The Theory used in ADINA is richly documented in the following books by K.J. Bathe and co-authors
Following are more than 700 publications — that we know of — with
reference to the use of ADINA. The pages give the Abstracts of some papers published since 1986 referring to ADINA. The most recent papers are listed first. All these papers may be searched using the box:
Cerebrospinal Fluid Flow Dynamics in the Central Nervous System
B. Sweetman and A.A. Linninger
Laboratory for Product and Process Design (LPPD), Department of Bioengineering, University of Illinois at Chicago, Science and Engineering Offices (SEO), Room 218 (M/C 063), 851 S Morgan St., Chicago, IL 60607-7052, USA
Annals of Biomedical Engineering, DOI: 10.1007/s10439-010-0141-0 (2010)
Abstract: Cine-phase-contrast-MRI was used to measure the three-dimensional cerebrospinal fluid (CSF) flow field inside the central nervous system (CNS) of a healthy subject. Image reconstruction and grid generation tools were then used to develop a three-dimensional fluid–structure interaction model of the CSF flow inside the CNS. The CSF spaces were discretized using the finite-element method and the constitutive equations for fluid and solid motion solved in ADINA-FSI 8.6. Model predictions of CSF velocity magnitude and stroke volume were found to be in excellent agreement with the experimental data. CSF pressure gradients and amplitudes were computed in all regions of the CNS. The computed pressure gradients and amplitudes closely match values obtained clinically. The highest pressure amplitude of 77 Pa was predicted to occur in the lateral ventricles. The pressure gradient between the lateral ventricles and the lumbar region of the spinal canal did not exceed 132 Pa (~1 mmHg) at any time during the cardiac cycle. The pressure wave speed in the spinal canal was predicted and found to agree closely with values previously reported in the literature. Finally, the forward and backward motion of the CSF in the ventricles was visualized, revealing the complex mixing patterns in the CSF spaces. The mathematical model presented in this article is a prerequisite for developing a mechanistic understanding of the relationships among vasculature pulsations, CSF flow, and CSF pressure waves in the CNS.
Keywords: Three-dimensional modeling - Central nervous system - Cerebrospinal fluid - Intracranial dynamics – Pressure wave speed - Computational fluid dynamics
Rheological Models of Blood: Sensitivity Analysis and Benchmark Simulations
D. Szeliga, P. Maciol, K. Banas, M. Kopernik and M. Pietrzyk
AGH University of Science and Technology, Department of Applied Computer Science and Modelling, al. Mickiewicza 30, 30-059 Krakow, Poland
NUMIFORM 2010, Proceedings of the 10th International Conference, 1184-1192, 2010
Abstract: Modeling of blood flow with respect to rheological parameters of the blood is the objective of this paper. Casson type equation was selected as a blood model and the blood flow was analyzed based on Backward Facing Step benchmark. The simulations were performed using ADINA CFD finite element code. Three output parameters were selected, which characterize the accuracy of flow simulation. Sensitivity analysis of the results with Morris Design method was performed to identify rheological parameters and the model output, which control the blood flow to significant extent. The paper is the part of the work on identification of parameters controlling process of clotting.
Keywords: blood rheology – CFD - sensitivity analysis
Arterial Luminal Curvature and Fibrous-Cap Thickness Affect Critical Stress Conditions Within Atherosclerotic Plaque: An In Vivo MRI-Based 2D Finite-Element Study
Z. Teng,1 U. Sadat,1 Z. Li,1,2 X. Huang,3 C. Zhu,1 V.E. Young,11 M. J. Graves,1 And J.H. Gillard1
1 University Department of Radiology, University of Cambridge, Cambridge, UK
Annals of Biomedical Engineering, 38(10): 3096–3101, 2010
Abstract—High mechanical stress in atherosclerotic plaques at vulnerable sites, called critical stress, contributes to plaque rupture. The site of minimum fibrous cap (FC) thickness (FCMIN) and plaque shoulder are well-documented vulnerable sites. The inherent weakness of the FC material at the thinnest point increases the stress, making it vulnerable, and it is the big curvature of the lumen contour over FC which may result in increased plaque stress. We aimed to assess critical stresses at FCMIN and the maximum lumen curvature over FC (LCMAX) and quantify the difference to see which vulnerable site had the highest critical stress and was, therefore, at highest risk of rupture. One hundred patients underwent high resolution carotid magnetic resonance (MR) imaging. We used 352 MR slices with delineated atherosclerotic components for the simulation study. Stresses at all the integral nodes along the lumen surface were calculated using the finite-element method. FCMIN and LCMAX were identified, and critical stresses at these sites were assessed and compared. Critical stress at FCMIN was significantly lower than that at LCMAX (median: 121.55 kPa; inter quartile range (IQR) = [60.70–180.32] kPa vs. 150.80 kPa; IQR = [91.39–235.75] kPa, p<0.0001). If critical stress at FCMIN was only used, then the stress condition of 238 of 352 MR slices would be underestimated, while if the critical stress at LCMAX only was used, then 112 out of 352 would be underestimated. Stress analysis at FCMIN and LCMAX should be used for a refined mechanical risk assessment of atherosclerotic plaques, since material failure at either site may result in rupture.
