@article{attarian_luo_luo_tran_xu_yi_yu_zhang_2023, title={Airplane Detection and Classification Based on Mask R-CNN and YOLO with Feature Engineering}, volume={543}, ISBN={["978-3-031-16077-6"]}, ISSN={["2367-3389"]}, DOI={10.1007/978-3-031-16078-3_52}, journal={INTELLIGENT SYSTEMS AND APPLICATIONS, VOL 2}, author={Attarian, Adam and Luo, Minxuan and Luo, Yangyang and Tran, Hien and Xu, Xingfei and Yi, Chunxiao and Yu, Yahe and Zhang, Fa}, year={2023}, pages={752–768} }
 @article{yu_tran_2022, title={An XGBoost-Based Fitted Q Iteration for Finding the Optimal STI Strategies for HIV Patients}, volume={6}, ISSN={["2162-2388"]}, url={https://doi.org/10.1109/TNNLS.2022.3176204}, DOI={10.1109/TNNLS.2022.3176204}, abstractNote={The computational algorithm proposed in this article is an important step toward the development of computational tools that could help guide clinicians to personalize the management of human immunodeficiency virus (HIV) infection. In this article, an XGBoost-based fitted Q iteration algorithm is proposed for finding the optimal structured treatment interruption (STI) strategies for HIV patients. Using the XGBoost-based fitted Q iteration algorithm, we can obtain acceptable and optimal STI strategies with fewer training data, when compared with the extra-tree-based fitted Q iteration algorithm, deep Q-networks (DQNs), and proximal policy optimization (PPO) algorithm. In addition, the XGBoost-based fitted Q iteration algorithm is computationally more efficient than the extra-tree-based fitted Q iteration algorithm.}, journal={IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS}, author={Yu, Yahe and Tran, Hien}, year={2022}, month={Jun} }
 @article{zhang_flores_tran_2021, title={Deep learning and regression approaches to forecasting blood glucose levels for type 1 diabetes}, volume={69}, ISSN={["1746-8108"]}, DOI={10.1016/j.bspc.2021.102923}, abstractNote={Objective: Controlling blood glucose in the euglycemic range is the main goal of developing the closed-loop insulin delivery system for type 1 diabetes patients. The closed-loop system delivers the amount of insulin dose determined by glucose predictions through the use of computational algorithms. A computationally efficient and accurate model that can capture the physiological nonlinear dynamics is critical for developing an efficient closed-loop system. Methods: Four data-driven models are compared, including different neural network architectures, a reservoir computing model, and a novel linear regression approach. Model predictions are evaluated over continuous 30 and 60 min time horizons using real-world data from wearable sensor measurements, a continuous glucose monitor, and self-reported events through mobile applications. The four data-driven models are trained on 12 data contributors for around 32 days, 8 days of data are used for validation, with an additional 10 days of data for out-of-sample testing. Model performance was evaluated by the root mean squared error and the mean absolute error. Results: A neural network model using an encoder-decoder architecture has the most stable performance and is able to recover missing dynamics in short time intervals. Regression models performed better at long-time prediction horizons (i.e., 60 min) and with lower computational costs. Significance: The performance of several distinct models was tested for individual-level data from a type 1 diabetes data set. These results may enable a feasible solution with low computational cost for the time-dependent adjustment of artificial pancreas for diabetes patients.}, journal={BIOMEDICAL SIGNAL PROCESSING AND CONTROL}, author={Zhang, Meng and Flores, Kevin B. and Tran, Hien T.}, year={2021}, month={Aug} }
 @article{williams_mehlsen_tran_olufsen_2019, title={An optimal control approach for blood pressure regulation during head-up tilt}, volume={113}, ISSN={["1432-0770"]}, DOI={10.1007/s00422-018-0783-9}, abstractNote={This paper presents an optimal control approach to modeling effects of cardiovascular regulation during head-up tilt (HUT). Many patients who suffer from dizziness or light-headedness are administered a head-up tilt test to explore potential deficits within the autonomic control system, which maintains the cardiovascular system at homeostasis. This system is complex and difficult to study in vivo, and thus we propose to use mathematical modeling to achieve a better understanding of cardiovascular regulation during HUT. In particular, we show the feasibility of using optimal control theory to compute physiological control variables, vascular resistance and cardiac contractility, quantities that cannot be measured directly, but which are useful to assess the state of the cardiovascular system. A non-pulsatile lumped parameter model together with pseudo- and clinical data are utilized in the optimal control problem formulation. Results show that the optimal control approach can predict time-varying quantities regulated by the cardiovascular control system. Our results compare favorable to our previous study using a piecewise linear spline approach, less a priori knowledge is needed, and results were obtained at a significantly lower computational cost.}, number={1-2}, journal={BIOLOGICAL CYBERNETICS}, author={Williams, Nakeya D. and Mehlsen, Jesper and Tran, Hien T. and Olufsen, Mette S.}, year={2019}, month={Apr}, pages={149–159} }
 @article{williams_brady_gilmore_gremaud_tran_ottesen_mehlsen_olufsen_2019, title={Cardiovascular dynamics during head-up tilt assessed via pulsatile and non-pulsatile models}, volume={79}, ISSN={0303-6812 1432-1416}, url={http://dx.doi.org/10.1007/s00285-019-01386-9}, DOI={10.1007/s00285-019-01386-9}, abstractNote={This study develops non-pulsatile and pulsatile models for the prediction of blood flow and pressure during head-up tilt. This test is used to diagnose potential pathologies within the autonomic control system, which acts to keep the cardiovascular system at homeostasis. We show that mathematical modeling can be used to predict changes in cardiac contractility, vascular resistance, and arterial compliance, quantities that cannot be measured but are useful to assess the system's state. These quantities are predicted as time-varying parameters modeled using piecewise linear splines. Having models with various levels of complexity formulated with a common set of parameters, allows us to combine long-term non-pulsatile simulations with pulsatile simulations on a shorter time-scale. We illustrate results for a representative subject tilted head-up from a supine position to a [Formula: see text] angle. The tilt is maintained for 5 min before the subject is tilted back down. Results show that if volume data is available for all vascular compartments three parameters can be identified, cardiovascular resistance, vascular compliance, and ventricular contractility, whereas if model predictions are made against arterial pressure and cardiac output data alone, only two parameters can be estimated either resistance and contractility or resistance and compliance.}, number={3}, journal={Journal of Mathematical Biology}, publisher={Springer Science and Business Media LLC}, author={Williams, Nakeya D. and Brady, Renee and Gilmore, Steven and Gremaud, Pierre and Tran, Hien T. and Ottesen, Johnny T. and Mehlsen, Jesper and Olufsen, Mette S.}, year={2019}, month={May}, pages={987–1014} }
 @article{murad_tran_banks_everett_rosenberg_2019, title={IMMUNOSUPPRESSANT TREATMENT DYNAMICS IN RENAL TRANSPLANT RECIPIENTS: AN ITERATIVE MODELING APPROACH}, volume={24}, ISSN={["1553-524X"]}, DOI={10.3934/dcdsb.2018274}, abstractNote={Finding the optimal balance between over-suppression and under-suppression of the immune response is difficult to achieve in renal transplant patients, all of whom require lifelong immunosuppression. Our ultimate goal is to apply control theory to adaptively predict the optimal amount of immunosuppression; however, we first need to formulate a biologically realistic model. The process of quantitively modeling biological processes is iterative and often leads to new insights with every iteration. We illustrate this iterative process of modeling for renal transplant recipients infected by BK virus. We analyze and improve on the current mathematical model by modifying it to be more biologically realistic and amenable for designing an adaptive treatment strategy.}, number={6}, journal={DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS-SERIES B}, author={Murad, Neha and Tran, H. T. and Banks, H. T. and Everett, R. A. and Rosenberg, Eric S.}, year={2019}, month={Jun}, pages={2781–2797} }
 @article{kennedy_king_tran_2019, title={Real-time implementation and analysis of a modified energy based controller for the swing-up of an inverted pendulum on a cart}, volume={50}, ISSN={["1435-5671"]}, DOI={10.1016/j.ejcon.2019.05.002}, abstractNote={In this paper we derive a modified energy based swing-up controller using Lyapunov functions. During the derivation, all effort has been made to use a more complex dynamical model for the single inverted pendulum (SIP) system than the simplified model that is most commonly used. We consider the electrodynamics of the DC motor that drives the cart, and incorporate viscous damping friction as seen at the motor pinion. Furthermore, we use a new method to account for the limitation of having a cart-pendulum system with a finite track length. Two modifications to the controller are also discussed to make the method more appropriate for real-time implementation. One of the modifications improves robustness using a modified Lyapunov function for the derivation, while the other one incorporates viscous damping as seen at the pendulum axis. We present both simulation and real-time experimental results implemented in MATLAB Simulink.}, journal={EUROPEAN JOURNAL OF CONTROL}, author={Kennedy, Emese and King, Ethan and Tran, Hien}, year={2019}, month={Nov}, pages={176–187} }
 @article{nguyen_tran_guillen_bui_matsunaga_2018, title={Acquisition War-Gaming Technique for Acquiring Future Complex Systems: Modeling and Simulation Results for Cost Plus Incentive Fee Contract}, volume={6}, ISSN={2227-7390}, url={http://dx.doi.org/10.3390/math6030043}, DOI={10.3390/math6030043}, abstractNote={This paper provides a high-level discussion and propositions of frameworks and models for acquisition strategy of complex systems. In particular, it presents an innovative system engineering approach to model the Department of Defense (DoD) acquisition process and offers several optimization modules including simulation models using game theory and war-gaming concepts. Our frameworks employ Advanced Game-based Mathematical Framework (AGMF) and Unified Game-based Acquisition Framework (UGAF), and related advanced simulation and mathematical models that include a set of War-Gaming Engines (WGEs) implemented in MATLAB statistical optimization models. WGEs are defined as a set of algorithms, characterizing the Program and Technical Baseline (PTB), technology enablers, architectural solutions, contract type, contract parameters and associated incentives, and industry bidding position. As a proof of concept, Aerospace, in collaboration with the North Carolina State University (NCSU) and University of Hawaii (UH), successfully applied and extended the proposed frameworks and decision models to determine the optimum contract parameters and incentives for a Cost Plus Incentive Fee (CPIF) contract. As a result, we can suggest a set of acquisition strategies that ensure the optimization of the PTB.}, number={3}, journal={Mathematics}, publisher={MDPI AG}, author={Nguyen, Tien and Tran, Hien and Guillen, Andy and Bui, Tung and Matsunaga, Sumner}, year={2018}, month={Mar}, pages={43} }
 @article{rutter_langdale_hokanson_hamilton_tran_grill_flores_2018, title={Detection of Bladder Contractions From the Activity of the External Urethral Sphincter in Rats Using Sparse Regression}, volume={26}, ISSN={1534-4320 1558-0210}, url={http://dx.doi.org/10.1109/tnsre.2018.2854675}, DOI={10.1109/tnsre.2018.2854675}, abstractNote={Bladder overactivity and incontinence and dysfunction can be mitigated by electrical stimulation of the pudendal nerve applied at the onset of a bladder contraction. Thus, it is important to predict accurately both bladder pressure and the onset of bladder contractions. We propose a novel method for prediction of bladder pressure using a time-dependent spectrogram representation of external urethral sphincter electromyographic (EUS EMG) activity and a least absolute shrinkage and selection operator regression model. There was a statistically significant improvement in prediction of bladder pressure compared with methods based on the firing rate of EUS EMG activity. This approach enabled prediction of the onset of bladder contractions with 91% specificity and 96% sensitivity and may be suitable for closed-loop control of bladder continence.}, number={8}, journal={IEEE Transactions on Neural Systems and Rehabilitation Engineering}, publisher={Institute of Electrical and Electronics Engineers (IEEE)}, author={Rutter, Erica M. and Langdale, Christopher L. and Hokanson, James A. and Hamilton, Franz and Tran, Hien and Grill, Warren M. and Flores, Kevin B.}, year={2018}, month={Aug}, pages={1636–1644} }
 @inproceedings{tran_arnold_2018, place={Hong Kong}, series={Lecture notes in engineering and computer science}, title={Ensemble Kalman Filtering for Inverse Optimal Control}, volume={II}, ISBN={9789881404886}, booktitle={International MultiConference of Engineers and Computer Scientists : IMECS 2018: 14-16 March, 2018, the Royal Garden Hotel, Kowloon, Hong Kong}, publisher={Newswood Limited, International Association of Engineers}, author={Tran, H. and Arnold, A.}, editor={Ao, Sio-long and Castillo, Oscar and Douglas, Craig and Feng, David Dagan and Korunsky, AlexanderEditors}, year={2018}, pages={526–530}, collection={Lecture notes in engineering and computer science} }
 @inbook{aston_cranfield_o’farrell_cassenote_mendes-correa_segurado_hoang_lankford_tran_2018, title={Hepatitis C Viral Dynamics Using a Combination Therapy of Interferon, Ribavirin, and Telaprevir: Mathematical Modeling and Model Validation}, ISBN={9781789842074 9781789842081}, url={http://dx.doi.org/10.5772/intechopen.75761}, DOI={10.5772/intechopen.75761}, abstractNote={Groundbreaking new drugs called direct acting antivirals have been introduced recently for 
the treatment of chronic Hepatitis C virus infection.We introduce a mathematical model for 
Hepatitis C dynamics treated with the direct acting antiviral drug, telaprevir, alongside 
traditional interferon and ribavirin treatments to understand how this combination therapy 
affects the viral load of patients exhibiting different types of response.We use sensitivity and 
identifiability techniques to determine which model parameters can be best estimated from 
viral load data. Parameter estimationwith these best estimable parameters is then performed 
to give patient-specific fits of the model to partial virologic response, sustained virologic 
response and breakthrough patients.}, booktitle={Hepatitis C - From Infection to Cure}, publisher={InTech}, author={Aston, Philip and Cranfield, Katie and O’Farrell, Haley and Cassenote, Alex and Mendes-Correa, Cassia J. and Segurado, Aluisio and Hoang, Phuong and Lankford, George and Tran, Hien}, year={2018}, month={Oct} }
