Browsing by Author "Pendar, Hodjat"

Now showing 1 - 9 of 9
  • Thumbnail Image
    Computational tools for inversion and uncertainty estimation in respirometry
    Cho, Taewon; Pendar, Hodjat; Chung, Julianne (PLoS, 2021-05-21)
    In many physiological systems, real-time endogeneous and exogenous signals in living organisms provide critical information and interpretations of physiological functions; however, these signals or variables of interest are not directly accessible and must be estimated from noisy, measured signals. In this paper, we study an inverse problem of recovering gas exchange signals of animals placed in a flow-through respirometry chamber from measured gas concentrations. For large-scale experiments (e.g., long scans with high sampling rate) that have many uncertainties (e.g., noise in the observations or an unknown impulse response function), this is a computationally challenging inverse problem. We first describe various computational tools that can be used for respirometry reconstruction and uncertainty quantification when the impulse response function is known. Then, we address the more challenging problem where the impulse response function is not known or only partially known. We describe nonlinear optimization methods for reconstruction, where both the unknown model parameters and the unknown signal are reconstructed simultaneously. Numerical experiments show the benefits and potential impacts of these methods in respirometry.
  • Thumbnail Image
    Effect of Kinematics and Caudal Fin Properties on Performance of a Freely-Swimming Fin
    Nayak, Anshul (Virginia Tech, 2020-12-23)
    Traditionally, underwater vehicles have been using propellers for locomotion but they are not only inefficient but generate large acoustic signature. Researchers have taken inspiration from efficient swimmers like fish to address the issue with alternate propulsion mechanism. Mostly, research on fish locomotion involved studying a foil tethered to a fixed point inside uniform flow. A major drawback of such study is that neither it resembles a freely swimming fish nor it takes into consideration the dynamics of moving fish on propulsive forces. Hence, in our current study, we focus on comparing the performance of a free swimming fin over tethered fin both experimentally and numerically. Experimentally, we focus on the oscillatory form of locomotion where the caudal fin pitches to generate necessary thrust as seen in boxfish. We intend to investigate the Caudal fin kinematics and its physical properties on locomotion performance. To better understand, we build an automated robo-physical model that swims in a circular path so as to carry extensive experiments. We focus on understanding the effect of flexibility, shape and thickness of caudal fin on performance. Currently, we have studied three different flexibility and for each flexibility, we studied three different shape. We found there must be an optimal flexibility for minimising the Cost of Transport (COT). We also propose that the steady forward speed linearly varies with tail tip velocity. Furthermore, we investigated the effect of thickness of fin and considered uniform and tapered fin with equal area moment of inertia. Numerically, we investigated the effect of phase offset between heave and pitch motion on the performance of a freely swimming fin and compared that to a tethered fin. A freely-swimming fin self propels and moves with steady speed while a tethered fin remains stationary and actuates under uniform flow. We model the fin as a rigid body undergoing prescribed motion in an inviscid fluid and solved for coupled interaction using panel method. We show the effect of phase offset for optimum performance and found a significant difference between tethered and freely swimming fin.
  • Thumbnail Image
    Effects of fish caudal fin sweep angle and kinematics on thrust production during low-speed thunniform swimming
    Matta, Alexander; Bayandor, Javid; Battaglia, Francine; Pendar, Hodjat (The Company of Biologists, 2019-06-12)
    Scombrid fish lunate caudal fins are characterized by a wide range of sweep angles. Scombrid that have small sweep-angle caudal fins move at higher swimming speeds, suggesting that smaller angles produce more thrust. Furthermore, scombrids occasionally use high angles of attack (AoA) suggesting this also has some thrust benefit. This work examined the hypothesis that a smaller sweep angle and higher AoA improved thrust in swimmers by experimentally analyzing a robophysical model. The robophysical model was tested in a water tunnel at speeds between 0.35 and 0.7 body lengths per second. Three swept caudal fins were analyzed at three different AoA, three different freestream velocities, and four different Strouhal numbers, for a total of 108 cases. Results demonstrated that the fin with the largest sweep angle of 50° resulted in lower thrust production than the 40° and 30° fins, especially at higher Strouhal numbers. Larger AoA up to 25° increased thrust production at the higher Strouhal numbers, but at lower Strouhal numbers, produced less thrust. Differences in thrust production due to fin sweep angle and AoAwere attributed to the variation in spanwise flowand leading edge vortex dynamics.
