Fluid–structure interaction simulations of patient-specific aortic dissection

Biomechanics and Modeling in Mechanobiology - Credible computational fluid dynamic (CFD) simulations of aortic dissection are challenging, because the defining parallel flow channels—the true...     

Fluid–structure interaction in aortic cross-clamping: Implications for vessel injury

Vascular cross-clamping is applied in many cardiovascular surgeries such as coronary bypass, aorta repair and valve procedures. Experimental studies have found that clamping of various degrees caused damage to arteries. This study examines the effects of popular clamps on vessel wall. Models of the aorta and clamp were created in Computer Assisted Design and Finite Element Analysis packages. The vessel wall was considered as a non-linear anisotropic material while the fluid was simulated as Newtonian with pulsatile flow. The clamp was applied through displacement time function. Fully coupled two-way solid–fluid interaction models were developed. It was found that the clamp design significantly affected the stresses in vessel wall. The clamp with a protrusion feature increased the overall Von Mises stress by about 60% and the compressive stress by more than 200%. Interestingly, when the protrusion clamp was applied, the Von Mises stress at the lumen (endothelium) side of artery wall was about twice that of the outer wall. This ratio was much higher than that of the plate-like clamp which was about 1.3. The flow reversal process was demonstrated during clamping. Vibrations, flow and wall shear stress oscillations were detected immediately before total vessel occlusion. The commonly used protrusion clamp increased stresses in vessel wall, especially the compressive stress. This design also significantly increased the stresses on endothelium, detrimental to vessel health. The present findings are relevant to surgical clamp design as well as the transient mechanical loading on the endothelium and potential injury. The deformation and stress analysis may provide valuable insights into the mode of tissue injury during cross-clamping.     

Fluid–structure interaction (FSI) modeling of bone marrow through trabecular bone structure under compression

Biomechanics and Modeling in Mechanobiology - The present study has sought to investigate the fluid characteristic and mechanical properties of trabecular bone using fluid–structure...     

Fluid–structure interaction analysis of turbulent pulsatile flow within a layered aortic wall as related to aortic dissection

Turbulent pulsatile flow and wall mechanics were studied numerically in an axisymmetric three-layered wall model of a descending aorta. The transport equations were solved using the finite element formulation based on the Galerkin method of weighted residuals. A fully-coupled fluid–structure interaction (FSI) analysis was utilized in this investigation. We calculated Von Mises wall stress, streamlines and fluid pressure contours. The findings of this study show that peak wall stress and maximum shear stress are highest in the media layer. The difference in the elastic properties of contiguous layers of the wall of the aorta probably determines the occurrence of dissection in the media layer. Moreover, the presence of aortic intramural hematoma is found to have a significant effect on the peak wall stress acting on the inner layer.     

Fluid–structure interaction analysis of the left coronary artery with variable angulation

The aim of this study is to elucidate the correlation between coronary artery branch angulation, local mechanical and haemodynamic forces at the vicinity of bifurcation. Using a coupled fluid–structure interaction (FSI) modelling approach, five idealized left coronary artery models with various angles ranging from 70° to 110° were developed to investigate the influence of branch angulations. In addition, one CT image-based model was reconstructed to further demonstrate the medical application potential of the proposed FSI coupling method. The results show that the angulation strongly alters its mechanical stress distribution, and the instantaneous wall shear stress distributions are substantially moderated by the arterial wall compliance. As high tensile stress is hypothesized to cause stenosis, the left circumflex side bifurcation shoulder is indicated to induce atherosclerotic changes with a high tendency for wide-angled models.     