 @article{arthur_attarian_hamilton_tran_2018, title={Nonlinear Kalman filtering for censored observations}, volume={316}, ISSN={0096-3003}, url={http://dx.doi.org/10.1016/j.amc.2017.08.002}, DOI={10.1016/j.amc.2017.08.002}, abstractNote={The use of Kalman filtering, as well as its nonlinear extensions, for the estimation of system variables and parameters has played a pivotal role in many fields of scientific inquiry where observations of the system are restricted to a subset of variables. However in the case of censored observations, where measurements of the system beyond a certain detection point are impossible, the estimation problem is complicated. Without appropriate consideration, censored observations can lead to inaccurate estimates. Motivated by previous work on censored filtering in linear systems, we develop a modified version of the extended Kalman filter to handle the case of censored observations in nonlinear systems. We validate this methodology in a simple oscillator system first, showing its ability to accurately reconstruct state variables and track system parameters when observations are censored. Finally, we utilize the nonlinear censored filter to analyze censored datasets from patients with hepatitis C and human immunodeficiency virus.}, journal={Applied Mathematics and Computation}, publisher={Elsevier BV}, author={Arthur, Joseph and Attarian, Adam and Hamilton, Franz and Tran, Hien}, year={2018}, month={Jan}, pages={155–166} }
 @article{murad_tran_banks_2018, title={Optimal control of immunosuppressants in renal transplant recipients susceptible to BKV infection}, volume={40}, ISSN={0143-2087}, url={http://dx.doi.org/10.1002/oca.2478}, DOI={10.1002/oca.2478}, abstractNote={Summary}, number={2}, journal={Optimal Control Applications and Methods}, publisher={Wiley}, author={Murad, Neha and Tran, H.T. and Banks, H.T.}, year={2018}, month={Nov}, pages={292–309} }
 @article{brady_frank-ito_tran_janum_møller_brix_ottesen_mehlsen_olufsen_2018, title={Personalized mathematical model of endotoxin-induced inflammatory responses in young men and associated changes in heart rate variability}, volume={13}, ISSN={0973-5348 1760-6101}, url={http://dx.doi.org/10.1051/mmnp/2018031}, DOI={10.1051/mmnp/2018031}, abstractNote={The objective of this study was to develop a personalized inflammatory model and estimate subject-specific parameters that could be related to changes in heart rate variability (HRV), a measure that can be obtained non-invasively in real time. An inflammatory model was developed and calibrated to measurements of interleukin-6 (IL-6), tumor necrosis factor (TNF-alpha), interleukin-8 (IL-8) and interleukin-10 (IL-10) over 8 hours in 20 subjects administered a low dose of lipopolysaccharide. For this model, we estimated 11 subject-specific parameters for all 20 subjects. Estimated parameters were correlated with changes in HRV, computed from ECG measurements using a built-in HRV module available in Labchart. Results revealed that patients could be separated into two groups expressing normal and abnormal responses to endotoxin. Abnormal responders exhibited increased HRV, most likely as a result of increased vagal firing. The observed correlation between the inflammatory response and HRV brings us a step further towards understanding if HRV predictions can be used as a marker for inflammation. Analyzing HRV parameters provides an easy, non-invasively obtained measure that can be used to assess the state of the subject, potentially translating to identifying a non-invasive marker that can be used to detect the onset of sepsis.}, number={5}, journal={Mathematical Modelling of Natural Phenomena}, publisher={EDP Sciences}, author={Brady, R. and Frank-Ito, D.O. and Tran, H.T. and Janum, S. and Møller, K. and Brix, S. and Ottesen, J.T. and Mehlsen, J. and Olufsen, M.S.}, editor={Maruta, K. and Minaev, S. and Il Kim, N. and Im, H. and Gubernov, V.Editors}, year={2018}, pages={42} }
 @inbook{nguyen_guillen_matsunaga_tran_bui_2018, title={War-Gaming Applications for Achieving Optimum Acquisition of Future Space Systems}, ISBN={9789535138037 9789535138006}, url={http://dx.doi.org/10.5772/intechopen.71044}, DOI={10.5772/intechopen.71044}, abstractNote={This chapter describes an innovative modeling and simulation approach using newly proposed Advanced Game-based Mathematical Framework (AGMF), Unified Game-based Acquisition Framework (UGAF) and a set of War-Gaming Engines (WGEs) to address future space systems acquisition challenges. Its objective is to assist the DoD Acquisition Authority (DAA) to understand the contractor’s perspective and to seek optimum Program-and-Technical-Baseline (PTB) solution and corresponding acquisition strategy under both the perspectives of the government and the contractors. The proposed approach calls for an interdisciplinary research that involves game theory, probability and statistics, and non-linear programming. The goal of this chapter is to apply the proposed war-gaming frameworks to develop and evaluate PTB solutions and associated acquisition strategies in the context of acquisition of future space systems. Our simulation results suggest that our optimization problem for the acquisition of future space systemsmeets the affordability and innovative requirements with minimum acquisition risk.}, booktitle={Simulation and Gaming}, publisher={InTech}, author={Nguyen, Tien M. and Guillen, Andy T. and Matsunaga, Sumner S. and Tran, Hien T. and Bui, Tung X.}, year={2018}, month={Feb} }
 @article{sawyer_tran_evans_2017, title={A physiologically based pharmacokinetic model of vitamin D}, volume={37}, ISSN={0260-437X}, url={http://dx.doi.org/10.1002/jat.3489}, DOI={10.1002/jat.3489}, abstractNote={Abstract}, number={12}, journal={Journal of Applied Toxicology}, publisher={Wiley}, author={Sawyer, Megan E. and Tran, Hien T. and Evans, Marina V.}, year={2017}, month={Jun}, pages={1448–1454} }
 @article{hamilton_setzer_chavez_tran_lloyd_2017, title={Adaptive filtering for hidden node detection and tracking in networks}, volume={27}, number={7}, journal={Chaos (Woodbury, N.Y.)}, author={Hamilton, F. and Setzer, B. and Chavez, S. and Tran, H. and Lloyd, A. L.}, year={2017} }
 @article{attarian_tran_2017, title={An Optimal Control Approach to Structured Treatment Interruptions for HIV Patients: A Personalized Medicine Perspective}, volume={08}, ISSN={2152-7385 2152-7393}, url={http://dx.doi.org/10.4236/am.2017.87074}, DOI={10.4236/am.2017.87074}, abstractNote={Highly Active Antiretroviral Therapy (HAART) has changed the course of human immunodeficiency virus (HIV) treatments since its introduction. However, for many patients, long term continuous HAART is expensive and can include problems with drug toxicity and side effects, as well as increased drug resistance. Because of these reasons, some HIV infected patients will voluntarily terminate HAART. Some of these patients will also interrupt the continuous prescribed therapies for short or long periods. After discontinuing HAART, patients will usually experience a rapid increase in viral load coupled with an immediate decline in CD4+ counts. The canonical example of a patient undergoing unsupervised breaks in HAART is that of the “Berlin patient”. In this case, the patient was able to control viral load in the absence of treatment by cycling HAART on and off due to non-related infections. Due to this patient, interest in the use of structured treatment interruptions (STI) as a mechanism to regulate an HIV infection piqued. This paper describes an optimal control approach to determine STI regimen for HIV patients. The optimal STI was implemented in the context of the receding horizon control (RHC) using a mathematical model for the in-vivo dynamics of an HIV type 1 infection. Using available clinical data, we calibrate the model by estimating on a patient specific basis, a best estimable set of parameters using sensitivity analysis and subset selection. We demonstrate how customized STI protocols can be designed through the variation of control parameters on a patient specific basis.}, number={07}, journal={Applied Mathematics}, publisher={Scientific Research Publishing, Inc,}, author={Attarian, Adam and Tran, Hien}, year={2017}, pages={934–955} }
 @article{arthur_tran_aston_2017, title={Feasibility of parameter estimation in hepatitis C viral dynamics models}, volume={25}, ISSN={["1569-3945"]}, DOI={10.1515/jiip-2014-0048}, abstractNote={Abstract}, number={1}, journal={JOURNAL OF INVERSE AND ILL-POSED PROBLEMS}, author={Arthur, Joseph G. and Tran, Hien T. and Aston, Philip}, year={2017}, month={Feb}, pages={69–80} }
 @article{tran_everett_banks_hu_murad_2017, place={Banks, R.A}, title={Mathematical and Statistical Model Misspecifications in Modeling Immune Response in Renal Transplant Recipients}, volume={26}, ISSN={1741-5977 1741-5985}, url={http://dx.doi.org/10.1080/17415977.2017.1312363}, DOI={10.1080/17415977.2017.1312363}, abstractNote={We examine uncertainty in clinical data from a kidney transplant recipient infected with BK virus and investigate mathematical model and statistical model misspecifications in the context of least squares methodology. A difference-based method is directly applied to data to determine the correct statistical model that represents the uncertainty in data. We then carry out an inverse problem with the corresponding iterative weighted least squares technique and use the resulting modified residual plots to detect mathematical model discrepancy. This process is implemented using both clinical and simulated data. Our results demonstrate mathematical model misspecification when both simpler and more complex models are assumed compared to data dynamics.}, number={2}, journal={Inverse Problems in Science and Engineering}, publisher={Informa UK Limited}, author={Tran, H. and Everett, R.A. and Banks, H.T. and Hu, S. and Murad, N.}, year={2017}, pages={1–18} }
 @inproceedings{tran_bernstein_2017, place={Hong Kong}, series={Lecture notes in engineering and computer science}, title={Real-Time Implementation of a LQR-Based Controller for the Stabilization of a Double Inverted Pendulum}, volume={I}, ISBN={978-988-14047-3-2}, number={Royal Garden Hotel, Kowloon, Hong Kong}, booktitle={International MultiConference of Engineers and Computer Scientists : IMECS 2017: 15-17 March, 2017, the Royal Garden Hotel, Kowloon, Hong Kong}, publisher={Newswood Limited}, author={Tran, H. and Bernstein, A.}, editor={Ao, Sio-long and Castillo, Oscar and Douglas, Craig and Feng, David Dagan and Korunsky, AlexanderEditors}, year={2017}, pages={245–250}, collection={Lecture notes in engineering and computer science} }
 @article{sidle_tran_2017, title={Using Multi-Class Classification Methods to Predict Baseball Pitch Types}, volume={4}, DOI={10.3233/JSA-170171}, abstractNote={. Since the introduction of PITCHf/x in 2006, there has been a plethora of data available for anyone who wants to access to the minute details of every baseball pitch thrown over the past nine seasons. Everything from the initial velocity and release point to the break angle and strike zone placement is tracked, recorded, and used to classify the pitch according to an algorithm developed by MLB Advanced Media (MLBAM). Given these classifications, we developed a model that would predict the next type of pitch thrown by a given pitcher, using only data that would be available before he even stepped to the mound. We used data from three recent MLB seasons (2013-2015) to compare individual pitcher predictions based on multi-class linear discriminant analysis, support vector machines, and classification trees to lead to the development of a real-time, live-game predictor. Using training data from the 2013, 2014, and part of the 2015 season, our best method achieved a mean out-of-sample predictive accuracy of 66.62%, and a real-time success rate of over 60%.}, number={1}, journal={Journal of Sports Analytics}, publisher={G. Sidle}, author={Sidle, G. and Tran, H.}, year={2017}, pages={85–93} }
 @inproceedings{vienhage_barcomb_marshall_black_coons_tran_nguyen_guillen_yoh_kizer_et al._2017, title={War-gaming application for future space systems acquisition: MATLAB implementation of war-gaming acquisition models and simulation results}, url={http://dx.doi.org/10.1117/12.2263247}, DOI={10.1117/12.2263247}, abstractNote={The paper describes the MATLAB (MathWorks) programs that were developed during the REU workshop1 to implement The Aerospace Corporation developed Unified Game-based Acquisition Framework and Advanced Game - based Mathematical Framework (UGAF-AGMF) and its associated War-Gaming Engine (WGE) models. Each game can be played from the perspectives of the Department of Defense Acquisition Authority (DAA) or of an individual contractor (KTR). The programs also implement Aerospace’s optimum “Program and Technical Baseline (PTB) and associated acquisition” strategy that combines low Total Ownership Cost (TOC) with innovative designs while still meeting warfighter needs. The paper also describes the Bayesian Acquisition War-Gaming approach using Monte Carlo simulations, a numerical analysis technique to account for uncertainty in decision making, which simulate the PTB development and acquisition processes and will detail the procedure of the implementation and the interactions between the games.}, booktitle={Sensors and Systems for Space Applications X}, publisher={SPIE}, author={Vienhage, Paul and Barcomb, Heather and Marshall, Karel and Black, William A. and Coons, Amanda and Tran, Hien T. and Nguyen, Tien M. and Guillen, Andy T. and Yoh, James and Kizer, Justin and et al.}, editor={Pham, Khanh D. and Chen, GensheEditors}, year={2017}, month={May} }
 @inproceedings{nguyen_tran_wang_coons_nguyen_lane_pham_chen_wang_2016, title={RFI modeling and prediction approach for SATOP applications: RFI prediction models}, volume={9838}, ISSN={["0277-786X"]}, url={http://dx.doi.org/10.1117/12.2223518}, DOI={10.1117/12.2223518}, abstractNote={This paper describes a technical approach for the development of RFI prediction models using carrier synchronization loop when calculating Bit or Carrier SNR degradation due to interferences for (i) detecting narrow-band and wideband RFI signals, and (ii) estimating and predicting the behavior of the RFI signals. The paper presents analytical and simulation models and provides both analytical and simulation results on the performance of USB (Unified S-Band) waveforms in the presence of narrow-band and wideband RFI signals. The models presented in this paper will allow the future USB command systems to detect the RFI presence, estimate the RFI characteristics and predict the RFI behavior in real-time for accurate assessment of the impacts of RFI on the command Bit Error Rate (BER) performance. The command BER degradation model presented in this paper also allows the ground system operator to estimate the optimum transmitted SNR to maintain a required command BER level in the presence of both friendly and un-friendly RFI sources.}, booktitle={Sensors and Systems for Space Applications IX}, publisher={SPIE}, author={Nguyen, Tien M. and Tran, Hien T. and Wang, Zhonghai and Coons, Amanda and Nguyen, Charles C. and Lane, Steven A. and Pham, Khanh D. and Chen, Genshe and Wang, Gang}, editor={Pham, Khanh D. and Chen, GensheEditors}, year={2016}, month={May} }
 @inproceedings{tran_kennedy_2016, place={Singapore}, title={Real-Time Stabilization of a Single Inverted Pendulum Using a Power Series Based Controller}, ISBN={978-981-10-0550-3}, booktitle={Transactions on engineering technologies : International MultiConference of Engineers and Computer Scientists 2015}, publisher={Springer}, author={Tran, H. and Kennedy, Emese A.}, editor={Yang, Gi-Chul and Ao, Sio-Iong and Huang, Xu and Castillo, OscarEditors}, year={2016}, pages={1–14} }