  • Thumbnail Image
    Estimation of Instantaneous Gas Exchange in Flow-Through Respirometry Systems: A Modern Revision of Bartholomew's Ztransform Method
    Pendar, Hodjat; Socha, John J. (PLOS, 2015-10-14)
    Flow-through respirometry systems provide accurate measurement of gas exchange over long periods of time. However, these systems have limitations in tracking rapid changes. When an animal infuses a metabolic gas into the respirometry chamber in a short burst, diffusion and airflow in the chamber gradually alter the original signal before it arrives at the gas analyzer. For single or multiple bursts, the recorded signal is smeared or mixed, which may result in dramatically altered recordings compared to the emitted signal. Recovering the original metabolic signal is a difficult task because of the inherent ill conditioning problem. Here, we present two new methods to recover the fast dynamics of metabolic patterns from recorded data. We first re-derive the equations of the well-known Z-transform method (ZT method) to show the source of imprecision in this method. Then, we develop a new model of analysis for respirometry systems based on the experimentally determined impulse response, which is the response of the system to a very short unit input. As a result, we present a major modification of the ZT method (dubbed the ‘EZT method’) by using a new model for the impulse response, enhancing its precision to recover the true metabolic signals. The second method, the generalized Z-transform (GZT) method, was then developed by generalizing the EZT method; it can be applied to any flow-through respirometry system with any arbitrary impulse response. Experiments verified that the accuracy of recovering the true metabolic signals is significantly improved by the new methods. These new methods can be used more broadly for input estimation in variety of physiological systems.
  • Thumbnail Image
    Exact protein distributions for stochastic models of gene expression using partitioning of Poisson processes
    Pendar, Hodjat; Platini, Thierry; Kulkarni, Rahul V. (American Physical Society, 2013-04-26)
    Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations; hence, there is considerable interest in quantifying noise in gene expression using stochastic models. However, obtaining exact analytical results for protein distributions has been an intractable task for all but the simplest models. Here, we invoke the partitioning property of Poisson processes to develop a mapping that significantly simplifies the analysis of stochastic models of gene expression. The mapping leads to exact protein distributions using results for mRNA distributions in models with promoter-based regulation. Using this approach, we derive exact analytical results for steady-state and time-dependent distributions for the basic two-stage model of gene expression. Furthermore, we show how the mapping leads to exact protein distributions for extensions of the basic model that include the effects of posttranscriptional and posttranslational regulation. The approach developed in this work is widely applicable and can contribute to a quantitative understanding of stochasticity in gene expression and its regulation.
  • Thumbnail Image
    Functional compartmentalization in the hemocoel of insects
    Pendar, Hodjat; Aviles, Jessica; Adjerid, Khaled; Schoenewald, Caroline; Socha, John J. (Springer Nature, 2019-04-15)
    The insect circulatory system contains an open hemocoel, in which the mechanism of hemolymph flow control is ambiguous. As a continuous fluidic structure, this cavity should exhibit pressure changes that propagate quickly. Narrow-waisted insects create sustained pressure differences across segments, but their constricted waist provides an evident mechanism for compartmentalization. Insects with no obvious constrictions between segments may be capable of functionally compartmentalizing the body, which could explain complex hemolymph flows. Here, we test the hypothesis of functional compartmentalization by measuring pressures in a beetle and recording abdominal movements. We found that the pressure is indeed uniform within the abdomen and thorax, congruent with the predicted behavior of an open system. However, during some abdominal movements, pressures were on average 62% higher in the abdomen than in the thorax, suggesting that functional compartmentalization creates a gradient within the hemocoel. Synchrotron tomography and dissection show that the arthrodial membrane and thoracic muscles may contribute to this dynamic pressurization. Analysis of volume change suggests that the gut may play an important role in regulating pressure by translating between body segments. Overall, this study suggests that functional compartmentalization may provide an explanation for how fluid flows are managed in an open circulatory system.
