Design of a mechanical larynx with agarose as a soft tissue substitute for vocal fold applications

Mechanical and computational models consisting of flow channels with convergent and oscillating constrictions have been applied to study the dynamics of human vocal fold vibration. To the best of our knowledge, no mechanical model has been studied using a material substitute with similar physical properties to the human vocal fold for surgical experimentation. In this study, we design and develop a mechanical larynx with agarose as a vocal fold substitute, and assess its suitability for surgical experimentation. Agarose is selected as a substitute for the vocal fold as it exhibits similar nonlinear hyperelastic characteristics to biological soft tissue. Through uniaxial compression and extension tests, we determined that agarose of 0.375% concentration most closely resembles the vocal fold mucosa and ligament of a 20-year old male for small tensile strain with an R(2) value of 0.9634 and root mean square error of 344.05±39.84?Pa. Incisions of 10 mm lengthwise and 3 mm in depth were created parallel to the medial edge on the superior surface of agar phantom. These were subjected to vibrations of 80, 130, and 180 Hz, at constant amplitude of 0.9 mm over a period of 10 min each in the mechanical larynx model. Lateral expansion of the incision was observed to be most significant for the lower frequency of 80 Hz. This model serves as a basis for future assessments of wound closure techniques during microsurgery to the vocal fold.     

Synthetic,Multi-Layer,Self-Oscillating Vocal Fold Model Fabrication

Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties ¹. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone ² and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders.Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes).Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry ^3,4, clinical instrument development ⁵, laryngeal aerodynamics ^6-9, vocal fold contact pressure ¹⁰, and subglottal acoustics ¹¹ (a more comprehensive list can be found in Kniesburges et al. ¹²)Existing synthetic vocal fold models, however, have either been homogenous (one-layer models) or have been fabricated using two materials of differing stiffness (two-layer models). This approach does not allow for representation of the actual multi-layer structure of the human vocal folds ¹ that plays a central role in governing vocal fold flow-induced vibratory response. Consequently, one- and two-layer synthetic vocal fold models have exhibited disadvantages ^3,6,8 such as higher onset pressures than what are typical for human phonation (onset pressure is the minimum lung pressure required to initiate vibration), unnaturally large inferior-superior motion, and lack of a "mucosal wave" (a vertically-traveling wave that is characteristic of healthy human vocal fold vibration).In this paper, fabrication of a model with multiple layers of differing material properties is described. The model layers simulate the multi-layer structure of the human vocal folds, including epithelium, superficial lamina propria (SLP), intermediate and deep lamina propria (i.e., ligament; a fiber is included for anterior-posterior stiffness), and muscle (i.e., body) layers ¹. Results are included that show that the model exhibits improved vibratory characteristics over prior one- and two-layer synthetic models, including onset pressure closer to human onset pressure, reduced inferior-superior motion, and evidence of a mucosal wave.     

Influence of asymmetric stiffness on the structural and aerodynamic response of synthetic vocal fold models

The influence of asymmetric vocal fold stiffness on voice production was evaluated using life-sized, self-oscillating vocal fold models with an idealized geometry based on the human vocal folds. The models were fabricated using flexible, materially-linear silicone compounds with Young's modulus values comparable to that of vocal fold tissue. The models included a two-layer design to simulate the vocal fold layered structure. The respective Young's moduli of elasticity of the “left” and “right” vocal fold models were varied to create asymmetric conditions. High-speed videokymography was used to measure maximum vocal fold excursion, vibration frequency, and left–right phase shift, all of which were significantly influenced by asymmetry. Onset pressure, a measure of vocal effort, increased with asymmetry. Particle image velocimetry (PIV) analysis showed significantly greater skewing of the glottal jet in the direction of the stiffer vocal fold model. Potential applications to various clinical conditions are mentioned, and suggestions for future related studies are presented.     

Optimization of 3D Poisson–Nernst‐Planck model for fast evaluation of diverse protein channels

We show the accuracy and applicability of our fast algorithmic implementation of a three‐dimensional Poisson–Nernst–Planck (3D‐PNP) flow model for characterizing different protein channels. Due to its high computational efficiency, our model can predict the full current‐voltage characteristics of a channel within minutes, based on the experimental 3D structure of the channel or its computational model structure. Compared with other methods, such as Brownian dynamics, which currently needs a few weeks of the computational time, or even much more demanding molecular dynamics modeling, 3D‐PNP is the only available method for a function‐based evaluation of very numerous tentative structural channel models. Flow model tests of our algorithm and its optimal parametrization are provided for five native channels whose experimental structures are available in the protein data bank (PDB) in an open conductive state, and whose experimental current‐voltage characteristics have been published. The channels represent very different geometric and structural properties, which makes it the widest test to date of the accuracy of 3D‐PNP on real channels. We test whether the channel conductance, rectification, and charge selectivity obtained from the flow model, could be sufficiently sensitive to single‐point mutations, related to unsignificant changes in the channel structure. Our results show that the classical 3D‐PNP model, under proper parametrization, is able to achieve a qualitative agreement with experimental data for a majority of the tested characteristics and channels, including channels with narrow and irregular conductivity pores. We propose that although the standard PNP model cannot provide insight into complex physical phenomena due to its intrinsic limitations, its semiquantitative agreement is achievable for rectification and selectivity at a level sufficient for the bioinformatical purpose of selecting the best structural models with a great advantage of a very short computational time. Proteins 2013; 81:1802–1822. © 2013 Wiley Periodicals, Inc.     