Fluid–structure interaction simulation of the brain–skull interface for acute subdural haematoma prediction

Traumatic brain injury is a leading cause of disability and mortality. Finite element-based head models are promising tools for enhanced head injury prediction, mitigation and prevention. The reliability of such models depends heavily on adequate representation of the brain–skull interaction. Nevertheless, the brain–skull interface has been largely simplified in previous three-dimensional head models without accounting for the fluid behaviour of the cerebrospinal fluid (CSF) and its mechanical interaction with the brain and skull. In this study, the brain–skull interface in a previously developed head model is modified as a fluid–structure interaction (FSI) approach, in which the CSF is treated on a moving mesh using an arbitrary Lagrangian–Eulerian multi-material formulation and the brain on a deformable mesh using a Lagrangian formulation. The modified model is validated against brain–skull relative displacement and intracranial pressure responses and subsequently imposed to an experimentally determined loading known to cause acute subdural haematoma (ASDH). Compared to the original model, the modified model achieves an improved validation performance in terms of brain–skull relative motion and is able to predict the occurrence of ASDH more accurately, indicating the superiority of the FSI approach for brain–skull interface modelling. The introduction of the FSI approach to represent the fluid behaviour of the CSF and its interaction with the brain and skull is crucial for more accurate head injury predictions.

     

The effect of the entry and re-entry size in the aortic dissection: a two-way fluid–structure interaction simulation

Biomechanics and Modeling in Mechanobiology - Aortic dissection (AD) is one of the most catastrophic cardiovascular diseases. AD occurs when a layer inside the aorta is disrupted and gives rise to...     

Probing the structure of Leishmania donovani chagasi DHFR-TS: comparative protein modeling and protein–ligand interaction studies

Dihydrofolate reductase (DHFR) has been used successfully as a drug target in the area of anti-bacterial, anti-cancer and anti-malarial therapy. It also acts as a drug target for Leishmaniasis. Inhibition of DHFR leads to cell death through lack of thymine (nucleotide metabolism). Although the crystal structures of Leishmania major and Trypanosoma cruzi DHFR-thymidylate synthase (TS) have been resolved, to date there is no three-dimensional (3D)-structural information on DHFR-TS of Leishmania donovani chagasi, which causes visceral leishmaniasis. Our aim in this study was to model the 3D structure of L. donovani chagasi DHFR-TS, and to investigate the structural requirements for its inhibition. In this paper we describe a highly refined homology model of L. donovani chagasi DHFR-TS based on available crystallographic structures by using the Homology module of Insight II. Structural refinement and minimization of the generated L. donovani chagasi DHFR-TS model employed the Discover 3 module of Insight II and molecular dynamic simulations. The model was further validated through use of the PROCHECK, Verify_3D, PROSA, PSQS and ERRAT programs, which confirm that the model is reliable. Superimposition of the model structure with the templates L. major A chain, L. major B chain And T. cruzi A chain showed root mean square deviations of 0.69 Å, 0.71 Å and 1.11 Å, respectively. Docking analysis of the L. donovani chagasi DHFR-TS model with methotrexate enabled us to identify specific residues, viz. Val156, Val30, Lys95, Lys75 and Arg97, within the L. donovani chagasi DHFR-TS binding pocket, that play an important role in ligand or substrate binding. Docking studies clearly indicated that these five residues are important determinants for binding as they have strong hydrogen bonding interactions with the ligand.     

Systolic fluid–structure interaction model of the congenitally bicuspid aortic valve: assessment of modelling requirements

A transient fluid–structure interaction (FSI) model of a congenitally bicuspid aortic valve has been developed which allows simultaneous calculation of fluid flow and structural deformation. The valve is modelled during the systolic phase (the stage when blood pressure is elevated within the heart to pump blood to the body). The geometry was simplified to represent the bicuspid aortic valve in two dimensions. A congenital bicuspid valve is compared within the aortic root only and within the aortic arch. Symmetric and asymmetric cusps were simulated, along with differences in mechanical properties. A moving arbitrary Lagrange–Euler mesh was used to allow FSI. The FSI model requires blood flow to induce valve opening and induced strains in the region of 10%. It was determined that bicuspid aortic valve simulations required the inclusion of the ascending aorta and aortic arch. The flow patterns developed were sensitive to cusp asymmetry and differences in mechanical properties. Stiffening of the valve amplified peak velocities, and recirculation which developed in the ascending aorta. Model predictions demonstrate the need to take into account the category, including any existing cusp asymmetry, of a congenital bicuspid aortic valve when simulating its fluid flow and mechanics.     