  • Thumbnail Image
    The mechanical linkage of abdominal movements and the respiratory system in beetles
    Pendar, Hodjat (Virginia Tech, 2015-03-11)
    Abdominal pumping is a well-known behavior in insects, thought to function largely in respiratory processes. In particular, the abdominal pump is considered to produce ventilation of air in the tracheal system, but the mechanistic link between abdominal movement and flow of air is not well understood. In this thesis, we explore the relationship between the abdominal pump and ventilation of air using pupal and adult forms of the darkling beetle Zophobas morio. First, we investigated the mechanical linkage between abdominal pumping and active ventilation in pupae by simultaneously measuring abdominal movement, hemolymph pressure, CO2 emission, and deformation of tracheal tubes. This study revealed that pupae with low metabolic rates do indeed exhibit tracheal compression, which is coincident with abdominal pumping and pressure pulsation. However, more than 63% of the abdominal pumps and associated pressure pulsations did not lead to tracheal compression. This result can be explained by the status of the spiracles; when the system is closed, little compression in the tracheae can occur. Therefore, we conclude that abdominal pumping in insects does not necessarily lead to ventilation and may serve other functions, such as producing hemolymph flow for circulation. Insects have an open circulatory system, with flow driven largely by the small dorsal vessel. Within the open coelom, hemolymph pressure should be mostly uniform, suggesting that abdominal pumping does not produce hemolymph flows within the main body cavity. We tested this assumption by simultaneously measuring hemolymph pressure in different locations in the coelom. Within the abdomen and thorax, hemolymph pressure is nearly uniform, as expected. However, hemolymph pressures are significantly different between the abdomen and thorax. This suggests that the coelom is compartmentalized, and that abdominal pumping can induce hemolymph flow within the coelom. Throughout these experiments, we faced a common difficulty inherent to flow-through respirometry systems: they are incapable of providing direct, instantaneous measurement of gas concentration. Previous methods are not able to reconstitute the rapid dynamical changes in respiratory signals that are required for precise temporal analysis. Therefore, we developed two new methods to accurately recover instantaneous gas exchange signals, based on new models of the impulse response of the system. These methods enabled us to accurately recover fast- changing respiratory signals with a higher fidelity than previously possible. Using these methods, we demonstrate the synchronization of respiratory data with other physiologically relevant signals, such as pressure and abdominal movement. This research was supported by NSF grant #0938047 and the Virginia Tech Institute for Critical Technology and Applied Science (ICTAS).
  • Thumbnail Image
    Recovering signals in physiological systems with large datasets
    Pendar, Hodjat (Virginia Tech, 2020-09-11)
    In many physiological studies, variables of interest are not directly accessible, requiring that they be estimated indirectly from noisy measured signals. Here, we introduce two empirical methods to estimate the true physiological signals from indirectly measured, noisy data. The first method is an extension of Tikhonov regularization to large-scale problems, using a sequential update approach. In the second method, we improve the conditioning of the problem by assuming that the input is uniform over a known time interval, and then we use a least-squares method to estimate the input. These methods were validated computationally and experimentally by applying them to flow-through respirometry data. Specifically, we infused CO2 in a flow-through respirometry chamber in a known pattern, and used the methods to recover the known input from the recorded data. The results from these experiments indicate that these methods are capable of sub-second accuracy. We also applied the methods on respiratory data from a grasshopper to investigate the exact timing of abdominal pumping, spiracular opening, and CO2 emission. The methods can be used more generally for input estimation of any linear system.
  • Thumbnail Image
    Recovering signals in physiological systems with large datasets
    Pendar, Hodjat; Socha, John J.; Chung, Julianne (Company of Biologists, 2016-08-15)
    In many physiological studies, variables of interest are not directly accessible, requiring that they be estimated indirectly from noisy measured signals. Here, we introduce two empirical methods to estimate the true physiological signals from indirectly measured, noisy data. The first method is an extension of Tikhonov regularization to large-scale problems, using a sequential update approach. In the second method, we improve the conditioning of the problem by assuming that the input is uniform over a known time interval, and then use a least-squares method to estimate the input. These methods were validated computationally and experimentally by applying them to flow-through respirometry data. Specifically, we infused CO2 in a flow-through respirometry chamber in a known pattern, and used the methods to recover the known input from the recorded data. The results from these experiments indicate that these methods are capable of subsecond accuracy. We also applied the methods on respiratory data from a grasshopper to investigate the exact timing of abdominal pumping, spiracular opening, and CO2 emission. The methods can be used more generally for input estimation of any linear system.