 @inproceedings{tran_kennedy_2016, place={Hong Kong}, title={Swing-up of an Inverted Pendulum on a Cart Using a Modified Energy Based Approach}, volume={I}, ISBN={978-988-19253-8-1 978-988-14047-6-3}, booktitle={International MultiConference of Engineers and Computer Scientists : IMECS 2016 : 16-18 March, 2016, the Royal Garden Hotel, Kowloon, Hong Kong}, publisher={Newswood Limited, International Association of Engineers}, author={Tran, H. and Kennedy, Emese}, year={2016}, pages={185–190} }
 @inproceedings{hoang_hamilton_murray_stafford_tran_2015, place={Cham, Switzerland}, series={Lecture Notes in Computer Science}, title={A Dynamic Feature Selection Based LDA Approach to Baseball Pitch Prediction}, volume={9441}, ISBN={["978-3-319-25659-7"]}, ISSN={["1611-3349"]}, DOI={10.1007/978-3-319-25660-3_11}, abstractNote={Baseball, which is one of the most popular sports in the world, has a uniquely discrete gameplay structure. This stop-and-go style of play creates a natural ability for fans and observers to record information about the game in progress, resulting in a wealth of data that is available for analysis. Major League Baseball (MLB), the professional baseball league in the US and Canada, uses a system known as PITCHf/x to record information about every individual pitch that is thrown in league play. We extend the classification to pitch prediction (fastball or nonfastball) by restricting our analysis to pre-pitch features. By performing significant feature analysis and introducing a novel approach for feature selection, moderate improvement over published results is achieved.}, booktitle={Trends and Applications in Knowledge Discovery and Data Mining}, publisher={Springer}, author={Hoang, P. and Hamilton, M. and Murray, J. and Stafford, C. and Tran, H.}, editor={Li, Xiao-Li and Cao, Tru and Lim, Ee-Peng and Zhou, Zhi-Hua and Ho, Tu-Bao and Cheung, DavidEditors}, year={2015}, pages={125–137}, collection={Lecture Notes in Computer Science} }
 @article{tran_lankford_read_ives_reppert_cline_guzman_2015, title={Optimization of Klystron Designs Using Deterministic Sampling Methods}, volume={62}, ISSN={0018-9383 1557-9646}, url={http://dx.doi.org/10.1109/ted.2015.2394479}, DOI={10.1109/ted.2015.2394479}, abstractNote={A method is presented for optimizing the design of klystron circuits. This automates the selection of cavity positions, resonant frequencies, quality factors, R/Q and other circuit parameters to maximize the efficiency with required gain. The method is based on deterministic sampling methods. In this paper, we describe the procedure and give several examples for both narrow-band and wideband klystrons, using the klystron codes AJDISK and TESLA.}, number={3}, journal={IEEE Transactions on Electron Devices}, publisher={Institute of Electrical and Electronics Engineers (IEEE)}, author={Tran, Hien and Lankford, George and Read, Michael E. and Ives, R. Lawrence and Reppert, Kelsey and Cline, Kayla and Guzman, Juan}, year={2015}, month={Mar}, pages={1032–1036} }
 @inproceedings{nguyen_tran_wang_coons_nguyen_lane_pham_chen_wang_2015, title={RFI modeling and prediction approach for SATOPS applications}, volume={9469}, ISSN={["1996-756X"]}, url={http://dx.doi.org/10.1117/12.2177955}, DOI={10.1117/12.2177955}, abstractNote={This paper describes innovative frameworks to develop RFI modeling and prediction models for (i) estimating the RFI characteristics, (ii) evaluating effectiveness of the existing Unified S-Band (USB) command waveforms employed by civil, commercial and military SATOPS ground stations, and (iii) predicting the impacts of RFI on USB command systems. The approach presented here will allow the communications designer to characterize both friendly and unfriendly RFI sources, and evaluate the impacts of RFI on civil, commercial and military USB SATOPS systems. In addition, the proposed frameworks allow the designer to estimate the optimum transmitted signal power to maintain a required USB SATOPS Quality-of-Service (QoS) in the presence of both friendly and unfriendly RFI sources.}, booktitle={Sensors and Systems for Space Applications VIII}, publisher={SPIE}, author={Nguyen, Tien M. and Tran, Hien T. and Wang, Zhonghai and Coons, Amanda and Nguyen, Charles C. and Lane, Steven A. and Pham, Khanh D. and Chen, Genshe and Wang, Gang}, editor={Pham, Khanh D. and Chen, GensheEditors}, year={2015}, month={May} }
 @inproceedings{real-time implementation of a power series based nonlinear controller for the balance of a single inverted pendulum_2015, place={Hong Kong}, volume={1}, ISBN={978-988-19253-2-9}, ISSN={2078-0958}, booktitle={International MultiConference of Engineers and Computer Scientists : IMECS 2015 : 18-20 March, 2015, the Royal Garden Hotel, Kowloon, Hong Kong}, publisher={Newswood Limited, International Association of Engineers}, year={2015}, pages={237–241} }
 @inproceedings{bui_read_lin_ives_tallis_tran_2015, title={Recent advances in beam optics analyzer}, DOI={10.1109/ivec.2015.7223806}, abstractNote={Recent advances in Beam Optics Analyzer (BOA) are reported to demonstrate its features and capabilities. BOA is a finite element particle-in-cell code with adaptive meshing. Its usage and detailed results for several electron gun simulations with optimization will be presented.}, booktitle={2015 ieee international vacuum electronics conference (ivec)}, author={Bui, T. and Read, M. and Lin, M. C. and Ives, R. L. and Tallis, B. and Tran, Hien}, year={2015} }
 @article{matzuka_chittenden_monteleone_tran_2015, title={Stochastic nonlinear mixed effects: a metformin case study}, volume={43}, ISSN={1567-567X 1573-8744}, url={http://dx.doi.org/10.1007/s10928-015-9456-7}, DOI={10.1007/s10928-015-9456-7}, abstractNote={In nonlinear mixed effect (NLME) modeling, the intra-individual variability is a collection of errors due to assay sensitivity, dosing, sampling, as well as model misspecification. Utilizing stochastic differential equations (SDE) within the NLME framework allows the decoupling of the measurement errors from the model misspecification. This leads the SDE approach to be a novel tool for model refinement. Using Metformin clinical pharmacokinetic (PK) data, the process of model development through the use of SDEs in population PK modeling was done to study the dynamics of absorption rate. A base model was constructed and then refined by using the system noise terms of the SDEs to track model parameters and model misspecification. This provides the unique advantage of making no underlying assumptions about the structural model for the absorption process while quantifying insufficiencies in the current model. This article focuses on implementing the extended Kalman filter and unscented Kalman filter in an NLME framework for parameter estimation and model development, comparing the methodologies, and illustrating their challenges and utility. The Kalman filter algorithms were successfully implemented in NLME models using MATLAB with run time differences between the ODE and SDE methods comparable to the differences found by Kakhi for their stochastic deconvolution.}, number={1}, journal={Journal of Pharmacokinetics and Pharmacodynamics}, publisher={Springer Science and Business Media LLC}, author={Matzuka, Brett and Chittenden, Jason and Monteleone, Jonathan and Tran, Hien}, year={2015}, month={Nov}, pages={85–98} }
 @article{matzuka_mehlsen_tran_olufsen_2015, title={Using Kalman Filtering to Predict Time-Varying Parameters in a Model Predicting Baroreflex Regulation During Head-Up Tilt}, volume={62}, ISSN={0018-9294 1558-2531}, url={http://dx.doi.org/10.1109/TBME.2015.2409211}, DOI={10.1109/tbme.2015.2409211}, abstractNote={The cardiovascular control system is continuously engaged to maintain homeostasis, but it is known to fail in a large cohort of patients suffering from orthostatic intolerance. Numerous clinical studies have been put forward to understand how the system fails, yet noninvasive clinical data are sparse, typical studies only include measurements of heart rate and blood pressure, as a result it is difficult to determine what mechanisms that are impaired. It is known, that blood pressure regulation is mediated by changes in heart rate, vascular resistance, cardiac contractility, and a number of other factors. Given that numerous factors contribute to changing these quantities, it is difficult to devise a physiological model describing how they change in time. One way is to build a model that allows these controlled quantities to change and to compare dynamics between subject groups. To do so, it requires more knowledge of how these quantities change for healthy subjects. This study compares two methods predicting time-varying changes in cardiac contractility and vascular resistance during head-up tilt. Similar to the study by Williams et al.[51], the first method uses piecewise linear splines, while the second uses the ensemble transform Kalman filter (ETKF) [1] , [11], [12], [33]. In addition, we show that the delayed rejection adaptive Metropolis (DRAM) algorithm can be used for predicting parameter uncertainties within the spline methodology, which is compared with the variability obtained with the ETKF. While the spline method is easier to set up, this study shows that the ETKF has a significantly shorter computational time. Moreover, while uncertainty of predictions can be augmented to spline predictions using DRAM, these are readily available with the ETKF.}, number={8}, journal={IEEE Transactions on Biomedical Engineering}, publisher={Institute of Electrical and Electronics Engineers (IEEE)}, author={Matzuka, Brett and Mehlsen, Jesper and Tran, Hien and Olufsen, Mette Sofie}, year={2015}, month={Aug}, pages={1992–2000} }
 @inproceedings{hamilton_hoang_layne_murray_padget_stafford_tran_2014, title={Applying Machine Learning Techniques to Baseball Pitch Prediction}, volume={1}, ISBN={9789897580185}, url={http://dx.doi.org/10.5220/0004763905200527}, DOI={10.5220/0004763905200527}, abstractNote={Major League Baseball, a professional baseball league in the US and Canada, is one of the most popular sports leagues in the world. Partially because of its popularity and the wide availability of data from games, baseball has become the subject of significant statistical and mathematical analysis. Pitch analysis is especially useful for helping a team better understand the pitch behavior it may face during a game, allowing the team to develop a corresponding batting strategy to combat the predicted pitch behavior. We apply several common machine learning classification methods to PITCHf/x data to classify pitches by type. We then extend the classification task to prediction by utilizing features only known before a pitch is thrown. By performing significant feature analysis and introducing a novel approach for feature selection, moderate improvement over former results is achieved.}, booktitle={Proceedings of the 3rd International Conference on Pattern Recognition Applications and Methods}, publisher={SCITEPRESS - Science and and Technology Publications}, author={Hamilton, M. and Hoang, P. and Layne, L. and Murray, J. and Padget, D. and Stafford, C. and Tran, H.}, editor={De Marsico, M. and Tabbone, A. and Fred, A.Editors}, year={2014}, pages={520–527} }
 @inbook{attarian_danis_gronsbell_iervolino_layne_padgett_tran_2014, title={Baseball pitch classification}, ISBN={9781138001367 9781315761817}, url={http://dx.doi.org/10.1201/b16763-43}, DOI={10.1201/b16763-43}, abstractNote={The development of monitoring and inventory system using Radio Frequency Identification (RFID) technology could answer these problems. Thus, this project has been conceived. It aimed to develop a monitoring and inventory system to control access of laboratory rooms. The study was based on a hierarchical structure that used wireless technology. The project would enable the staff to have ready access to all information on the status of the equipment such as previous and current borrowers, condition of the equipment, date of purchase, received date, location of the equipment, etc. In this manner, monitoring and inventory system of all equipment could be improved.}, booktitle={IAENG Transactions on Engineering Sciences}, publisher={CRC Press}, author={Attarian, A and Danis, G and Gronsbell, J and Iervolino, G and Layne, L and Padgett, D and Tran, H}, year={2014}, month={Apr}, pages={393–399} }
 @article{tran_attarian_danis_gronsbell_iervolino_2013, place={Hong Kong}, series={Lecture Notes in Engineering and Computer Science}, title={A Comparison of Feature Selection and Classification Algorithms in Identifying Baseball Pitches}, journal={International MultiConference of Engineers and Computer Scientists : IMECS 2013 : 13-15 March, 2013, the Royal Garden Hotel, Kowloon, Hong Kong}, publisher={Newswood Ltd. : International Association of Engineers,}, author={Tran, H. and Attarian, A. and Danis, G. and Gronsbell, J. and Iervolino, G.}, editor={Ao, S.I. and Castillo, O. and Douglas, C. and Feng, D.D. and Lee, Jeong-A.Editors}, year={2013}, pages={263–268}, collection={Lecture Notes in Engineering and Computer Science} }
 @article{attarian_batzel_matzuka_tran_2013, title={Application of the Unscented Kalman Filtering to Parameter Estimation}, volume={2064}, ISBN={["978-3-642-32881-7"]}, ISSN={["0075-8434"]}, DOI={10.1007/978-3-642-32882-4_4}, abstractNote={Filtering is a methodology used to combine a set of observations with a model to obtain the optimal state. This technique can be extended to estimate the state of the system as well as the unknown model parameters. Estimating the model parameters given a set of data is often referred to as the inverse problem. Filtering provides many benefits to the inverse problem by providing estimates in real time and allowing model errors to be taken into account. Assuming a linear model and Gaussian noises, the optimal filter is the Kalman filter. However, these assumptions rarely hold for many problems of interest, so a number of extensions have been proposed in the literature to deal with nonlinear dynamics. In this chapter, we illustrate the application of one approach to deal with nonlinear model dynamics, the so-called unscented Kalman filter. In addition, we will also show how some of the tools for model validation discussed in other chapters of this volume can be used to improve the estimation process.}, journal={MATHEMATICAL MODELING AND VALIDATION IN PHYSIOLOGY: APPLICATIONS TO THE CARDIOVASCULAR AND RESPIRATORY SYSTEMS}, author={Attarian, Adam and Batzel, Jerry J. and Matzuka, Brett and Tran, Hien}, year={2013}, pages={75–88} }
 @inproceedings{tran_williams_olufsen_2013, title={Cardiovascular Dynamics during Head-up Tilt assessed Via a Pulsatile and Non-pulsatile Model}, volume={1}, ISBN={9789898565693}, url={http://dx.doi.org/10.5220/0004624006730680}, DOI={10.5220/0004624006730680}, booktitle={Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications}, publisher={SciTePress - Science and and Technology Publications}, author={Tran, H. and Williams, N. and Olufsen, M.S.}, year={2013}, pages={673–680} }
 @inproceedings{tran_matzuka_mehlsen_olufsen_williams_2012, title={A Kalman Filtering Based Approach for the Modeling of the Cardiovascular Regulation System}, ISBN={978-88-97999-13-3}, booktitle={Proceeding of The 1st international workshop on innovative simulation for healthcare, I-WISH}, author={Tran, H. and Matzuka, B. and Mehlsen, J. and Olufsen, M. and Williams, N.}, editor={Backfrieder, W. and Bruzzone, A. and Longo, F. and Novak, V. and Rosen, J.Editors}, year={2012}, pages={107–112} }