Keywords: Curvature - Atherosclerosis - Stress - Plaque rupture - MRI
Stress Analysis of Carotid Plaque Based on in Vivo MRI of Acute Symptomatic and Asymptomatic Patients
Z.Y. Li1,2, C. Zhu2, Z. Teng2, and J.H. Gillard2
1 School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
WCB 2010, IFMBE Proceedings 31, 891-894, 2010
Abstract: Stress analysis within carotid plaques based on in vivo MR imaging has shown to be useful for the identification of vulnerable atheroma. This study is to investigate whether magnetic resonance imaging (MRI) based biomechanical stress analysis of carotid plaques can differentiate acute symptomatic and asymptomatic patients. 54 asymptomatic and 45 acute symptomatic patients underwent in vivo multi-contrast MRI of the carotid arteries. Plaque geometry used for finite element analysis was derived from in vivo MR images at the site of maximum and minimum plaque burden. In total 198 slices were used for the computational simulations. A pre shrink technique was used to refine the simulation. Maximum principle stress at the vulnerable plaque sites (i.e. critical stress) was extracted for the selected slices and a comparison was performed between the two groups. Critical stress at the site of maximum plaque burden is significantly higher in acute symptomatic patients as compared to asymptomatic patients [median: 198.0kPa (inter quartile range (IQR) = (119.8 - 359.0) vs. 138.4kPa (83.8, 242.6), p=0.04]. No significant difference was found at the minimum plaque burden site between the two groups [196.7kPa (133.3- 282.7) vs. 182.4kPa (117.2 - 310. 6), p=0.82). Stress analysis at the site of maximal plaque burden can be effectively used for differentiating acute symptomatic carotid plaques from asymptomatic plaques. This maybe potentially used for development of biomechanical risk stratification criteria based on plaque burden in future studies.
Keywords: Atherosclerosis - plaque rupture - stress analysis - MRI
Impact of plaque haemorrhage and its age on structural stresses in atherosclerotic plaques of patients with carotid artery disease: an MR imaging-based finite element simulation study
U. Sadat, Z. Teng, V.E. Young, C. Zhu, T.Y. Tang, M.J. Graves, J.H. Gillard
University Department of Radiology, University of Cambridge, Addenbrooke’s Hospital, Box 218, Level 5, Hills Road, Cambridge CB2 0QQ, UK
Abstract :Plaque haemorrhage (PH) in atherosclerotic plaques is associated with recurrent thromboembolic ischaemic events. The healing process predominantly involves the repair of the plaque rupture site and the replacement of fresh PH with chronic PH, which is either reabsorbed or replaced by fibrous tissue. The extent to which the presence of PH, and its type i.e. fresh or chronic, affects plaque stability remains unexplored. Finite element analysis (FEA)-based biomechanical stress simulations can provide quantification of the percentage contribution of PH and its types to the biomechanical stresses of plaques, thereby providing information about its role in plaque stability. Fifty-two patients with atherosclerotic carotid disease underwent high resolution magnetic resonance (MR) imaging of their carotid arteries in a 1.5 Tesla MR system. Twenty-three patients had MR identifiable PH and were selected. Only those images of these patients were used for simulations, which had evidence of PH. Manual segmentation of plaque components, such as lipid pool, fibrous tissue, calcium and PH, was done using carotid MR images. Plaque components and vessel wall were modelled as isotropic, incompressible hyperelastic materials with non-linear properties undergoing deformation under patient-specific blood pressure loading. Two dimensional structure-only FEA was used for quantification of maximum critical stress (M-CStress) of plaques. The median M-CStress of symptomatic patients with fresh PH was 159 kPa (IQR: 114–253). Because PH usually occurs within the lipid pool, when the simulation was repeated with lipid pool replacing fresh PH to simulate the pre-rupture plaque state, M-CStress was reduced by 26% [118 kPa (IQR: 79–189) (P = 0.001)]. When fresh PH was replaced with chronic PH it resulted in a 30% reduction in the M-CStress [118 kP (IQR: 79–189), (P = 0.001)]. PH affects stresses within atheroma to various degrees depending on its type, thereby influencing plaque stability to a different extent, with fresh PH significantly increasing the biomechanical stresses. Plaque component dependent stress analysis has the potential of identifying the critical nature of various plaque components.