Thermal analysis of the dentine tubule under hot and cold stimuli using fluid–structure interaction simulation

The objective of this study is to compare the thermal stress changes in the tooth microstructures and the hydrodynamic changes of the dental fluid under hot and cold stimuli. The dimension of the microstructures of eleven cats’ teeth was measured by scanning electron microscopy, and the changes in thermal stress during cold and hot stimulation were calculated by 3D fluid–structure interaction modeling. Evaluation of results, following data validation, indicated that the maximum velocities in cold and hot stimuli were ??410.2?±?17.6 and +?205.1?±?8.7 µm/s, respectively. The corresponding data for maximum thermal stress were ??20.27?±?0.79 and +?10.13?±?0.24 cmHg, respectively. The thermal stress caused by cold stimulus could influence almost 2.9 times faster than that caused by hot stimulus, and the durability of the thermal stress caused by hot stimulus was 71% greater than that by cold stimulus under similar conditions. The maximum stress was on the tip of the odontoblast, while the stress in lateral walls of the odontoblast and terminal fibril was very weak. There is hence a higher possibility of pain transmission with activation of stress-sensitive ion channels at the tip of the odontoblast. The maximum thermal stress resulted from the cold stimulus is double that produced by the hot stimulus. There is a higher possibility of pain transmission in the lateral walls of the odontoblast and terminal fibril by releasing mediators during the cold stimulation than the hot stimulation. These two reasons can be associated with a greater pain sensation due to intake of cold liquids.     

Modulation of the albumin–paraoxon interaction sites by fatty acids: Analysis by the molecular modeling methods

It is known that albumin can break the ester bonds in organophosphorus compounds (OPs). Amino acids responsible for esterase and pseudoesterase activity of albumin towards OPs are still not determined. It is assumed that Sudlow’s site I with residue Tyr150 exhibits the “true” esterase activity; and Sudlow’s site II containing residue Tyr411, a pseudoesterase one. Binding of fatty acids to albumin affects the efficiency of its interaction with xenobiotics; however, the effect of fatty acids on the interaction of albumin with OPs was not studied. The purpose of this work was to study the interaction of OPs with potential sites of albumin enzymatic activity and to examine the effect of fatty acids on the efficiency of such interaction using the molecular modeling methods by the example of paraoxon, a known inhibitor of acetylcholinesterase, and oleic acid. The structures of the protein complexes with paraoxon and oleic acid were determined by the molecular docking procedure; the conformational changes were calculated by the molecular dynamics method. It has been shown that sorption of oleic acid in one of the fatty acid-binding sites leads to the conformational changes in Sudlow’s sites I and II due to a “reversal” of the side chains of Arg410 and Arg257 residues by 90°. It has been found that this change in geometry reduces the affinity of Sudlow’s site I and increases the Sudlow’s site II affinity to paraoxon. The amino acid residue Ser193, which was previously identified as a site of possible albumin esterase activity, is not able to bind paraoxon efficiently. It is assumed that its activity can be affected by the interaction of the oleic acid molecules with other fatty acid-binding sites. It is hypothesized that the lesser toxicity of paraoxon compared to soman may be associated not only with its lower inhibitory activity against cholinesterases, but also with the increased affinity of paraoxon to albumin. It was concluded that albumin may serve as an alternative means of OP detoxification.     

Numerical simulation of fluid–structure interaction in bypassed DeBakey III aortic dissection

It was found that bypass graft alone could achieve great effects in treating aortic dissection. In order to investigate the mechanical mechanism and the haemodynamic validity of the bypassing treatment for DeBakey III aortic dissection, patient-specific models of DeBakey III aortic dissection treated with different bypassing strategies were constructed. One of the bypassing strategies is bypassing between ascending aorta and abdominal aorta, and the other is bypassing between left subclavian artery and abdominal aorta. Numerical simulations under physiological flow conditions based on fluid–structure interaction were performed using finite element method. The results show that blood flow velocity, pressure and vessel wall displacement of false lumen are all reduced after bypassing. This phenomenon indicates that bypassing is an effective surgery for the treatment of DeBakey III aortic dissection. The effectiveness to cure through lumen is better when bypassing between left subclavian artery and abdominal aorta, while the effectiveness to cure blind lumen is better when bypassing between ascending aorta and abdominal aorta.     