Investigating the Three-dimensional Flow Separation Induced by a Model Vocal Fold Polyp

The fluid-structure energy exchange process for normal speech has been studied extensively, but it is not well understood for pathological conditions. Polyps and nodules, which are geometric abnormalities that form on the medial surface of the vocal folds, can disrupt vocal fold dynamics and thus can have devastating consequences on a patient''s ability to communicate. Our laboratory has reported particle image velocimetry (PIV) measurements, within an investigation of a model polyp located on the medial surface of an in vitro driven vocal fold model, which show that such a geometric abnormality considerably disrupts the glottal jet behavior. This flow field adjustment is a likely reason for the severe degradation of the vocal quality in patients with polyps. A more complete understanding of the formation and propagation of vortical structures from a geometric protuberance, such as a vocal fold polyp, and the resulting influence on the aerodynamic loadings that drive the vocal fold dynamics, is necessary for advancing the treatment of this pathological condition. The present investigation concerns the three-dimensional flow separation induced by a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, i.e. a model vocal fold polyp, using an oil-film visualization technique. Unsteady, three-dimensional flow separation and its impact of the wall pressure loading are examined using skin friction line visualization and wall pressure measurements.     

Geometry of human vocal folds and glottal channel for mathematical and biomechanical modeling of voice production

Current models of the vocal folds derive their shape from approximate information rather than from exactly measured data. The objective of this study was to obtain detailed measurements on the geometry of human vocal folds and the glottal channel in phonatory position. A non-destructive casting methodology was developed to capture the vocal fold shape from excised human larynges on both medial and superior surfaces. Two female larynges, each in two different phonatory configurations corresponding to low and high fundamental frequency of the vocal fold vibrations, were measured. A coordinate measuring machine was used to digitize the casts yielding 3D computer models of the vocal fold shape. The coronal sections were located in the models, extracted and fitted by piecewise-defined cubic functions allowing a mathematical expression of the 2D shape of the glottal channel. Left-right differences between the cross-sectional shapes of the vocal folds were found in both the larynges.     

Mechanical stress during phonation in a self-oscillating finite-element vocal fold model

The stress information during phonation in the vocal folds is helpful in understanding the etiologies of vocal trauma and its related vocal diseases, such as nodules. In this paper, a self-oscillating finite-element model, which combines aerodynamic properties, tissue mechanics, airflow-tissue interactions, and vocal fold collisions, was used to simulate the vocal fold vibration during phonation. The spatial and temporal characteristics of mechanical stress in the vocal folds were predicted by this model. Temporally, it was found that mechanical stress periodically undulates with vibration of the vocal folds and that vocal fold impact causes a jump in the normal stress value. Spatially, the normal stress is significantly higher on the vocal fold surface than inside of the vocal folds. At the midpoint of the medial surface, the peak-to-peak amplitude of the normal stress reaches its maximum value. Using different lung pressures (0-1.5kPa) to drive the self-oscillating model, we found that lower lung pressure can effectively decrease the mechanical stress in the vocal folds. This study supports the fatigue damage hypothesis of vocal trauma. With this hypothesis and the numerical simulation in this study, the clinical observations of vocal fold trauma risk can be explained. This implies the mechanical stress predicted by this self-oscillating model could be valuable for predicting, preventing, and treating vocal fold injury.     

Modeling mechanical stresses as a factor in the etiology of benign vocal fold lesions

Vocal fold tissue lesions such as nodules and polyps are thought to develop in response to mechanical stress that occurs during vocal fold collision. Two computational models of vocal fold collision during voice production are used to investigate this hypothesis. A one-dimensional lumped mass model, whose parameters are derived from vocal fold tissue dimensions and material properties, predicts stress perpendicular to the direction of impact (normal stress). A previously published three-dimensional finite element model that incorporates the same dimensions and properties predicts the entire stress tensor. The hypothesis is supported by predictions from the finite element model that three components of normal stress and one component of shear stress are increased during collision in the typical location of lesions (i.e. the center of the superior medial edge of the vocal fold in the middle of the vibrating and contact region). The lumped mass model predicts that mechanical stress is negatively correlated with mucosal thickness (increased by voice warm-up and hydration), is positively correlated with driving force (proportional to voice intensity), and is affected by voice production method. These relationships are consistent with clinical observations of vocal fold lesion risk factors and have implications for improving prevention and treatment of benign vocal fold lesions.     