Keywords: Magnetic resonance imaging - Stroke - Transient Ischaemic attacks – Atherosclerosis – Finite element analysis - Biomechanical stress – Plaque - Haemorrhage
Conformational dynamics of supramolecular protein assemblies
Do.-N. Kim, C.-T. Nguyen, M. Bathe
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Journal of Structural Biology, In press, 2010
Abstract: Supramolecular protein assemblies including molecular motors, cytoskeletal filaments, chaperones, and ribosomes play a central role in a broad array of cellular functions ranging from cell division and motility to RNA and protein synthesis and folding. Single-particle reconstructions of such assemblies have been growing rapidly in recent years, providing increasingly high resolution structural information under native conditions. While the static structure of these assemblies provides essential insight into their mechanism of biological function, their dynamical motions provide additional important information that cannot be inferred from structure alone. Here we present an unsupervised computational framework for the analysis of high molecular weight assemblies and use it to analyze the conformational dynamics of structures deposited in the Electron Microscopy Data Bank. Protein assemblies are modeled using a recently introduced coarse-grained modeling framework based on the finite element method, which is used to compute equilibrium thermal fluctuations, elastic strain energy distributions associated with specific conformational transitions, and dynamical correlations in distant molecular domains. Results are presented in detail for the ribosome-bound termination factor RF2 from Escherichia coli, the nuclear pore complex from Dictyostelium discoideum, and the chaperonin GroEL from E. coli. Elastic strain energy distributions reveal hinge regions associated with specific conformational change pathways, and correlations in collective molecular motions reveal dynamical coupling between distant molecular domains that suggest new, as well as confirm existing, allosteric mechanisms. Results are publicly available for use in further investigation and interpretation of biological function including cooperative transitions, allosteric communication, and molecular mechanics, as well as in further classification and refinement of electron microscopy based structures.
Keywords: Electron Microscopy Data Bank - Normal mode analysis - Finite element method
Evaluation by Fluid/Structure-Interaction Spinal-Cord Simulation of the Effects of Subarachnoid-Space Stenosis on an Adjacent Syrinx
Biofluid Mechanics Laboratory, Faculty of Engineering, University of New South Wales, Australia
Journal of Biomechanical Engineering, 132: 061009-1, 2010
Abstract: A finite-element numerical model was constructed of the spinal cord, pia mater, filum terminale, cerebrospinal fluid in the spinal subarachnoid space (SSS), and dura mater. The cord was hollowed out by a thoracic syrinx of length 140 mm, and the SSS included a stenosis of length 30 mm opposite this syrinx. The stenosis severity was varied from 0% to 90% by area. Pressure pulse excitation was applied to the model either at the cranial end of the SSS, simulating the effect of cranial arterial pulsation, or externally to the abdominal dura mater, simulating the effect of cough. A very short pulse was used to examine wave propagation; a pulse emulating cardiac systole was used to examine the effects of fluid displacement. Additionally, repetitive sinusoidal excitation was applied cranially. Bulk fluid flow past the stenosis gave rise to prominent longitudinal pressure dissociation (“suck”) in the SSS adjacent to the syrinx. However, this did not proportionally increase the longitudinal motion of fluid in the syrinx. The inertia of the fluid in the SSS, together with the compliance of this space, gave a resonance capable of being excited constructively or destructively by cardiac or coughing impulses. The main effect of mild stenosis was to lower the frequency of this resonance; severe stenosis damped out to-and-fro motions after the end of the applied excitation. Syrinx fluid motion indicated the fluid momentum and thus the pressure developed when the fluid was stopped by the end of the syrinx; however, the tearing stress in the local cord material depended also on the instantaneous local SSS pressure and was therefore not well predicted by syrinx fluid motion. Stenosis was also shown to give rise to a one-way valve effect causing raised SSS pressure caudally and slight average cord displacement cranially. The investigation showed that previous qualitative predictions of the effects of suck neglected factors that reduced the extent of the resulting syrinx fluid motion and of the cord tearing stress, which ultimately determines whether the syrinx lengthens.