Fluid flow in the osteocyte mechanical environment: a fluid–structure interaction approach

Osteocytes are believed to be the primary sensor of mechanical stimuli in bone, which orchestrate osteoblasts and osteoclasts to adapt bone structure and composition to meet physiological loading demands. Experimental studies to quantify the mechanical environment surrounding bone cells are challenging, and as such, computational and theoretical approaches have modelled either the solid or fluid environment of osteocytes to predict how these cells are stimulated in vivo. Osteocytes are an elastic cellular structure that deforms in response to the external fluid flow imposed by mechanical loading. This represents a most challenging multi-physics problem in which fluid and solid domains interact, and as such, no previous study has accounted for this complex behaviour. The objective of this study is to employ fluid–structure interaction (FSI) modelling to investigate the complex mechanical environment of osteocytes in vivo. Fluorescent staining of osteocytes was performed in order to visualise their native environment and develop geometrically accurate models of the osteocyte in vivo. By simulating loading levels representative of vigorous physiological activity ( $3,000\,\upmu \upvarepsilon $ compression and 300 Pa pressure gradient), we predict average interstitial fluid velocities $(\sim 60.5\,\upmu \text{ m/s })$ and average maximum shear stresses $(\sim 11\, \text{ Pa })$ surrounding osteocytes in vivo. Interestingly, these values occur in the canaliculi around the osteocyte cell processes and are within the range of stimuli known to stimulate osteogenic responses by osteoblastic cells in vitro. Significantly our results suggest that the greatest mechanical stimulation of the osteocyte occurs in the cell processes, which, cell culture studies have indicated, is the most mechanosensitive area of the cell. These are the first computational FSI models to simulate the complex multi-physics mechanical environment of osteocyte in vivo and provide a deeper understanding of bone mechanobiology.     

An anisotropic constitutive model for immersogeometric fluid–structure interaction analysis of bioprosthetic heart valves

This paper considers an anisotropic hyperelastic soft tissue model, originally proposed for native valve tissue and referred to herein as the Lee–Sacks model, in an isogeometric thin shell analysis framework that can be readily combined with immersogeometric fluid–structure interaction (FSI) analysis for high-fidelity simulations of bioprosthetic heart valves (BHVs) interacting with blood flow. We find that the Lee–Sacks model is well-suited to reproduce the anisotropic stress–strain behavior of the cross-linked bovine pericardial tissues that are commonly used in BHVs. An automated procedure for parameter selection leads to an instance of the Lee–Sacks model that matches biaxial stress–strain data from the literature more closely, over a wider range of strains, than other soft tissue models. The relative simplicity of the Lee–Sacks model is attractive for computationally-demanding applications such as FSI analysis and we use the model to demonstrate how the presence and direction of material anisotropy affect the FSI dynamics of BHV leaflets.     

An integrated fluid–structure interaction and thrombosis model for type B aortic dissection

False lumen thrombosis (FLT) in type B aortic dissection has been associated with the progression of dissection and treatment outcome. Existing computational models mostly assume rigid wall behavior which ignores the effect of flap motion on flow and thrombus formation within the FL. In this study, we have combined a fully coupled fluid–structure interaction (FSI) approach with a shear-driven thrombosis model described by a series of convection–diffusion reaction equations. The integrated FSI-thrombosis model has been applied to an idealized dissection geometry to investigate the interaction between vessel wall motion and growing thrombus. Our simulation results show that wall compliance and flap motion can influence the progression of FLT. The main difference between the rigid and FSI models is the continuous development of vortices near the tears caused by drastic flap motion up to 4.45 mm. Flap-induced high shear stress and shear rates around tears help to transport activated platelets further to the neighboring region, thus speeding up thrombus formation during the accelerated phase in the FSI models. Reducing flap mobility by increasing the Young’s modulus of the flap slows down the thrombus growth. Compared to the rigid model, the predicted thrombus volume is 25% larger using the FSI-thrombosis model with a relatively mobile flap. Furthermore, our FSI-thrombosis model can capture the gradual effect of thrombus growth on the flow field, leading to flow obstruction in the FL, increased blood viscosity and reduced flap motion. This model is a step closer toward simulating realistic thrombus growth in aortic dissection, by taking into account the effect of intimal flap and vessel wall motion.