 @inproceedings{olsen_mehlsen_otteson_tran_olufsen_2012, title={Global Sensitivity and Identifiability Analysis Applied to a Model Predicting Baroreflex Regulation During Head-up Tilt}, ISBN={978-88-97999-13-3}, booktitle={Proceeding of The 1st international workshop on innovative simulation for healthcare, I-WISH}, author={Olsen, C.H. and Mehlsen, J. and Otteson, J. and Tran, H. and Olufsen, M.S.}, editor={Backfrieder, W. and Bruzzone, A. and Longo, F. and Novak, V. and Rosen, J.Editors}, year={2012}, pages={81–86} }
 @article{banks_bliss_tran_2012, title={Modeling Red Blood Cell and Iron Dynamics in Patients with Chronic Kidney Disease}, volume={75}, number={1}, journal={International Journal of Pure and Applied Mathematics}, author={Banks, H.T. and Bliss, K.M. and Tran, H.}, year={2012}, pages={103–140} }
 @inbook{tran_2012, place={Berkeley, CA}, title={Optimal Control Theory}, ISBN={9780520951785}, booktitle={Encyclopedia of Theoretical Ecology}, publisher={University of California Press}, author={Tran, H.}, editor={Hastings, A. and Gross, L.Editors}, year={2012}, pages={519–523} }
 @article{banks_beeler_kwon_lewis_toivanen_tran_2011, title={An SDRE-Based Approach for HIV Feedback Control and Control of Thin Film Growth in a CVD Reactor}, volume={44}, ISSN={1474-6670}, url={http://dx.doi.org/10.3182/20110828-6-it-1002.03412}, DOI={10.3182/20110828-6-it-1002.03412}, abstractNote={Abstract A number of computational methodologies have been proposed in the literature to design and synthesize feedback controls when the plant is modeled by nonlinear dynamical systems. One of the highly promising and rapidly emerging methodologies for designing nonlinear controllers is the state-dependent Riccati equation (SDRE) method in the context of the nonlinear regulator problem. In essence, SDRE mimics the linear quadratic regulator theory by using direct parametrization to rewrite the nonlinear state function as a product of a state-dependent coefficient matrix with the state vector. This paper presents an overview of our successful effort on the application of SDRE for the regulation of the growth of thin films in a high pressure chemical vapor deposition (CVD) and for the development of optimal dynamic multi-drug therapies for human immunodeficiency virus (HIV) infection.}, number={1}, journal={IFAC Proceedings Volumes}, publisher={Elsevier BV}, author={Banks, H.T. and Beeler, S.C. and Kwon, Hee-Dae and Lewis, B.M. and Toivanen, J.A. and Tran, H.T.}, year={2011}, month={Jan}, pages={9601–9606} }
 @article{david_tran_banks_2011, title={Receding Horizon Control of HIV}, volume={32}, ISSN={["1099-1514"]}, DOI={10.1002/oca.969}, abstractNote={Abstract}, number={6}, journal={OPTIMAL CONTROL APPLICATIONS & METHODS}, author={David, John and Tran, Hien and Banks, H. T.}, year={2011}, pages={681–699} }
 @article{manning_schlosser_tran_2010, title={A Multicompartment Liver-based Pharmacokinetic Model for Benzene and its Metabolites in Mice}, volume={72}, ISSN={["0092-8240"]}, DOI={10.1007/s11538-009-9459-x}, abstractNote={Benzene is a highly flammable, colorless liquid. Ubiquitous exposures result from its presence in gasoline vapors, cigarette smoke, and industrial processes. After uptake into the body, benzene undergoes a series of metabolic transformations to multiple metabolites that exert toxic effects on the bone marrow. We developed a physiologically based pharmacokinetic model for the uptake and elimination of benzene in mice to relate the concentration of inhaled and orally administered benzene to the tissue doses of benzene and its key metabolites. This model takes into account the zonal distribution of enzymes and metabolism in the liver rather than treating the liver as one homogeneous compartment, and considers metabolism in tissues other than the liver. Analysis was done to examine the existence and uniqueness of solutions of the system. We then formulated an inverse problem to obtain estimates for the unknown parameters; data from multiple laboratories and experiments were used. Despite the sources of variability, the model simulations matched the data reasonably well in most cases. Our study shows that the multicompartment metabolism model does improve predictions over the previous model (Cole et al. in J. Toxicol. Environ. Health, 439-465, 2001) and that in vitro metabolic constants can be successfully extrapolated to predict in vivo data for benzene metabolism and dosimetry.}, number={3}, journal={BULLETIN OF MATHEMATICAL BIOLOGY}, author={Manning, Cammey C. and Schlosser, Paul M. and Tran, Hien T.}, year={2010}, month={Apr}, pages={507–540} }
 @article{banks_hu_kenz_tran_2010, title={A comparison of nonlinear filtering approaches in the context of an HIV model}, volume={7}, ISSN={1551-0018}, url={http://dx.doi.org/10.3934/mbe.2010.7.213}, DOI={10.3934/mbe.2010.7.213}, abstractNote={In this paper three different filtering methods, the Extended Kalman Filter (EKF), the Gauss-Hermite Filter (GHF), and the Unscented Kalman Filter (UKF), are compared for state-only and coupled state and parameter estimation when used with log state variables of a model of the immunologic response to the human immunodeficiency virus (HIV) in individuals. The filters are implemented to estimate model states as well as model parameters from simulated noisy data, and are compared in terms of estimation accuracy and computational time. Numerical experiments reveal that the GHF is the most computationally expensive algorithm, while the EKF is the least expensive one. In addition, computational experiments suggest that there is little difference in the estimation accuracy between the UKF and GHF. When measurements are taken as frequently as every week to two weeks, the EKF is the superior filter. When measurements are further apart, the UKF is the best choice in the problem under investigation.}, number={2}, journal={Mathematical Biosciences and Engineering}, publisher={American Institute of Mathematical Sciences (AIMS)}, author={Banks, H. and Hu, Shuhua and Kenz, Zackary and Tran, Hien}, year={2010}, month={Apr}, pages={213–236} }
 @article{ives_attarian_tallis_andujar_forstall_tran_read_bui_2010, title={Design of Doubly Convergent Multiple-Beam Electron Guns}, volume={38}, ISSN={["0093-3813"]}, DOI={10.1109/tps.2010.2046501}, abstractNote={In an effort to achieve higher power RF source performance, designers are utilizing distributed beam devices, such as sheet beams and multiple beams. A limitation is the amount of current that can be emitted by the cathode while still achieving long cathode lifetimes. The desire is to develop distributed beam devices that utilize fundamental mode cavities in the RF circuit. For multiple-beam devices, where the individual beams propagate at the same radius as the cathode, a limitation is reached, where the size of the cathode becomes limited by the space available. A solution is to place the cathodes at a larger radius and compress the beams toward the radius required for fundamental mode cavities. This paper describes the design of a multiple-beam gun where the ensemble of beams is compressed toward the device axis while still achieving parallel propagation through the RF circuit.}, number={6}, journal={IEEE TRANSACTIONS ON PLASMA SCIENCE}, author={Ives, R. Lawrence and Attarian, Adam and Tallis, William and Andujar, Cynthia and Forstall, Virginia and Tran, Hien and Read, Michael and Bui, Thuc}, year={2010}, month={Jun}, pages={1337–1344} }
 @article{ives_attarian_bui_read_david_tran_tallis_davis_gadson_blach_et al._2009, title={Computational design of asymmetric electron beam devices}, volume={56}, DOI={10.1109/TED.2009.2015421}, abstractNote={Three-dimensional design codes are allowing the development of more complex electron beam devices with significant performance improvements over axially symmetric devices. Distributed beam RF devices, including multiple-beam and sheet-beam designs, allow significant reduction in operating voltage with improved efficiency and bandwidth. The increased parameter space, however, makes the design process extremely complicated and costly. This paper describes optimization techniques to automate the most time-consuming tasks of the design, which is searching the available parameter space to optimize performance. Both sheet-beam and multiple-beam designs are considered.}, number={5}, journal={IEEE Transactions on Electron Devices}, author={Ives, R. L. and Attarian, A. and Bui, T. and Read, M. and David, J. and Tran, Hien and Tallis, W. J. and Davis, S. and Gadson, S. E. and Blach, N. and et al.}, year={2009}, pages={753–761} }
 @article{david_tran_banks_2009, title={HIV Model Analysis and Estimation Implementation Under Optimal Control Based Treatment Strategies}, volume={57}, number={3}, journal={International Journal of Pure and Applied Mathematics}, author={David, J. and Tran, H. and Banks, H.T.}, year={2009}, pages={357–392} }
 @book{banks_tran_2009, title={Mathematical and experimental modeling of physical and biological processes}, ISBN={9781420073379}, publisher={Boca Raton : CRC Press}, author={Banks, H. T. and Tran, H. T.}, year={2009} }
 @inproceedings{aoi_gremaud_tran_novak_olufsen_2009, title={Modeling cerebral blood flow and regulation}, url={http://dx.doi.org/10.1109/IEMBS.2009.5334057}, DOI={10.1109/IEMBS.2009.5334057}, abstractNote={Cerebral autoregulation is a homeostatic mechanism which maintains blood flow despite changes in blood pressure in order to meet local metabolic demands. Several mechanisms play a role in cerebral autoregulation in order to adjust vascular tone and caliber of the cerebral vessels, but the exact etiology of the dynamics of these mechanism is not well understood. In this study, we discuss two patient specific models predicting cerebral blood flow velocity during postural change from sitting to standing. One model characterises cerebral autoregulation, the other describes the beat-to-beat distribution of blood flow to the major regions of the brain. Both models have been validated against experimental data from a healthy young subject.}, booktitle={2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society}, publisher={IEEE}, author={Aoi, M. and Gremaud, P. and Tran, H.T. and Novak, V. and Olufsen, M.S.}, year={2009}, month={Sep} }
 @article{fink_batzel_tran_2008, title={A respiratory system model: Parameter estimation and sensitivity analysis}, volume={8}, ISSN={["1567-8822"]}, DOI={10.1007/s10558-007-9051-7}, abstractNote={In this paper we compare several approaches to identifying certain key respiratory control parameters relying on data normally available from non-invasive measurements. We consider a simple model of the respiratory control system and describe issues related to numerical estimates of key parameters involved in respiratory function such as central and peripheral control gains, transport delay, and lung compartment volumes. The combination of model-specific structure and limited data availability influences the parameter estimation process. Methods for studying how to improve the parameter estimation process are examined including classical and generalized sensitivity analysis, and eigenvalue grouping. These methods are applied and compared in the context of clinically available data. These methods are also compared in conjunction with specialized tests such as the minimally invasive single-breath CO2 test that can improve the estimation, and the enforced fixed breathing test, which opens the control loop in the system. The analysis shows that it is impossible to estimate central and peripheral gain simultaneously without usage of ventilation measurement and a controlled perturbation of the respiratory system, such as the CO2 test. The numerical results are certainly model dependent, but the illustrated methods, the nature of the comparisons, and protocols will carry over to other models and data configurations.}, number={2}, journal={CARDIOVASCULAR ENGINEERING}, author={Fink, Martin and Batzel, Jerry J. and Tran, Hien}, year={2008}, month={Jun}, pages={120–134} }
 @article{david_ives_tran_bui_read_2008, title={Computer optimized design of electron guns}, volume={36}, ISSN={["1939-9375"]}, DOI={10.1109/TPS.2007.913884}, abstractNote={This paper considers the problem of designing electron guns using computer optimization techniques. Several different design parameters are manipulated while considering multiple design criteria, including beam and gun properties. The optimization routines are described. Examples of guns designed using these techniques are presented. Future research is also described.}, number={1}, journal={IEEE TRANSACTIONS ON PLASMA SCIENCE}, author={David, John and Ives, R. Lawrence and Tran, Hien T. and Bui, Thuc and Read, Michael E.}, year={2008}, month={Feb}, pages={156–168} }
 @inproceedings{ives_bui_read_david_attarian_tran_2008, title={Computer optimized design of electron guns}, ISBN={9781424417155}, url={http://dx.doi.org/10.1109/ivelec.2008.4556399}, DOI={10.1109/ivelec.2008.4556399}, abstractNote={Calabazas Creek Research, Inc. (CCR) and North Carolina State University are developing optimization techniques for advanced, 3D, electron guns. Our approach uses advanced solid modeling CAD programs capable of controlling geometrical parameters with design tables manipulated by an optimization control program. Geometrical and parametric changes are simulated using a 3D, finite element, adaptive meshing charged particle program. Results of the beam analysis are analyzed and an optimization routine modifies the parameters to obtain user-defined performance goals. These techniques are applied to a number of gun geometries, and the results are described.}, booktitle={2008 IEEE International Vacuum Electronics Conference}, publisher={IEEE}, author={Ives, R. Lawrence and Bui, Thuc and Read, Michael and David, John and Attarian, Adam and Tran, Hien}, year={2008}, month={May} }
 @inproceedings{david_ives_tran_bui_read_attarian_posth_2008, place={New York}, title={Implementation of Computer Optimization for Design of Electron Guns}, booktitle={'Proceedings of the 9th IEEE International Vacuum Electronics Conference}, publisher={IEEE}, author={David, J. and Ives, R.L. and Tran, H. and Bui, T. and Read, M. and Attarian, A. and Posth, M.}, year={2008} }
 @inproceedings{ives_bui_attarian_davis_gadson_tallis_tran_read_posth_2008, title={Implementation of computer optimization for design of electron guns}, ISBN={9781424421190}, url={http://dx.doi.org/10.1109/icimw.2008.4665480}, DOI={10.1109/icimw.2008.4665480}, abstractNote={Computer optimization can dramatically reduce the time and cost to design electron beam devices. It also allows design of complex, 3D devices that would be impractical with manual design. Recent implementation of a magnetic solver into a 3D finite element electron beam trajectory code is allowing optimized design of the electrostatic, optical and magnetic configuration of 3D device. The process and examples will be presented.}, booktitle={2008 33rd International Conference on Infrared, Millimeter and Terahertz Waves}, publisher={IEEE}, author={Ives, R. Lawrence and Bui, Thuc and Attarian, Adam and Davis, Steven and Gadson, Sean and Tallis, William and Tran, Hien and Read, Michael and Posth, Mattie}, year={2008}, month={Sep} }