Numerical analysis and comparison of flow fields in normal larynx and larynx with unilateral vocal fold paralysis

In this study, laryngeal flow fields are investigated and compared in normal larynx and models of larynx with unilateral vocal fold paralysis (UVFP). In paralytic models, three fixed initial glottal gaps are considered to understand the positive or probable negative impacts of surgical operation on unilaterally paralytic larynx, by which the paralyzed vocal fold is brought closer to the mid-plane. Various features of the flow fields have been discussed in detail including glottal gap width, glottal flow rate, glottal exit pressure pattern and glottal jet evolution. The numerical solution of fluid-structure interaction is carried out using ANSYS, and the results confirm some of the favorable effects of surgery on the patient’s larynx. It is also shown that by tightening the glottal gap, some of the problems caused by the presence of a motionless vocal fold, such as leakage through glottal gap in the closure phase resulting in breathy voice can be moderated, although some of the symptoms of this disorder remain relatively unchanged.     

The effects of the false vocal fold gaps on intralaryngeal pressure distributions and their effects on phonation

Human phonation does not merely depend on the vibration of the vocal folds. Research by clinical and computer simulations has demonstrated that the false vocal fold (FVF) is an important laryngeal con-striction that plays a vital role during human voice production. This study explored the effects of the FVF gaps using both the three-dimensional Plexiglas model and the numerical computation methods. Twelve FVF gaps (ranging from 0.02 to 2.06 cm) were used in this study at three glottal angles (uniform and convergent/divergent 40°), two minimal glottal diameters (Dg) (0.04 cm and 0.06 cm) separately, and the constant subglottal pressure (8 cm H2O). The results suggested that (1) the intralaryngeal pressure was the lowest and the flow was the highest (least flow resistance) when the FVF gap was 1.5-2 times greater than Dg; (2) the divergent glottal angle gave lower pressure and greater flow than the conver-gent and uniform glottal angle as there were no FVF conditions; (3) the presence of the FVF decreased the effects of the glottal angle to a certain extent; and more importantly, (4) the presence of the FVF also moved the separation points downstream, straightened the glottal jet for a longer distance, decreased the overall laryngeal resistance, and reduced the energy dissipation, suggesting the significance of FVF in efficient voice production. These results may be incorporated in the phonatory models (physical or computational) for better understanding of vocal mechanics. The results might also be helpful in exploring the surgical and rehabilitative intervention of related voice problems.     

LaDIVA: A neurocomputational model providing laryngeal motor control for speech acquisition and production

Many voice disorders are the result of intricate neural and/or biomechanical impairments that are poorly understood. The limited knowledge of their etiological and pathophysiological mechanisms hampers effective clinical management. Behavioral studies have been used concurrently with computational models to better understand typical and pathological laryngeal motor control. Thus far, however, a unified computational framework that quantitatively integrates physiologically relevant models of phonation with the neural control of speech has not been developed. Here, we introduce LaDIVA, a novel neurocomputational model with physiologically based laryngeal motor control. We combined the DIVA model (an established neural network model of speech motor control) with the extended body-cover model (a physics-based vocal fold model). The resulting integrated model, LaDIVA, was validated by comparing its model simulations with behavioral responses to perturbations of auditory vocal fundamental frequency (f_o) feedback in adults with typical speech. LaDIVA demonstrated capability to simulate different modes of laryngeal motor control, ranging from short-term (i.e., reflexive) and long-term (i.e., adaptive) auditory feedback paradigms, to generating prosodic contours in speech. Simulations showed that LaDIVA’s laryngeal motor control displays properties of motor equivalence, i.e., LaDIVA could robustly generate compensatory responses to reflexive vocal f_o perturbations with varying initial laryngeal muscle activation levels leading to the same output. The model can also generate prosodic contours for studying laryngeal motor control in running speech. LaDIVA can expand the understanding of the physiology of human phonation to enable, for the first time, the investigation of causal effects of neural motor control in the fine structure of the vocal signal.     

