and pathological-condition dependent FLs (estimated based on detailed musculoskeletal finite element (MS-FE) models). In these novel force–displacement control FE models,... 

The aim of this study was to use finite element analysis (FEA) to assess the influence of microthread design at the implant neck on stress distribution in the surrounding bone. A commercially available implant with 3.5 mm diameter and 10.5 mm length was selected and used as a model. For the purpose of designing the microthread implant model, microthreads were added to the implant neck in a computerized model. A force measuring 100 N was then applied to the entire surface of the abutment in the vertical direction. The results showed that in both models, stress was mainly concentrated at the cortical bone adjacent to the neck of the implant. Maximum stress values in the cortical bone... 

Airflow simulation of the whole respiratory system is still unfeasible due to the geometrical complexity of the lung airways and the diversity of the length scales involved in the problem. Even the new CT imaging system is not capable of providing accurate 3D geometries for smaller tubes, and a complete 3D simulation is impeded by the limited computational resources available. The aim of this study is to develop a fully coupled 3D-1D model to make accurate prediction of airflow and particle deposition in the whole respiratory track, with reasonable computational cost and efficiency. In the new proposed method, the respiratory tree is divided into three parts to be dealt with using different... 

Background: Asymmetric lifting activities are associated with low back pain. Methods: A finite element biomechanical model is used to estimate spinal loads during one- and two-handed asymmetric static lifting activities. Model input variables are thorax flexion angle, load magnitude as well as load sagittal and lateral positions while response variables are L4-L5 and L5-S1 disc compression and shear forces. A number of levels are considered for each input variable and all their possible combinations are introduced into the model. Robust yet user-friendly predictive equations that relate model responses to its inputs are established. Findings: Predictive equations with adequate... 

A modelling of the anaerobic digestion process of molasses was conducted in a 70-L multistage anaerobic biofilm reactor or hybrid anaerobic baffled reactor with six compartments at an operating temperature of 26 °C. Five hydraulic retention times (6, 16, 24, 72 and 120 h) were studied at a constant influent COD concentration of 10,000 mg/L. Two different kinetic models (one was based on a dispersion model with first-order kinetics for substrate consumption and the other based on a modification of the Young equation) were evaluated and compared to predict the organic matter removal efficiency or fractional conversion. The first-order kinetic constant obtained with the dispersion model was... 

Response surface methodology is used to establish robust and user-friendly predictive equations that relate responses of a complex detailed trunk finite element biomechanical model to its input variables during sagittal symmetric static lifting activities. Four input variables (thorax flexion angle, lumbar/pelvis ratio, load magnitude, and load position) and four model responses (L4-L5 and L5-S1 disc compression and anterior-posterior shear forces) are considered. Full factorial design of experiments accounting for all combinations of input levels is employed. Quadratic predictive equations for the spinal loads at the L4-S1 disc mid-heights are obtained by regression analysis with adequate... 

Paraplegic users of mechanical walking orthoses, e.g. advanced reciprocating gait orthosis (ARGO), often face high energy expenditure and extreme upper body loading during locomotion. We studied the effect of kinematical pattern on the mechanical performance of paraplegic locomotion, in search for an improved gait pattern that leads to lower muscular efforts. A three-dimensional, four segment, six-degrees-of-freedom skeletal model of the advanced reciprocating gait orthosis-assisted paraplegic locomotion was developed based on the data acquired from an experimental study on a single subject. The effect of muscles was represented by ideal joint torque generators. A response surface analysis... 

We propose a new image recovery method to improve the resolution in microwave imaging applications. Scattered field data obtained from a simplified breast model with closely located targets is used to formulate an electromagnetic inverse scattering problem, which is then solved using the Distorted Born Iterative Method (DBIM). At each iteration of the DBIM method, an underdetermined set of linear equations is solved using our proposed sparse recovery algorithm, IMATCS. Our results demonstrate the ability of the proposed method to recover small targets in cases where traditional DBIM approaches fail. Furthermore, in order to regularize the sparse recovery algorithm, we propose a novel... 

Different lifting analysis tools are commonly used to assess spinal loads and risk of injury. Distinct musculoskeletal models with various degrees of accuracy are employed in these tools affecting thus their relative accuracy in practical applications. The present study aims to compare predictions of six tools (HCBCF, LSBM, 3DSSPP, AnyBody, simple polynomial, and regression models) for the L4-L5 and L5-S1 compression and shear loads in twenty-six static activities with and without hand load. Significantly different spinal loads but relatively similar patterns for the compression (R2>0.87) were computed. Regression models and AnyBody predicted intradiscal pressures in closer agreement with... 

The human motor system is organized for execution of various motor tasks in a different and flexible manner. The kinetic redundancy in the human musculoskeletal system is a significant property by which the central nervous system achieves many complementary goals. An equilibrium-based biomechanical model of isometric three-dimensional exertions of trunk muscles has been developed. Following the definition and role of the uncontrolled manifold, the kinetic redundancy concept is explored in mathematical terms. The null space of the kinetically redundant system when a certain joint moment and/or stiffness are needed is derived and discussed. The aforementioned concepts have been illustrated,... 

Degenerative disc disease, associated with discrete structural changes in the peripheral annulus and vertebral endplate, is one of the most common pathological triggers of acute and chronic low back pain, significantly depreciating an individual's quality of life and instigating huge socioeconomic costs. Novel emerging therapeutic techniques are hence of great interest to both research and clinical communities alike. Exogenous crosslinking, such as Genipin, and platelet-rich plasma therapies have been recently demonstrated encouraging results for the repair and regeneration of degenerated discs, but there remains a knowledge gap regarding the quantitative degree of effectiveness and... 

Bacterial transport parameters play a fundamental role in microbial population dynamics, biofilm formation and bacteria dispersion. In this study, the novel model was extended based on the capability of microsized microbial fuel cells (MFCs) as amperometric biosensors to predict the cells' chemotactic and bioelectrochemical properties. The model prediction results coincide with the experimental data of Shewanella oneidensis and chemotaxis mutant of P. aeruginosa bdlA and pilT strains, indicating the complementary role of numerical predictions for bioscreening applications of microsized MFCs. Considering the general mechanisms for electron transfer, substrate biodegradation, microbial growth...