 @article{batzel_novak_kappel_olufsen_tran_2008, title={Introduction to the special issues: Short-term cardiovascular-respiratory control mechanisms}, volume={8}, ISSN={["1567-8822"]}, DOI={10.1007/s10558-007-9053-5}, abstractNote={This and the following issue of Cardiovascular Engineering are special issues reflecting research discussed during an interdisciplinary focused workshop entitled Short-term Cardiovascular–Respiratory Control Mechanisms. The workshop was organized by Mette Olufsen and Hien Tran at the Department of Mathematics at North Carolina State University, Jerry Batzel and Franz Kappel at the Institute for Mathematics and Scientific Computing, University of Graz, and Vera Novak at the Department of Gerontology at Harvard Medical School, and hosted by the American Institute of Mathematics (AIM), Palo Alto, California, October 9–13, 2006. The workshop was co-sponsored by AIM and the National Science Foundation.}, number={1}, journal={CARDIOVASCULAR ENGINEERING}, author={Batzel, Jerry J. and Novak, Vera and Kappel, Franz and Olufsen, Mette S. and Tran, Hien T.}, year={2008}, month={Mar}, pages={1–4} }
 @article{olufsen_alston_tran_ottesen_novak_2008, title={Modeling heart rate regulation - Part I: Sit-to-stand versus head-up tilt}, volume={8}, ISSN={["1573-6806"]}, DOI={10.1007/s10558-007-9050-8}, abstractNote={In this study we describe a model predicting heart rate regulation during postural change from sitting to standing and during head-up tilt in five healthy elderly adults. The model uses blood pressure as an input to predict baroreflex firing-rate, which in turn is used to predict efferent parasympathetic and sympathetic outflows. The model also includes the combined effects of vestibular and central command stimulation of muscle sympathetic nerve activity, which is increased at the onset of postural change. Concentrations of acetylcholine and noradrenaline, predicted as functions of sympathetic and parasympathetic outflow, are then used to estimate the heart rate response. Dynamics of the heart rate and the baroreflex firing rate are modeled using a system of coupled ordinary delay differential equations with 17 parameters. We have derived sensitivity equations and ranked sensitivities of all parameters with respect to all state variables in our model. Using this model we show that during head-up tilt, the baseline firing-rate is larger than during sit-to-stand and that the combined effect of vestibular and central command stimulation of muscle sympathetic nerve activity is less pronounced during head-up tilt than during sit-to-stand.}, number={2}, journal={CARDIOVASCULAR ENGINEERING}, author={Olufsen, Mette S. and Alston, April V. and Tran, Hien T. and Ottesen, Johnny T. and Novak, Vera}, year={2008}, month={Jun}, pages={73–87} }
 @article{ellwein_tran_zapata_novak_olufsen_2008, title={Sensitivity analysis and model assessment: Mathematical models for arterial blood flow and blood pressure}, volume={8}, ISSN={["1573-6806"]}, DOI={10.1007/s10558-007-9047-3}, abstractNote={The complexity of mathematical models describing the cardiovascular system has grown in recent years to more accurately account for physiological dynamics. To aid in model validation and design, classical deterministic sensitivity analysis is performed on the cardiovascular model first presented by Olufsen, Tran, Ottesen, Ellwein, Lipsitz and Novak (J Appl Physiol 99(4):1523-1537, 2005). This model uses 11 differential state equations with 52 parameters to predict arterial blood flow and blood pressure. The relative sensitivity solutions of the model state equations with respect to each of the parameters is calculated and a sensitivity ranking is created for each parameter. Parameters are separated into two groups: sensitive and insensitive parameters. Small changes in sensitive parameters have a large effect on the model solution while changes in insensitive parameters have a negligible effect. This analysis was successfully used to reduce the effective parameter space by more than half and the computation time by two thirds. Additionally, a simpler model was designed that retained the necessary features of the original model but with two-thirds of the state equations and half of the model parameters.}, number={2}, journal={CARDIOVASCULAR ENGINEERING}, author={Ellwein, Laura M. and Tran, Hien T. and Zapata, Cheryl and Novak, Vera and Olufsen, Mette S.}, year={2008}, month={Jun}, pages={94–108} }
 @article{yokley_tran_schlosser_2008, title={Sensory irritation response in rats: Modeling, analysis and validation}, volume={70}, ISSN={["0092-8240"]}, DOI={10.1007/s11538-007-9268-z}, abstractNote={Inhaled gases can cause respiratory depression by irritating (stimulating) nerves in the nasal cavity. Respiratory depression, in turn, decreases the rate of delivery of those gases to the stimulated nerves, potentially leading to a complex feedback response. In order to better understand how the nervous system responds to such chemicals, a mathematical model is created to describe how the presence of irritants affects respiration in the rat. The ordinary differential equation model describes the dosimetry of these reactive gases in the respiratory tract, with particular focus on the physiology of the upper respiratory tract, and on the neurological control of respiration rate due to signaling from the irritant-responsive nerves in the nasal cavity. The ventilation equation is altered to account for an apparent change in dynamics between the initial ventilation decrease and the recovery to steady state as seen in formaldehyde exposure data. Further, the model is evaluated and improved through optimization of particular parameters to describe formaldehyde-induced respiratory response data and through sensitivity analysis. The model predicts the formaldehyde data well, and hence the model is thought to be a reasonable description of the physiological system of sensory irritation. The model is also expected to translate well to other irritants.}, number={2}, journal={BULLETIN OF MATHEMATICAL BIOLOGY}, author={Yokley, Karen A. and Tran, Hien and Schlosser, Paul M.}, year={2008}, month={Feb}, pages={555–588} }
 @book{batzel_novak_kappel_olufsen_tran_2008, title={Special Issues: Short-term Cardiovascular–Respiratory Control Mechanisms}, volume={9}, number={1}, journal={Journal of Cardiovascular Engineering}, year={2008}, month={Mar}, pages={1–71} }
 @article{zagera_schlosser_tran_2007, title={A delayed nonlinear PBPK model for genistein dosimetry in rats}, volume={69}, ISSN={["1522-9602"]}, DOI={10.1007/s11538-006-9068-x}, abstractNote={Genistein is an endocrine-active compound (EAC) found in soy products. It has been linked to beneficial effects such as mammary tumor growth suppression and adverse endocrine-related effects such as reduced birth weight in rats and humans. In its conjugated form, genistein is excreted in the bile, which is a significant factor in its pharmacokinetics. Experimental data suggest that genistein induces a concentration-dependent suppression of biliary excretion. In this article, we describe a physiologically based pharmacokinetic (PBPK) model that focuses on biliary excretion with the goal of accurately simulating the observed suppression. The mathematical model is a system of nonlinear differential equations with state-dependent delay to describe biliary excretion. The model was analyzed to examine local existence and uniqueness of a solution to the equations. Furthermore, unknown parameters were estimated, and the mathematical model was compared against published experimental data.}, number={1}, journal={BULLETIN OF MATHEMATICAL BIOLOGY}, author={Zagera, Michael G. and Schlosser, Paul M. and Tran, Hien T.}, year={2007}, month={Jan}, pages={93–117} }
 @misc{batzel_kappel_schneditz_tran_2007, title={Cardiovascular and Respiratory Systems}, ISBN={9780898716177 9780898717457}, url={http://dx.doi.org/10.1137/1.9780898717457}, DOI={10.1137/1.9780898717457}, abstractNote={Preface 1. The cardiovascular system under an ergometric workload 2. Respiratory modeling 3. Cardio-Respiratory Modeling 4. Blood volume and the venous system 5. Future directions Appendix A. Supplemental calculations B. A Nonlinear feedback law C. Retarded functional differential equations: Basic theory Bibliography Index.}, publisher={Society for Industrial and Applied Mathematics}, author={Batzel, Jerry J. and Kappel, Franz and Schneditz, Daniel and Tran, Hien T.}, year={2007}, month={Jan} }
 @inproceedings{ives_bui_david_tran_read_2007, title={Computer optimization of electron gun designs}, ISBN={9781424414383}, url={http://dx.doi.org/10.1109/icimw.2007.4516435}, DOI={10.1109/icimw.2007.4516435}, abstractNote={Computer optimization is applied to three dimensional design of electron guns. The resulting designs exhibit improved performance with significantly reduced design cost compared to manual design. Design tables update geometric parameters in a solid modeling program, including dimensions for points defining spline surfaces. Algorithms then modified the geometry and other parameters based on goal functions defining the desired performance. Optimal designs were achieved by automatic execution of the optimization loop. Results for confined flow Pierce guns, sheet beam guns, and multiple beam guns will be described.}, booktitle={2007 Joint 32nd International Conference on Infrared and Millimeter Waves and the 15th International Conference on Terahertz Electronics}, publisher={IEEE}, author={Ives, R.L. and Bui, Thuc and David, J. and Tran, Hien and Read, M.}, year={2007}, month={Sep} }
 @article{david_kory_tran_ives_chernin_2007, title={Enhanced features for design of traveling wave tubes using CHRISTINE-1D}, volume={35}, ISSN={["0093-3813"]}, DOI={10.1109/TPS.2007.902128}, abstractNote={Traveling wave tubes (TWTs) are vacuum devices invented in the early 1940s for amplification of radio frequency power. These devices are critical for radar, communications, and electronic warfare missions in the military, as well as in commercial applications. The physics-based design and simulation code CHRISTINE-1D was used in the past to explore different TWT circuit designs and to automate the process of parameter estimation. However, the current capability of CHRISTINE-1D allows optimization of only helix TWT designs and includes a limited number of optimization goal functions. In addition, the current optimizer in CHRISTINE-1D employs a modified steepest descent method to carry out the optimization process. The objectives of this paper are threefold: (1) to investigate optimization techniques that may be better suited for this problem (for example, simplex type methods such as Nelder-Mead and Dividing Rectangles); (2) to allow optimization of nonhelix TWTs; and (3) to implement new optimization goal functions. Finally, to show the feasibility of our approach, we apply our optimization algorithms to the problem of designing a folded waveguide slow-wave circuit.}, number={4}, journal={IEEE TRANSACTIONS ON PLASMA SCIENCE}, author={David, John A. and Kory, Carol L. and Tran, Hien T. and Ives, R. Lawrence and Chernin, David}, year={2007}, month={Aug}, pages={1056–1064} }
 @article{banks_lewis_tran_2007, title={Nonlinear feedback controllers and compensators: a state-dependent Riccati equation approach}, volume={37}, ISSN={["1573-2894"]}, DOI={10.1007/s10589-007-9015-2}, abstractNote={State-dependent Riccati equation (SDRE) techniques are rapidly emerging as general design and synthesis methods of nonlinear feedback controllers and estimators for a broad class of nonlinear regulator problems. In essence, the SDRE approach involves mimicking standard linear quadratic regulator (LQR) formulation for linear systems. In particular, the technique consists of using direct parameterization to bring the nonlinear system to a linear structure having state-dependent coefficient matrices. Theoretical advances have been made regarding the nonlinear regulator problem and the asymptotic stability properties of the system with full state feedback. However, there have not been any attempts at the theory regarding the asymptotic convergence of the estimator and the compensated system. This paper addresses these two issues as well as discussing numerical methods for approximating the solution to the SDRE. The Taylor series numerical methods works only for a certain class of systems, namely with constant control coefficient matrices, and only in small regions. The interpolation numerical method can be applied globally to a much larger class of systems. Examples will be provided to illustrate the effectiveness and potential of the SDRE technique for the design of nonlinear compensator-based feedback controllers.}, number={2}, journal={COMPUTATIONAL OPTIMIZATION AND APPLICATIONS}, author={Banks, H. T. and Lewis, B. M. and Tran, H. T.}, year={2007}, month={Jun}, pages={177–218} }
 @article{lewis_tran_2007, title={Real-time implementation of a frequency shaping controller on a cantilever beam}, volume={57}, ISSN={["0168-9274"]}, DOI={10.1016/j.apnum.2006.07.017}, abstractNote={In this paper, we present the real time implementation of a control methodology for the attenuation of beam vibrations in a smart structure paradigm caused by a narrow-band exogenous force. By narrow-band exogenous force we mean a periodic force over a narrow frequency band or a particular harmonic. The particular control method is based on the minimization of a frequency dependent quadratic cost functional. This control method has been used successfully in various applications; however, this investigation differs from other works in that it emphasizes the real-time implementation of this model-based control methodology using real-time partial state measurements.}, number={5-7}, journal={APPLIED NUMERICAL MATHEMATICS}, author={Lewis, B. M. and Tran, H. T.}, year={2007}, pages={778–790} }
 @article{fink_attarian_tran_2007, title={Subset selection for parameter estimation in an HIV model}, volume={7}, ISSN={1617-7061 1617-7061}, url={http://dx.doi.org/10.1002/pamm.200700319}, DOI={10.1002/pamm.200700319}, abstractNote={Abstract}, number={1}, journal={PAMM}, publisher={Wiley}, author={Fink, Martin and Attarian, Adam and Tran, Hien}, year={2007}, month={Dec}, pages={1121501–1121502} }
 @article{banks_kwon_toivanen_tran_2006, title={A state-dependent Riccati equation-based estimator approach for HIV feedback control}, volume={27}, ISSN={["1099-1514"]}, DOI={10.1002/oca.773}, abstractNote={Abstract}, number={2}, journal={OPTIMAL CONTROL APPLICATIONS & METHODS}, author={Banks, HT and Kwon, HD and Toivanen, JA and Tran, HT}, year={2006}, pages={93–121} }
 @inproceedings{ives_read_bui_david_tran_2006, title={Computer Optimized Gun Design}, ISBN={1424403995 1424404002}, url={http://dx.doi.org/10.1109/icimw.2006.368358}, DOI={10.1109/icimw.2006.368358}, abstractNote={Computer optimization can explore a wider parameter space than practical with manual design, particularly for 3D geometries. This allows rapid, economical development of higher performance devices. The proliferation of parametric solid modeling programs allows optimization of both geometry and operating parameters. This presentation described computer optimization in the 3D trajectory code beam optics analysis (BOA). This is possible because meshing in BOA is completely automatic, allowing the program to be controlled by the optimization routines.}, booktitle={2006 Joint 31st International Conference on Infrared Millimeter Waves and 14th International Conference on Teraherz Electronics}, publisher={IEEE}, author={Ives, R. L. and Read, M.E. and Bui, Thuc and David, John and Tran, Hien}, year={2006}, month={Sep} }
 @inproceedings{tran_banks_david_toivanen_kwon_2006, place={Kyoto}, title={Dynamic Multidrug Therapies for HIV: Feedback and Structured Treatment Interruption Control Approaches}, booktitle={MTNS 2006 : proceedings of the 17th international symposium on mathematical theory of networks and systems, Kyoto, Japan, 24-28.07.2006.}, publisher={Kyoto University}, author={Tran, H. and Banks, H.T. and David, John and Toivanen, J.A. and Kwon, Hae-Dae}, year={2006} }