Keywords: syringomyelia - finite-element model - cerebrospinal fluid - wave propagation
Morphometric and Simulation Analyses of Right Hepatic Vein Reconstruction in Adult Living Donor Liver Transplantation Using Right Lobe Grafts
S. Hwang,1 S.-G. Lee,1 C.-S. Ahn,1 D.-B. Moon,1 K.-H. Kim,1 K.-B. Sung,2 G.-Y. Ko,2 T.-Y. Ha,1 G.-W. Song,1 D.-H. Jung,1 D.-I. Gwon,2 K.-W. Kim,2 N.-K. Choi,1 K.-W. Kim,1 Y.-D. Yu,1 and G.-C. Park1
1 Division of Hepatobiliary Surgery and Liver Transplantation, Department of Surgery
Liver Transplantation, 16:639-648, 2010
The incidence of clinically significant right hepatic vein (RHV) stenosis after adult living donor liver transplantation has been higher than expected. In this study, an assessment of the risk factors for the development of RHV stenosis in this context was undertaken. Hepatic anatomy, surgical techniques, and the incidence of RHV stenosis 1 year after transplantation were evaluated retrospectively in 225 recipients of right lobe grafts. These patients underwent independent RHV reconstruction, which was facilitated by the application of computed tomography morphometry and computational simulation analyses. Three types of preparation of the orifice of the graft RHV and 7 types of preparation for venoplasty of the recipient RHV were used. The frequency of high, middle, and low sites of RHV insertion into the inferior vena cava (IVC) was 56.0%, 36.4%, and 7.6%, respectively, for donors, and 26.7%, 58.7%, and 14.7%, respectively, for recipients. Nine patients (4%) developed RHV stenosis of early onset that required stent insertion during the first 2 postoperative weeks; in 12 patients (5.3%), RHV stenosis of delayed onset occurred. Inappropriate matching of RHV sites of insertion correlated with the incidence of stenosis of early onset (P = 0.039). Technical refinements to avoid adverse consequences of inappropriate ventrodorsal matching of RHV sites of insertion include making the recipient RHV orifice wide and enlarging the recipient IVC by a customized incision and patch venoplasty after anatomical assessment of the RHV and IVC of the graft and recipient.
Advanced human carotid plaque progression correlates positively with flow shear stress using follow-up scan data: An in vivo MRI multi-patient 3D FSI study
C. Yang1,2, G.Canton3, C. Yuan3, M. Ferguson3, T.S. Hatsukami3,4, D. Tang2
1 School of Mathematical Sciences, Beijing Normal University, Lab of Math and Complex Systems, Ministry of Education, Beijing, China
Journal of Biomechanics, 43(13):2530-2538, 2010
Abstract: Although it has been well-accepted that atherosclerosis initiation and early progression correlate negatively with flow wall shear stresses (FSS), increasing evidence suggests mechanisms governing advanced plaque progression are not well understood. Fourteen patients were scanned 2–4 times at 18 month intervals using a histologically validated multi-contrast magnetic resonance imaging (MRI) protocol to acquire carotid plaque progression data. Thirty-two scan pairs (baseline and follow-up scans) were formed with slices matched for model construction and analysis. 3D fluid–structure interaction (FSI) models were constructed and plaque wall stress (PWS) and flow shear stress (FSS) were obtained from all matching lumen data points (400–1000 per plaque; 100 points per matched slice) to quantify correlations with plaque progression measured by vessel wall thickness increase (WTI). Using FSS and PWS data from follow-up scan, 21 out of 32 scan pairs showed a significant positive correlation between WTI and FSS (positive/negative/no significance ratio=21/8/3), and 26 out of 32 scan pairs showed a significant negative correlation between WTI and PWS (positive/negative/no significance ratio=2/26/4). The mean FSS value of lipid core nodes (n=5294) from all 47 plaque models was 63.5 dyn/cm2, which was 45% higher than that from all normal vessel nodes (n=27553, p<0.00001). The results from this intensive FSI study indicate that flow shear stress from follow-up scan correlates positively with advanced plaque progression which is different from what has been observed in plaque initiation and early-stage progression. It should be noted that the correlation results do not automatically lead to any causality conclusions.