Improving sequence-based fold recognition by using 3D model quality assessment

MOTIVATION: The ability of a simple method (MODCHECK) to determine the sequence-structure compatibility of a set of structural models generated by fold recognition is tested in a thorough benchmark analysis. Four Model Quality Assessment Programs (MQAPs) were tested on 188 targets from the latest LiveBench-9 automated structure evaluation experiment. We systematically test and evaluate whether the MQAP methods can successfully detect native-like models. RESULTS: We show that compared with the other three methods tested MODCHECK is the most reliable method for consistently performing the best top model selection and for ranking the models. In addition, we show that the choice of model similarity score used to assess a model's similarity to the experimental structure can influence the overall performance of these tools. Although these MQAP methods fail to improve the model selection performance for methods that already incorporate protein three dimension (3D) structural information, an improvement is observed for methods that are purely sequence-based, including the best profile-profile methods. This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information. CONTACT: d.jones@cs.ucl.ac.uk     

3D reconstruction of the pelvis from bi-planar radiography

3D personalized models are more and more requested for clinical and biomechanical studies. Techniques based on bi-planar X-rays present the advantage of a low radiation dose for the patient. However, up to now, such techniques have shown limited accuracy in the case of pelvis reconstruction. This study proposes and validates a method providing accurate 3D personalized model of the pelvis from bi-planar X-rays. The algorithm is based on the fast computation of an initial solution followed by local deformations based on 2D anatomical points and contours that are digitized in both radiographs. Results were close to CT-scan reconstructions (mean difference 1.6 mm and differences under 4.3 mm for 95% of the points). Moreover, 3D morphometry of the pelvis could be obtained with an accuracy of 5%. This technique provides 3D patient specific model with a low radiation dose.     

Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species

Vocal folds are used as sound sources in various species, but it is unknown how vocal fold morphologies are optimized for different acoustic objectives. Here we identify two main variables affecting range of vocal fold vibration frequency, namely vocal fold elongation and tissue fiber stress. A simple vibrating string model is used to predict fundamental frequency ranges across species of different vocal fold sizes. While average fundamental frequency is predominantly determined by vocal fold length (larynx size), range of fundamental frequency is facilitated by (1) laryngeal muscles that control elongation and by (2) nonlinearity in tissue fiber tension. One adaptation that would increase fundamental frequency range is greater freedom in joint rotation or gliding of two cartilages (thyroid and cricoid), so that vocal fold length change is maximized. Alternatively, tissue layers can develop to bear a disproportionate fiber tension (i.e., a ligament with high density collagen fibers), increasing the fundamental frequency range and thereby vocal versatility. The range of fundamental frequency across species is thus not simply one-dimensional, but can be conceptualized as the dependent variable in a multi-dimensional morphospace. In humans, this could allow for variations that could be clinically important for voice therapy and vocal fold repair. Alternative solutions could also have importance in vocal training for singing and other highly-skilled vocalizations.     

Modeling viscous dissipation during vocal fold contact: the influence of tissue viscosity and thickness with implications for hydration

The mechanics of vocal fold contact during phonation is known to play a crucial role in both normal and pathological speech production, though the underlying physics is not well understood. Herein, a viscoelastic model of the stresses during vocal fold contact is developed. This model assumes the cover to be a poroelastic structure wherein interstitial fluid translocates in response to mechanical squeezing. The maximum interstitial fluid pressure is found to generally increase with decreasing viscous dissipation and/or decreasing tissue elasticity. A global minimum in the total contact stress, comprising interstitial fluid pressure and elastic stress in the tissue, is observed over the studied dimensionless parameter range. Interestingly, physiologically reasonable estimates for the governing parameters fall within this global minimum region. The model is validated against prior experimental and computational work, wherein the predicted contact stress magnitude and impact duration agree well with published results. Lastly, observations of the potential relationship between vocal fold hydration and increased risk of tissue damage are discussed based upon model predictions of stress as functions of cover layer thickness and viscosity.     

Development of novel statistical potentials for protein fold recognition

The need to perform large-scale studies of protein fold recognition, structure prediction and protein-protein interactions has led to novel developments of residue-level minimal models of proteins. A minimum requirement for useful protein force-fields is that they be successful in the recognition of native conformations. The balance between the level of detail in describing the specific interactions within proteins and the accuracy obtained using minimal protein models is the focus of many current protein studies. Recent results suggest that the introduction of explicit orientation dependence in a coarse-grained, residue-level model improves the ability of inter-residue potentials to recognize the native state. New statistical and optimization computational algorithms can be used to obtain accurate residue-dependent potentials for use in protein fold recognition and, more importantly, structure prediction.     

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem

Background  

The protein folding problem is a fundamental problems in computational molecular biology and biochemical physics. Various optimisation methods have been applied to formulations of the ab-initio folding problem that are based on reduced models of protein structure, including Monte Carlo methods, Evolutionary Algorithms, Tabu Search and hybrid approaches. In our work, we have introduced an ant colony optimisation (ACO) algorithm to address the non-deterministic polynomial-time hard (NP-hard) combinatorial problem of predicting a protein's conformation from its amino acid sequence under a widely studied, conceptually simple model – the 2-dimensional (2D) and 3-dimensional (3D) hydrophobic-polar (HP) model.