 @article{olufsen_tran_ottesen_lipsitz_novak_2006, title={Modeling baroreflex regulation of heart rate during orthostatic stress}, volume={291}, ISSN={["1522-1490"]}, DOI={10.1152/ajpregu.00205.2006}, abstractNote={ During orthostatic stress, arterial and cardiopulmonary baroreflexes play a key role in maintaining arterial pressure by regulating heart rate. This study presents a mathematical model that can predict the dynamics of heart rate regulation in response to postural change from sitting to standing. The model uses blood pressure measured in the finger as an input to model heart rate dynamics in response to changes in baroreceptor nerve firing rate, sympathetic and parasympathetic responses, vestibulo-sympathetic reflex, and concentrations of norepinephrine and acetylcholine. We formulate an inverse least squares problem for parameter estimation and successfully demonstrate that our mathematical model can accurately predict heart rate dynamics observed in data obtained from healthy young, healthy elderly, and hypertensive elderly subjects. One of our key findings indicates that, to successfully validate our model against clinical data, it is necessary to include the vestibulo-sympathetic reflex. Furthermore, our model reveals that the transfer between the nerve firing and blood pressure is nonlinear and follows a hysteresis curve. In healthy young people, the hysteresis loop is wide, whereas, in healthy and hypertensive elderly people, the hysteresis loop shifts to higher blood pressure values, and its area is diminished. Finally, for hypertensive elderly people, the hysteresis loop is generally not closed, indicating that, during postural change from sitting to standing, baroreflex modulation does not return to steady state during the first minute of standing. }, number={5}, journal={AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY}, author={Olufsen, Mette S. and Tran, Hien T. and Ottesen, Johnny T. and Lipsitz, Lewis A. and Novak, Vera}, year={2006}, month={Nov}, pages={R1355–R1368} }
 @article{yokley_tran_pekari_rappaport_riihimaki_rothman_waidyanatha_schlosser_2006, title={Physiologically-based pharmacokinetic modeling of benzene in humans: A Bayesian approach}, volume={26}, ISSN={["0272-4332"]}, DOI={10.1111/j.1539-6924.2006.00789.x}, abstractNote={Benzene is myelotoxic and leukemogenic in humans exposed at high doses (>1 ppm, more definitely above 10 ppm) for extended periods. However, leukemia risks at lower exposures are uncertain. Benzene occurs widely in the work environment and also indoor air, but mostly below 1 ppm, so assessing the leukemia risks at these low concentrations is important. Here, we describe a human physiologically‐based pharmacokinetic (PBPK) model that quantifies tissue doses of benzene and its key metabolites, benzene oxide, phenol, and hydroquinone after inhalation and oral exposures. The model was integrated into a statistical framework that acknowledges sources of variation due to inherent intra‐ and interindividual variation, measurement error, and other data collection issues. A primary contribution of this work is the estimation of population distributions of key PBPK model parameters. We hypothesized that observed interindividual variability in the dosimetry of benzene and its metabolites resulted primarily from known or estimated variability in key metabolic parameters and that a statistical PBPK model that explicitly included variability in only those metabolic parameters would sufficiently describe the observed variability. We then identified parameter distributions for the PBPK model to characterize observed variability through the use of Markov chain Monte Carlo analysis applied to two data sets. The identified parameter distributions described most of the observed variability, but variability in physiological parameters such as organ weights may also be helpful to faithfully predict the observed human‐population variability in benzene dosimetry.}, number={4}, journal={RISK ANALYSIS}, author={Yokley, Karen and Tran, Hien T. and Pekari, Kaija and Rappaport, Stephen and Riihimaki, Vesa and Rothman, Nat and Waidyanatha, Suramya and Schlosser, Paul M.}, year={2006}, month={Aug}, pages={925–943} }
 @article{olufsen_ottesen_tran_ellwein_lipsitz_novak_2005, title={Blood pressure and blood flow variation during postural change from sitting to standing: model development and validation}, volume={99}, ISSN={["1522-1601"]}, DOI={10.1152/japplphysiol.00177.2005}, abstractNote={ Short-term cardiovascular responses to postural change from sitting to standing involve complex interactions between the autonomic nervous system, which regulates blood pressure, and cerebral autoregulation, which maintains cerebral perfusion. We present a mathematical model that can predict dynamic changes in beat-to-beat arterial blood pressure and middle cerebral artery blood flow velocity during postural change from sitting to standing. Our cardiovascular model utilizes 11 compartments to describe blood pressure, blood flow, compliance, and resistance in the heart and systemic circulation. To include dynamics due to the pulsatile nature of blood pressure and blood flow, resistances in the large systemic arteries are modeled using nonlinear functions of pressure. A physiologically based submodel is used to describe effects of gravity on venous blood pooling during postural change. Two types of control mechanisms are included: 1) autonomic regulation mediated by sympathetic and parasympathetic responses, which affect heart rate, cardiac contractility, resistance, and compliance, and 2) autoregulation mediated by responses to local changes in myogenic tone, metabolic demand, and CO2 concentration, which affect cerebrovascular resistance. Finally, we formulate an inverse least-squares problem to estimate parameters and demonstrate that our mathematical model is in agreement with physiological data from a young subject during postural change from sitting to standing. }, number={4}, journal={JOURNAL OF APPLIED PHYSIOLOGY}, author={Olufsen, MS and Ottesen, JT and Tran, HT and Ellwein, LM and Lipsitz, LA and Novak, V}, year={2005}, month={Oct}, pages={1523–1537} }
 @article{adams_banks_davidian_kwon_tran_wynne_rosenberg_2005, title={HIV dynamics: Modeling, data analysis, and optimal treatment protocols}, volume={184}, ISSN={["1879-1778"]}, DOI={10.1016/j.cam.2005.02.004}, abstractNote={We present an overview of some concepts and methodologies we believe useful in modeling HIV pathogenesis. After a brief discussion of motivation for and previous efforts in the development of mathematical models for progression of HIV infection and treatment, we discuss mathematical and statistical ideas relevant to Structured Treatment Interruptions (STI). Among these are model development and validation procedures including parameter estimation, data reduction and representation, and optimal control relative to STI. Results from initial attempts in each of these areas by an interdisciplinary team of applied mathematicians, statisticians and clinicians are presented.}, number={1}, journal={JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS}, author={Adams, BM and Banks, HT and Davidian, M and Kwon, HD and Tran, HT and Wynne, SN and Rosenberg, ES}, year={2005}, month={Dec}, pages={10–49} }
 @article{lee_tran_2005, title={Reduced-order-based feedback control of the Kuramoto–Sivashinsky equation}, volume={173}, ISSN={0377-0427}, url={http://dx.doi.org/10.1016/j.cam.2004.02.021}, DOI={10.1016/j.cam.2004.02.021}, abstractNote={In this paper, we consider the Kuramoto–Sivashinsky equation (KSE), which describes the long-wave motions of a thin film over a vertical plane. Solution procedures for the KSE often yield a large or infinite-dimensional nonlinear system. We first discuss two reduced-order methods, the approximate inertial manifold and the proper orthogonal decomposition, and show that these methods can be used to obtain a reduced-order system that can accurately describe the dynamics of the KSE. Moreover, from this resulting reduced-order system, the feedback controller can readily be designed and synthesized. For our control techniques, we use the linear and nonlinear quadratic regulator methods, which are the first- and second-order approximated solutions of the Hamilton–Jacobi–Bellman equation, respectively. Numerical simulations comparing the performance of the reduced-order-based linear and nonlinear controllers are presented.}, number={1}, journal={Journal of Computational and Applied Mathematics}, publisher={Elsevier BV}, author={Lee, C.H. and Tran, H.T.}, year={2005}, month={Jan}, pages={1–19} }
 @article{lewis_tran_read_ives_2004, title={Design of an electron gun using computer optimization}, volume={32}, ISSN={["1939-9375"]}, DOI={10.1109/TPS.2004.827572}, abstractNote={This paper considers an optimization technique in which the objective is attained via alterations to the physical geometry of the system. This optimization framework, to be considered in the context of electron guns, is known as optimal shape design. Optimal shape design has been used in a number of applications including wing design, magnetic tape design, and nozzle design, among others. In this investigation, we use the methods of shape optimization to design the cathode of an electron gun. The dynamical equations modeling the electron particle path as well as the generalized shape optimization problem will be presented. Illustrative examples of the technique on gun designs that were previously limited to spherical cathodes will be given.}, number={3}, journal={IEEE TRANSACTIONS ON PLASMA SCIENCE}, author={Lewis, BM and Tran, HT and Read, ME and Ives, RL}, year={2004}, month={Jun}, pages={1242–1250} }
 @article{adams_banks_kwon_tran_2004, title={Dynamic multidrug therapies for HIV: Optimal and STI control approaches}, volume={1}, DOI={10.3934/mbe.2004.1.223}, abstractNote={We formulate a dynamic mathematical model that describes the interaction of the immune system with the human immunodeficiency virus (HIV) and that permits drug "cocktail " therapies. We derive HIV therapeutic strategies by formulating and analyzing an optimal control problem using two types of dynamic treatments representing reverse transcriptase (RT) in hibitors and protease inhibitors (PIs). Continuous optimal therapies are found by solving the corresponding optimality systems. In addition, using ideas from dynamic programming, we formulate and derive suboptimal structured treatment interruptions (STI)in antiviral therapy that include drug-free periods of immune-mediated control of HIV. Our numerical results support a scenario in which STI therapies can lead to long-term control of HIV by the immune response system after discontinuation of therapy.}, number={2}, journal={Mathematical Biosciences and Engineering}, author={Adams, B. M. and Banks, H. T. and Kwon, H. D. and Tran, Hien}, year={2004}, pages={223–241} }
 @article{ackleh_deng_cole_tran_2004, title={Existence-uniqueness and monotone approximation for an erythropoiesis age-structured model}, volume={289}, ISSN={["0022-247X"]}, DOI={10.1016/j.jmaa.2003.08.037}, abstractNote={We develop a monotone approximation to the solution of an age-structured model which describes the regulation of erythropoiesis, the process in which red blood cells are developed. The convergence of this approximation to the unique solution of the model is also established.}, number={2}, journal={JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS}, author={Ackleh, AS and Deng, K and Cole, CE and Tran, HT}, year={2004}, month={Jan}, pages={530–544} }
 @inproceedings{tran_lewis_2004, title={From Concept to Real-time Implementation: POD Based Reduced Order Control of a Cantilever Beam}, booktitle={Proceedings of the 16th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2004)}, author={Tran, H. and Lewis, B.M.}, editor={De Moor, B. and Motmans, Bart and Willems, J. and Van Dooren, Paul and Blondel, VincentEditors}, year={2004} }
 @article{olufsen_tran_ottesen_2004, title={Modeling Cerebral Blood Flow Control During Posture Change from Sitting to Standing}, volume={4}, ISSN={1567-8822}, url={http://dx.doi.org/10.1023/b:care.0000025122.46013.1a}, DOI={10.1023/b:care.0000025122.46013.1a}, abstractNote={Hypertension, decreased cerebral blood flow, and diminished cerebral blood flow velocity regulation, are among the first signs indicating the presence of cerebral vascular disease. In this paper, we will present a mathematical model that can predict blood flow and pressure during posture change from sitting to standing. The mathematical model uses a compartmental approach to describe pulsatile blood flow velocity and pressure in a number of compartments representing the systemic circulation. Our model includes compartments representing the trunk and upper extremities, the lower extremities, the brain, and the heart. We use physiologically based control mechanisms to describe the regulation of cerebral blood flow velocity and arterial pressure in response to orthostatic hypotension resulting from postural change. To justify the fidelity of our mathematical model and control mechanisms development, we will show validation results of our model against experimental data from a young subject.}, number={1}, journal={Cardiovascular Engineering}, publisher={Springer Nature}, author={Olufsen, Mette and Tran, Hien and Ottesen, Johnny}, year={2004}, month={Mar}, pages={47–58} }
 @article{banks_cole_schlosser_tran_2004, title={Modeling and optimal regulation of erythropoiesis subject to benzene intoxication}, volume={1}, ISSN={["1547-1063"]}, DOI={10.3934/mbe.2004.1.15}, abstractNote={Benzene (C(6)H(6)) is a highly flammable, colorless liquid. Ubiquitous exposures result from its presence in gasoline vapors, cigarette smoke, and industrial processes. Benzene increases the incidence of leukemia in humans when they are exposed to high doses for extended periods; however, leukemia risks in humans subjected to low exposures are uncertain. The exposure-dose- response relationship of benzene in humans is expected to be nonlinear because benzene undergoes a series of metabolic transformations, detoxifying and activating, resulting in various metabolites that exert toxic effects on the bone marrow. Since benzene is a known human leukemogen, the toxicity of benzene in the bone marrow is of most importance. And because blood cells are produced in the bone marrow, we investigated the effects of benzene on hematopoiesis (blood cell production and development). An age-structured model was used to examine the process of erythropoiesis, the development of red blood cells. This investigation proved the existence and uniqueness of the solution of the system of coupled partial and ordinary differential equations. In addition, we formulated an optimal control problem for the control of erythropoiesis and performed numerical simulations to compare the performance of the optimal feedback law and another feedback function based on the Hill function.}, number={1}, journal={MATHEMATICAL BIOSCIENCES AND ENGINEERING}, author={Banks, HT and Cole, CE and Schlosser, PM and Tran, HT}, year={2004}, month={Jun}, pages={15–48} }
 @inbook{banks_tran_wynne_2003, title={A well-posedness Result for a Shear Wave Propagation Model}, ISBN={9783034893992 9783034880015}, url={http://dx.doi.org/10.1007/978-3-0348-8001-5_2}, DOI={10.1007/978-3-0348-8001-5_2}, abstractNote={We consider a nonlinear model for propagation of shear waves in viscoelastic tissue. Existence and uniqueness results for solutions are established.}, booktitle={Control and Estimation of Distributed Parameter Systems}, publisher={Birkhäuser Basel}, author={Banks, H. T. and Tran, H. and Wynne, S.}, year={2003}, pages={25–40} }