Keywords: Plaque progression – Blood flow – Atherosclerosis – Plaque rupture – Fluid-structure interaction
Numerical investigation of the aerodynamic characteristics of a hovering Coleopteran insect
T.Q. Le1, D. Byun1, Saputra1, J.H. Ko1, H.Ch. Park2, M. Kim3
1 Department of Aerospace and Information Engineering, Konkuk University, Seoul, Republic of Korea
Journal of Theoretical Biology, 266:485–495, 2010
Abstract: The aerodynamic characteristics of the Coleopteran beetle species Epilachna quadricollis, a species with flexible hind wings and stiff elytra (fore wings), are investigated in terms of hovering flight. The flapping wing kinematics of the Coleopteran insect are modeled through experimental observations with a digital high-speed camera and curve fitting from an ideal harmonic kinematics model. This model numerically simulates flight by estimating a cross section of the wing as a two-dimensional elliptical plane. There is currently no detailed study on the role of the elytron or how the elytron–hind wing interaction affects aerodynamic performance. In the case of hovering flight, the relatively small vertical or horizontal forces generated by the elytron suggest that the elytron makes no significant contribution to aerodynamic force.
Keywords: Insect hovering flight - flapping – kinematics
Dynamic behavior of valve system in linear compressor based on fluid-structure interaction
Y. Choi1, J. Lee1, W. Jeong1, and I. Kim2
1 School of Mechanical Engineering, Pusan National University, 30 Jangjeon-dong, Geumjeong-gu, Pusan 609-735, Korea
Journal of Mechanical Science and Technology, 24(7):1371-1377, 2010
Abstract: In refrigerator designs, the linear compressor is preferable to the recipro-type compressor, due to its higher energy efficiency. The linear compressor’s valve system, however, causes significant noise, not only in the steady state but also in the transient state. To accurately predict the behavior of the suction and discharge valve system in both states, the interaction between the fluid flowing through the valves and the structural deformation of the valves needs to be understood. In the present study, the steady-state behaviors of the valve system were numerically analyzed using ADINA software, which takes fluid-structure interaction (FSI) into account. This computational
Keywords: Fluid-structure interaction - Linear compressor - Valve system - Dynamic behavior
Modelling and simulation of acoustic pulse interaction with a fluid-filled hollow elastic sphere through numerical Laplace inversion
S.M. Hasheminejad, A. Bahari, S. Abbasion
Acoustics Research Laboratory, Department of Mechanical Engineering, Iran University of Science and Technology, Narmak, Tehran 16844, Iran
Applied Mathematical Modelling, 35:22–49, 2010
A detailed study is undertaken to analyze the non-steady interaction of plane progressive pressure pulses with an isotropic, homogeneous, fluid-filled and submerged spherical elastic shell of arbitrary wall thickness within the scope of linear acoustics. The formulation is based on the general three dimensional equations of linear elasticity and the wave equation for the internal and external acoustic domains. The Laplace transform with respect to the time coordinate is invoked, and the classical method of separation of variables is used to obtain the transformed solutions in the form of partial-wave expansions in terms of Legendre polynomials. The inversion of Laplace transforms have been carried out numerically using Durbin’s approach based on Fourier series expansion. Special convergence enhancement techniques are invoked to completely eradicate spurious oscillations (Gibbs’ phenomenon), and obtain uniformly convergent solutions. Detailed numerical results for the transient and vibratory responses of water-submerged steel shells of selected wall thickness parameters with various internal fluid loadings under an exponential wave excitation are presented. Many of the interesting dynamic features in the transient shell–shock interaction such as shock transparency, shell-radiated negative pressure waves, formation of triple points, and focusing of the reflected waves are examined using appropriate 2D images of the internal pressure field. Also, the temporal behavior of the specularly-reflected, the lowest symmetric S0- and antisymmetric A0-Lamb waves, as well as appearance of the Franz’s creeping waves are discussed through proper visualization of the external scattered field. Likelihood of cavitation is addressed and regions proned to cavitation are identified. Moreover, the effects of internal fluid impedance in addition to shell wall thickness on the dynamic stress concentrations induced within the shell are analyzed. Limiting cases are considered and fair agreements with well-known solutions are established.