     

Fluid–structure interactions in micro-interlocked regions of the cement–bone interface

Experimental tests and computational modelling were used to explore the fluid dynamics at the trabeculae–cement interlock regions found in the tibial component of total knee replacements. A cement–bone construct of the proximal tibia was created to simulate the immediate post-operative condition. Gap distributions along nine trabeculae–cement regions ranged from 0 to 50.4 μm (mean = 12 μm). Micro-motions ranged from 0.56 to 4.7 μm with a 1 MPa compressive load to the cement. Fluid–structure analysis between the trabeculae and the cement used idealised models with parametric evaluation of loading direction, gap closing fraction (GCF), gap thickness, loading frequency and fluid viscosity. The highest fluid shear stresses (926 Pa) along the trabecular surface were found for conditions with very thin and large GCFs, much larger than reported physiological levels (～1–5 Pa). A second fluid–structure model was created with a provision for bone resorption using a constitutive model with resorption velocity proportional to fluid shear rate. A lower cut-off was used, below which bone resorption would not occur (50 s^? 1). Results showed that there was initially high shear rates (>1000 s^? 1) that diminished after initial trabecular resorption. Resorption continued in high shear rate regions, resulting in a final shape with bone left deep in the cement layer, and is consistent with morphology found in post-mortem retrievals. Small gaps between the trabecular surface and the cement in the immediate post-operative state produce fluid flow conditions that appear to be supra-physiologic; these may cause fluid-induced lysis of trabeculae in the micro-interlock regions.     

Numerical evaluation of transcatheter aortic valve performance during heart beating and its post-deployment fluid–structure interaction analysis

Biomechanics and Modeling in Mechanobiology - Transcatheter aortic valve replacement (TAVR) is a minimally invasive procedure that provides an effective alternative to open-heart surgical valve...     

Modeling of the structure of protein–DNA complexes using the data from FRET and footprinting experiments

We discuss the question of constructing three-dimensional models of DNA in complex with proteins using computer modeling and indirect methods of studying the conformation of macromolecules. We consider the methods of interpreting the experimental data obtained by indirect methods of studying the three-dimensional structure of biomolecules. We discuss some aspects of integrating such data into the process of constructing the molecular models of DNA–protein complexes based on the geometric characteristics of DNA. We propose an algorithm for estimating conformations of such complexes based on the information about the local flexibility of DNA and on the experimental data obtained by Forster resonance energy transfer (FRET) and hydroxyl footprinting. Finally, we use this algorithm to predict the hypothetical configuration of DNA in a nucleosome bound with histone H1.     

Comparison between Generalized-Born and Poisson–Boltzmann methods in physics-based scoring functions for protein structure prediction

Continuum solvent models such as Generalized-Born and Poisson–Boltzmann methods hold the promise to treat solvation effect efficiently and to enable rapid scoring of protein structures when they are combined with physics-based energy functions. Yet, direct comparison of these two approaches on large protein data set is lacking. Building on our previous work with a scoring function based on a Generalized-Born (GB) solvation model, and short molecular-dynamics simulations, we further extended the scoring function to compare with the MM-PBSA method to treat the solvent effect. We benchmarked this scoring function against seven publicly available decoy sets. We found that, somewhat surprisingly, the results of MM-PBSA approach are comparable to the previous GB-based scoring function. We also discussed the effect to the scoring function accuracy due to presence of large ligands and ions in some native structures of the decoy sets.