 @inproceedings{bui_vogler_ives_shephard_klaas_remacle_kapraun_tran_2003, title={Beam optics analysis - a 3D finite element charged particle code with adaptive meshing}, ISBN={0780372565}, url={http://dx.doi.org/10.1109/ivelec.2002.999314}, DOI={10.1109/ivelec.2002.999314}, abstractNote={Development of the next generation of RF devices is in progress with research on sheet beam and multiple beam devices on-going at several institutions. Analysis of inherently three dimensional devices requires a new set of analytical tools to model the electromagnetic fields and the behavior of electron and ion beams. Existing codes, such as HFSS and MAFIA, are widely used to model the electromagnetic fields in these devices, but there is a need for simple, accurate, and efficient codes to model the behavior of charged particles in 3D geometries and fields. Calabazas Creek Research, Inc. (CCR) is funded by the U.S. Department of Energy to develop a finite element, charged particle, analysis code suitable for the next generation of RF devices. The principle feature of the new program is adaptive meshing, which removes the burden for mesh generation from the user and assigns responsibility to field solver and particle pusher routines.}, booktitle={Third IEEE International Vacuum Electronics Conference (IEEE Cat. No.02EX524)}, publisher={IEEE}, author={Bui, T. and Vogler, B. and Ives, L. and Shephard, M. and Klaas, O. and Remacle, J.-F. and Kapraun, D. and Tran, H.}, year={2003}, month={Jun} }
 @article{whitaker_tran_portier_2003, title={Development of a biologically-based controlled growth and differentiation model for developmental toxicology}, volume={46}, ISSN={["0303-6812"]}, DOI={10.1007/s00285-002-0164-8}, abstractNote={Amathematical model is developed with a highly controlled birth and death process for precursor cells. This model is both biologically- and statistically-based. The controlled growth and differentiation (CGD) model limits the number of replications allowed in the development of a tissue or organ and thus, more closely reflects the presence of a true stem cell population. Leroux et al. (1996) presented a biologically-based dose-response model for developmental toxicology that was derived from a partial differential equation for the generating function. This formulation limits further expansion into more realistic models of mammalian development. The same formulae for the probability of a defect (a system of ordinary differential equations) can be derived through the Kolmogorov forward equations due to the nature of this Markov process. This modified approach is easily amenable to the expansion of more complicated models of the developmental process such as the one presented here. Comparisons between the Leroux et al. (1996) model and the controlled growth and differentiation (CGD) model as developed in this paper are also discussed.}, number={1}, journal={JOURNAL OF MATHEMATICAL BIOLOGY}, author={Whitaker, SY and Tran, HT and Portier, CJ}, year={2003}, month={Jan}, pages={1–16} }
 @article{nguyen_yoh_lee_tran_johnson_2003, title={Modeling of HPA and HPA linearization through a predistorter: Global Broadcasting Service applications}, volume={49}, ISSN={["0018-9316"]}, DOI={10.1109/TBC.2003.813650}, abstractNote={This paper presents a technique to linearize the high power amplifier (HPA) through a predistorter (PD). The characteristics of the PD circuit are derived based on the extension of Saleh's model for HPA and a simple linear-log model. Numerical results are shown for Global Broadcasting Service (GBS) applications.}, number={2}, journal={IEEE TRANSACTIONS ON BROADCASTING}, author={Nguyen, TM and Yoh, J and Lee, CH and Tran, HT and Johnson, DM}, year={2003}, month={Jun}, pages={132–141} }
 @inproceedings{kapraun_tran_ives_vogler_bui_2003, title={SCATTER - a new computer code for modeling reflected electrons from surfaces}, ISBN={0780372565}, url={http://dx.doi.org/10.1109/ivelec.2002.999300}, DOI={10.1109/ivelec.2002.999300}, abstractNote={Calabazas Creek Research, Inc. is funded by the U.S. Department of Energy to develop an advanced charged particle code using adaptive meshing. One of the tasks in that program is to model secondary and reflected electrons in collectors. The Center for Research in Scientific Computing (CRSC) received a subcontract to develop a 3D Monte Carlo technique for modeling these electrons. Taking into account the energy and direction of an incident electron, as well as the atomic number, atomic mass and density of the solid, the program calculates a statistically reasonable path for the electron through the solid via Monte Carlo techniques. When applied to large numbers of electrons, the algorithm provides statistically accurate results. The success of the effort resulted in a stand-alone code that could be use to investigate the effect of various materials and coatings to reduce the emission and there by achieve higher depressed collector efficiencies.}, booktitle={Third IEEE International Vacuum Electronics Conference (IEEE Cat. No.02EX524)}, publisher={IEEE}, author={Kapraun, D. and Tran, H. and Ives, R.L. and Vogler, W. and Bui, T.}, year={2003}, month={Jun} }
 @inproceedings{banks_beeler_tran_2003, place={Birkhäuser}, series={ISNM International Series of Numerical Mathematics}, title={State Estimation and Tracking Control of Nonlinear Dynamical Systems}, volume={143}, DOI={10.1007/978-3-0348-8001-5_1}, abstractNote={In this paper state estimation and feedback tracking control methods for nonlinear systems are presented. The methods, which are based on the “state-dependent Riccati equation”, allow the construction of nonlinear estimators and nonlinear feedback tracking controls for a wide class of systems. Our emphasis will be on development of computational methods that are easily implementable as well as efficient. Simulation results of the performance of the nonlinear estimator and tracking control are included. In addition, comparisons with the linear estimator and linear tracking control found through the linearized system are also made.}, booktitle={Control and Estimation of Distributed Parameter Systems}, publisher={Basel/Springer}, author={Banks, H.T. and Beeler, S.C. and Tran, H.T.}, editor={Desch, W. and Kappel, F. and Kunisch, K.Editors}, year={2003}, month={Jul}, pages={1–24}, collection={ISNM International Series of Numerical Mathematics} }
 @inproceedings{nguyen_tran_yoh_nguyen_lewis_2002, title={Diversity and Combining Techniques for 2G and 3G PCS Systems}, ISBN={9781624101113}, url={http://dx.doi.org/10.2514/6.2002-1859}, DOI={10.2514/6.2002-1859}, abstractNote={This paper provides an overview of the diversity and combining techniques for the second (2G) and third (3G) generation Personal Communication Systems (PCS). The 2G system employs path diversity with maximum combining ratio combining technique. On the other hand, the 3G system uses antenna diversity along with path diversity and the maximal ratio combining (MRC) technique. Both of these systems use convolutional code to combat channel errors. The paper also presents simulation results describing the performance of the diversity and combining techniques for a 2G PCS system.}, booktitle={20th AIAA International Communication Satellite Systems Conference and Exhibit}, publisher={American Institute of Aeronautics and Astronautics}, author={Nguyen, Tien and Tran, Hien and Yoh, James and Nguyen, Hung and Lewis, Brian}, year={2002}, month={May} }
 @article{banks_barnes_eberhardt_tran_wynne_2002, title={Modeling and Computation of Propagating Waves from Coronary Stenoses}, volume={21}, number={3}, journal={Computational & Applied Mathematics}, author={Banks, H.T. and Barnes, J.H. and Eberhardt, A. and Tran, H. and Wynne, S.}, year={2002}, pages={767–788} }
 @article{ly_tran_2002, title={Proper orthogonal decomposition for flow calculations and optimal control in a horizontal CVD reactor}, volume={60}, ISSN={["1552-4485"]}, DOI={10.1090/qam/1939004}, abstractNote={Proper orthogonal decomposition (which is also known as the Karhunen-Loève decomposition) is a reduction method that is used to obtain low-dimensional dynamic models of distributed parameter systems. Roughly speaking, proper orthogonal decomposition (POD) is an optimal technique of finding a basis that spans an ensemble of data, collected from an experiment or a numerical simulation of a dynamical system, in the sense that when these basis functions are used in a Galerkin procedure, they will yield a finite-dimensional system with the smallest possible degrees of freedom. Thus, the technique is well suited to treat optimal control and parameter estimation of distributed parameter systems. In this paper, the method is applied to analyze the complex flow phenomenon in a horizontal chemical vapor deposition (CVD) reactor. In particular, we show that POD can be used to efficiently approximate solutions to the compressible viscous flows coupled with the energy and the species equations. In addition, we also examine the feasibility and efficiency of the POD method in the optimal control of the source vapors to obtain the most uniform deposition profile at the maximum growth rate. Finally, issues concerning the implementation of the method and numerical calculations are discussed.}, number={4}, journal={QUARTERLY OF APPLIED MATHEMATICS}, author={Ly, HV and Tran, HT}, year={2002}, month={Dec}, pages={631–656} }
 @article{banks_rosario_tran_2002, title={Proper orthogonal decomposition-based control of transverse beam vibrations: Experimental implementation}, volume={10}, ISSN={["1063-6536"]}, DOI={10.1109/TCST.2002.801793}, abstractNote={Linear quadratic Gaussian (LQG) compensator control of transverse vibrations was implemented on an aluminum cantilevered beam in a "smart structure" paradigm. The beam was mounted with two self-sensing self-actuating piezoceramic patches. The Euler-Bernoulli beam equation was discretized via a Galerkin type approximation (referred to as the full-order model). To reduce the size of the resulting finite-dimensional approximating system, the proper orthogonal decomposition (POD) was employed as a reduced basis method. A reduction of dimension from 34 to 2 was obtained through the model reduction technique. Feedback control based on the reduced order system was implemented in real time using a dSpace DS1103 control system. Experimental results indicate that POD-based control achieves comparable control attenuation with full-order model-based control.}, number={5}, journal={IEEE TRANSACTIONS ON CONTROL SYSTEMS TECHNOLOGY}, author={Banks, HT and Rosario, RCH and Tran, HT}, year={2002}, month={Sep}, pages={717–726} }
 @inproceedings{tran_yoh_nguyen_johnson_lee_2002, title={RFI modeling of satellite communications}, ISBN={0780365216}, url={http://dx.doi.org/10.1109/milcom.2000.904950}, DOI={10.1109/milcom.2000.904950}, abstractNote={This paper describes the development of an analytical model for predicting the interference experienced by a generic satellite communications receiving station due to an interfering satellite. In these initial studies, both satellites, the desired as well as the interfering satellite, are considered to be in circular orbits. Furthermore, the unknown parameters in the model are assumed to be random, and the mean of the radio frequency interference (RFI) duration, time between RFI and fraction of time there is RFI are also statistically estimated.}, booktitle={MILCOM 2000 Proceedings. 21st Century Military Communications. Architectures and Technologies for Information Superiority (Cat. No.00CH37155)}, publisher={IEEE}, author={Tran, H.T. and Yoh, J. and Nguyen, T.M. and Johnson, D.M. and Lee, C.H.}, year={2002}, month={Nov} }
 @article{banks_beeler_kepler_tran_2002, title={Reduced order modeling and control of thin film growth in an HPCVD reactor}, volume={62}, ISSN={["1095-712X"]}, DOI={10.1137/S0036139901383280}, abstractNote={This paper describes the development of a reduced order model-based feedback control methodology for regulation of the growth of thin films in a high-pressure chemical vapor deposition (HPCVD) reactor. Precise control of the film thickness and composition is highly desirable, making real-time control of the deposition process very important. The source vapor species transport is modeled by the standard gas dynamics partial differential equations, with species decomposition reactions, reduced down to a small number of ordinary differential equations through use of the proper orthogonal decomposition technique. This system is coupled with a reduced order model of the surface reactions involved in the source vapor decomposition and film growth on the substrate. Also modeled is the real-time observation technique used to obtain a partial measurement of the deposition process.The utilization of reduced order models greatly simplifies the mathematical formulation of the physical process so that it can be solved...}, number={4}, journal={SIAM JOURNAL ON APPLIED MATHEMATICS}, author={Banks, HT and Beeler, SC and Kepler, GM and Tran, HT}, year={2002}, month={Apr}, pages={1251–1280} }
 @inproceedings{nguyen_nguyen_tran_jocic_lewis_2002, title={Survey on Diversity and Combining Techniques}, ISBN={9781624101113}, url={http://dx.doi.org/10.2514/6.2002-1858}, DOI={10.2514/6.2002-1858}, booktitle={20th AIAA International Communication Satellite Systems Conference and Exhibit}, publisher={American Institute of Aeronautics and Astronautics}, author={Nguyen, Tien and Nguyen, Hung and Tran, Hien and Jocic, Lubo and Lewis, Brian}, year={2002}, month={May} }
 @inproceedings{tran_2002, place={Centreville, VA}, title={The Human Respiratory Control System: Models, Applications, and Analysis}, booktitle={VACETS VTIC 2002 : George Mason University, May 10-11, 2002 : proceedings}, publisher={VACETS}, author={Tran, H.}, year={2002} }
 @inproceedings{ives_bui_vogler_remacle_shephard_beall_kapraun_tran_2002, title={User-friendly, economical, 3D charged particle code with adaptive meshing}, ISBN={0780371410}, url={http://dx.doi.org/10.1109/ppps.2001.960847}, DOI={10.1109/ppps.2001.960847}, abstractNote={Summary form only given, as follows. Calabazas Creek Research, Inc., in association with Rensselaer Polytechnic Institute (RPI) and Simmetrix, Inc., is developing a user-friendly 3-D, finite element, charged particle code with adaptive meshing. This program builds on the particle pusher and emission algorithms developed during the 2-D development, which demonstrated that the technical approach provided the functionality and accuracy required. The 2-D and 3-D charged particle codes use unstructured meshes that are not restricted in terms of size or density and are ideal for adaptive meshing. The size of the mesh in any particular region is primarily determined by the local field gradients and the presence of the beam. This reduces the number of nodes by orders of magnitude, allowing modeling of problems that were previously impractical to analyze. The adaptive meshing feature allows the field solver and particle pusher to automatically determine the minimum mesh density required throughout the problem domain based on user specified error criteria. This capability allows the codes to solve problems involving fine structures, such as the grid region in gridded electron guns, or for modeling thin hollow beams far from axis, such as those in high power gyrotrons. The menu driven user interface will be incorporated in AutoCAD and Solid Works. Mesh generation will be accomplished using the MeshSim toolkit produced by Simmetrix Inc. The error estimation and mesh adaptation procedures are being developed by RPI's Scientific Computation Research Center. This presentation will provide details of the code operation and capabilities.}, booktitle={IEEE Conference Record - Abstracts. PPPS-2001 Pulsed Power Plasma Science 2001. 28th IEEE International Conference on Plasma Science and 13th IEEE International Pulsed Power Conference (Cat. No.01CH37255)}, publisher={IEEE}, author={Ives, L. and Bui, T. and Vogler, W. and Remacle, J.-F. and Shephard, M.S. and Beall, M.W. and Kapraun, D.F. and Tran, H.T.}, year={2002}, month={Nov} }