Keywords: Thick-walled sphere - Shock wave loading - 3D elasticity solution - Inverse Laplace transform - Sound field visualization - Lamb waves
Application of Computational Fluid Dynamics and Fluid–Structure Interaction Method to the Lubrication Study of a Rotor–Bearing System
H. Liu1,2, H. Xu1, P.J. Ellison2, Z. Jin2
1 Theory of Lubrication and Bearing Institute, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, China
Tribol. Lett., 38:325–336, 2010
Abstract: Computational methods were used to analyse the elasto-hydrodynamic lubrication of a complex rotor–bearing system. The methodology employed computational fluid dynamics (CFD), based on the Navier–Stokes equation and a fluid–structure interaction (FSI) technique. A series of models representing the system were built using the CFD–FSI methodology to investigate the interaction between the lubrication of the fluid film, and elastic dynamics of the rotor and journal bearing. All models followed an assumption of isothermal behaviour. The FSI methodology was implemented by setting nodal forces and displacements to equilibrium at the fluid–structure interface, therefore allowing the lubrication of the fluid and the elastic deformation of structures to be solved simultaneously. This is significantly different to the more common techniques—such as the Reynolds equation method—that use an iterative solution to balance the imposed load and the force resulting from the pressure of the fluid film to within a set tolerance. Predictions using the CFD–FSI method were compared with the results of an experimental study and the predictions from an ‘in-house’ lubrication code based on the Reynolds equation. The dynamic response of the system was investigated with both rigid and flexible bodies for a range of different bearing materials and dynamic unbalanced loads. Cavitation within the fluid film was represented in the CFD–FSI method using a simplified phase change boundary condition. This allowed the transition between the liquid and vapour phases to be derived from the lubricant’s properties as a function of pressure. The combination of CFD and FSI was shown to be a useful tool for the investigation of the hydrodynamic and elasto-hydrodynamic lubrications of a rotor–bearing system. The elastic deformation of the bearing and dynamic unbalanced loading of the rotor had significant effects on the position of its locus.
Keywords: Fluid–structure interaction - Computational fluid dynamics - Elasto-hydrodynamic lubrication - Rotor–bearing system -Dynamic unbalanced response
Respiration Simulation of Human Upper Airway for Analysis of Obstructive Sleep Apnea Syndrome
R. Huang and Q. Rong
College of Engineering, Peking University, Beijing 100871, P.R. China
LSMS/ICSEE 2010, LNBI 6330, pp. 588-596, 2010
Abstract: Obstructive sleep apnea syndrome (OSAS) is a disease that the pharyngeal portion collapses repeatedly during sleep and finally results in the cessation of breathing. So far the potential pathogenesis factors that may cause OSAS are discussed from two main aspects: anatomic abnormalities of the upper airway and the weak or absence of nerve control mechanism. In this study, a three-dimensional finite element model which possesses high geometrical similarity with the real anatomical structure is built. By making use of the pressure in upper airway measured in normal expiration and apnea episode, the fluid field in upper airway and the displacement of the soft tissue around the airway are calculated using fluid-structure coupled algorithm, and then the result between binormal respiration and apnea episode are compared. According to the result, the region where the maximum negative pressure and the largest displacement occur will be the most domains the airway collapses and breath apnea appears.
Keywords: OSAS - upper airway - fluid-structure interaction - FEM