 @inbook{tran_lee_2001, place={Oxford, England}, edition={2nd}, title={Chemical Vapor Deposition Processes: Reduced-order Modeling}, DOI={10.1016/B0-08-043152-6/00221-7}, booktitle={Encyclopedia of Materials: Science and Technology}, publisher={Elsevier Science Ltd}, author={Tran, H. and Lee, C.H.}, editor={Jürgen Buschow, K.H. and Flemings, Merton C. and Kramer, Edward J. and Veyssière, Patrick and Cahn, Robert W. and Ilschner, Bernhard and Mahajan, SubhashEditors}, year={2001}, pages={1183–1187} }
 @article{kepler_tran_banks_2001, title={Compensator control for chemical vapor deposition film growth using reduced-order design models}, volume={14}, ISSN={["1558-2345"]}, DOI={10.1109/66.939820}, abstractNote={We present a summary of investigations on the use of proper orthogonal decomposition techniques as a reduced basis method for computation of feedback controls and compensators in a high-pressure chemical vapor deposition (HPCVD) reactor. These investigations incorporate multiple species and controls, gas phase reactions, and time dependent tracking signals that are consistent with pulsed vapor reactant inputs. Numerical implementation of the model-based feedback control uses a reduced-order state estimator, based on partial state observations of the fluxes of reactants at the substrate center, which can be achieved with current sensing technology. We demonstrate that the reduced-order state estimator or compensator system is capable of substantial control authority when applied to the full system.}, number={3}, journal={IEEE TRANSACTIONS ON SEMICONDUCTOR MANUFACTURING}, author={Kepler, GM and Tran, HT and Banks, HT}, year={2001}, month={Aug}, pages={231–241} }
 @inproceedings{banks_beeler_kepler_tran_2001, title={Feedback control of thin film growth in an HPCVD reactor via reduced order models}, ISBN={0780370619}, url={http://dx.doi.org/10.1109/cdc.2001.981123}, DOI={10.1109/cdc.2001.981123}, abstractNote={This paper describes the development of a reduced order model-based feedback control methodology for the regulation of the growth of thin films in a high-pressure chemical vapor deposition (HPCVD) reactor. This is achieved in the context of gas dynamics coupled with a nonlinear reduced order model of the surface reactions involved in the source vapor decomposition and film growth on the substrate. Also modeled is the realtime observation technique used to obtain a partial measurement of the deposition process. The control problems are optimal tracking problems of the film thickness that employ state-dependent Riccati gains with nonlinear observations and the resulting dual state dependent Riccati equations for the compensator gains.}, booktitle={Proceedings of the 40th IEEE Conference on Decision and Control (Cat. No.01CH37228)}, publisher={IEEE}, author={Banks, H.T. and Beeler, S.C. and Kepler, G.M. and Tran, H.T.}, year={2001}, month={Jul} }
 @article{ly_tran_2001, title={Modeling and control of physical processes using proper orthogonal decomposition}, volume={33}, ISSN={["1872-9479"]}, DOI={10.1016/S0895-7177(00)00240-5}, abstractNote={The proper orthogonal decomposition (POD) technique (or the Karhunan Loève procedure) has been used to obtain low-dimensional dynamical models of many applications in engineering and science. In principle, the idea is to start with an ensemble of data, called snapshots , collected from an experiment or a numerical procedure of a physical system. The POD technique is then used to produce a set of basis functions which spans the snapshot collection. When these basis functions are used in a Galerkin procedure, they yield a finite-dimensional dynamical system with the smallest possible degrees of freedom. In this context, it is assumed that the physical system has a mathematical model, which may not be available for many physical and/or industrial applications. In this paper, we consider the steady-state Rayleigh-Bénard convection whose mathematical model is assumed to be unknown, but numerical data are available. The aim of the paper is to show that, using the obtained ensemble of data, POD can be used to model accurately the natural convection. Furthermore, this approach is very efficient in the sense that it uses the smallest possible number of parameters, and thus, is suited for process control. Particularly, we consider two boundary control problems 1. (a) tracking problem, and 2. (b) avoiding hot spot in a certain region of the domain.}, number={1-3}, journal={MATHEMATICAL AND COMPUTER MODELLING}, author={Ly, HV and Tran, HT}, year={2001}, pages={223–236} }
 @article{cole_tran_schlosser_2001, title={Physiologically based pharmacokinetic modeling of benzene metabolism in mice through extrapolation from in vitro to in vivo}, volume={62}, ISSN={["1528-7394"]}, DOI={10.1080/00984100150501178}, abstractNote={Benzene (C6H6) is a highly flammable, colorless liquid. Ubiquitous exposures result from its presence in gasoline vapors, cigarette smoke, and industrial processes. Benzene increases the incidence of leukemia in humans when they are exposed to high doses for extended periods; however, leukemia risks in humans at low exposures are uncertain. The exposure-dose-response relationship of benzene in humans is expected to be nonlinear because benzene undergoes a series of metabolic transformations, detoxifying and activating, in the liver, resulting in multiple metabolites that exert toxic effects on the bone marrow. We developed a physiologically based pharmacokinetic model for the uptake and elimination of benzene in mice to relate the concentration of inhaled and orally administered benzene to the tissue doses of benzene and its key metabolites, benzene oxide, phenol, and hydroquinone. As many parameter values as possible were taken from the literature; in particular, metabolic parameters obtained from in vitro studies with mouse liver were used since comparable parameters are also available for humans. Parameters estimated by fitting the model to published data were first-order rate constants for pathways lacking in vitro data and the concentrations of microsomal and cytosolic protein, which effectively alter overall enzyme activity. The model was constrained by using the in vitro metabolic parameters (maximum velocities, first-order rate constants, and saturation parameters), and data from multiple laboratories and experiments were used. Despite these constraints and sources of variability, the model simulations matched the data reasonably well in most cases, showing that in vitro metabolic constants can be successfully extrapolated to predict in vivo data for benzene metabolism and dosimetry. Therefore in vitro metabolic constants for humans can subsequently be extrapolated to predict the dosimetry of benzene and its metabolites in humans. This will allow us to better estimate the risks of adverse effects from low-level benzene exposures.}, number={6}, journal={JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH-PART A}, author={Cole, CE and Tran, HT and Schlosser, PM}, year={2001}, month={Mar}, pages={439–465} }
 @inbook{banks_tran_2001, title={Reduced Order Based Compensator Control of Thin Film Growth in a CVD Reactor}, ISBN={9783034894562 9783034881487}, url={http://dx.doi.org/10.1007/978-3-0348-8148-7_1}, DOI={10.1007/978-3-0348-8148-7_1}, abstractNote={This paper reports on an interdisciplinary effort, which involves applied mathematicians, material scientists and physicists at North Carolina State University, to integrate new intelligent processing approaches with advanced mathematical modeling, optimization, and control theory to guide the construction and experimental implementation of a series of high pressure (up to 100 atm) organometallic chemical vapor deposition (CVD) reactors. An integral component of this research program is the design of the reactor so that control and sensing are a basic component of the optimal design efforts for the reactor. We report here on the successful use of mathematics in a fundamental role in the development of linear and nonlinear feedback control methods for real-time implementation on the reactor. This is achieved in the required context of gas dynamics coupled with nonlinear surface deposition processes. The problems are optimal tracking problems (for the chemical component fluxes over the substrate) that employ state-dependent Riccati gains with nonlinear observations and the resulting dual state dependent Riccati equations for the compensator gains This control methodology is successfully combined with reduced order model methods based on proper orthogonal decomposition techniques. Computational results to support the efficacy of our approach and methods are also included.}, booktitle={Optimal Control of Complex Structures}, publisher={Birkhäuser Basel}, author={Banks, H. T. and Tran, H. T.}, year={2001}, pages={1–17} }
 @article{dietz_beeler_schmidt_tran_2001, title={Surface reaction kinetics of Ga1-xInxP growth during pulsed chemical beam epitaxy}, volume={178}, ISSN={["1873-5584"]}, DOI={10.1016/S0169-4332(01)00302-6}, abstractNote={The understanding of thin film growth processes and their control requires the development of surface-sensitive real-time optical characterization techniques that are able to provide insight into the surface reaction kinetics during an organometallic deposition process. These insights will allow us to move the control point closer to the point where the growth occurs, which in a chemical beam epitaxy (CBE) process is a surface reaction layer (SRL), built up of physisorbed and chemisorbed precursor fragments between the ambient and film interface. This contribution presents results on parameter estimations of rate constants and optical response factors in a reduced order surface kinetics (ROSK) model, which has been developed to describe the decomposition and growth kinetics of the involved organometallic precursors and their incorporation in the film deposition. As a real-time characterization technique, we applied p-polarized reflectance spectroscopy (PRS) during low temperature growth of epitaxial Ga1−xInxP heterostructures on Si(0 0 1) substrates by pulsed chemical beam epitaxy (PCBE). The high surface sensitivity of PRS allows us to follow alterations in composition and thickness of the SRL as they are encountered during periodic precursor supply. The linkage of the PRS response to the ROSK model provides the base for the parameter estimation, giving insights into the organometallic precursor decomposition and growth kinetics.}, number={1-4}, journal={APPLIED SURFACE SCIENCE}, author={Dietz, N and Beeler, SC and Schmidt, JW and Tran, HT}, year={2001}, month={Jul}, pages={63–74} }
 @article{beeler_tran_banks_2000, title={Feedback control methodologies for nonlinear systems}, volume={107}, ISSN={["0022-3239"]}, DOI={10.1023/A:1004607114958}, abstractNote={A number of computational methods have been proposed in the literature to design and synthesize feedback controls when the plant is modeled by nonlinear dynamics. However, it is not immediately clear which is the best method for a given problem; this may depend on the nature of the nonlinearities, size of the system, whether the amount of control used or time needed for the method is a concern, and other factors. In this paper, a comprehensive comparison study of five methods for the synthesis of nonlinear control systems is carried out. The performance of the methods on several test problems are studied, and some recommendations are made as to which feedback control method is best to use under various conditions.}, number={1}, journal={JOURNAL OF OPTIMIZATION THEORY AND APPLICATIONS}, author={Beeler, SC and Tran, HT and Banks, HT}, year={2000}, month={Oct}, pages={1–33} }
 @book{gremaud_li_smith_tran_2000, place={Philadelphia, PA}, title={Industrial Mathematics: The 1998 CRSC Workshop}, publisher={SIAM Publications}, year={2000}, month={Oct} }
 @misc{batzel_tran_2000, title={Modeling instability in the control system for human respiration: applications to infant non-REM sleep}, volume={110}, ISSN={["0096-3003"]}, DOI={10.1016/s0096-3003(99)00112-5}, abstractNote={Mathematical models of the human respiratory control system have been developed since 1940 to study a wide range of features of this complex system. The phenomena collectively referred to as periodic breathing (including Cheyne–Stokes respiration and apneustic breathing) have important medical implications. The hypothesis that periodic breathing is the result of delay in the feedback signals to the respiratory control system has been studied since the work of F.S. Grodins, J. Gray, A.I. Norins, R.W. Jones [J. Appl. Physiol. 1 (1954) 283–308] in the early 1950s. The purpose of this paper is to extend the model presented by M.C.K. Khoo, R.E. Kronauer, K.P. Strohl, A.S. Slutsky [J. Appl. Physiol. 53 (3) (1982) 644–659] in 1991 to include variable delay in the feedback control loop and to study the phenomena of periodic breathing and apnea as they occur during quiet sleep in infant sleep respiration at around 4 months of age. The nonlinear mathematical model consists of a feedback control system of five delay differential equations. Numerical simulations are performed to study instabilities in the control system and the occurrence of periodic breathing and apnea in the above case which is a time frame of high incidence of sudden infant death syndrome (SIDS).}, number={1}, journal={APPLIED MATHEMATICS AND COMPUTATION}, author={Batzel, JJ and Tran, HT}, year={2000}, month={Apr}, pages={1–51} }
 @article{kepler_tran_banks_2000, title={Reduced order model compensator control of species transport in a CVD reactor}, volume={21}, ISSN={["0143-2087"]}, DOI={10.1002/1099-1514(200007/08)21:4<143::AID-OCA671>3.0.CO;2-Y}, abstractNote={We propose the use of proper orthogonal decomposition (POD) techniques as a reduced basis method for computation of feedback controls and compensators in a high-pressure chemical vapour deposition (HPCVD) reactor. In this paper, we present a proof-of-concept computational implementation of this method with a simplified growth example for III–V layers in which we implement Dirichlet boundary control of a dilute Group III reactant transported by convection and diffusion to an absorbing substrate with no reactions. We implement the model-based feedback control using a reduced order state estimator based on observations of the flux of reactant at the substrate centre. This is precisely the type of measurements available with current sensing technology. We demonstrate that the reduced order state estimator or compensator system is capable of substantial control authority when applied to a high-order system. In principle, these ideas can be extended to more general HPCVD control situations by including multiple species with gas-phase reactions and surface reactions. Copyright © 2000 John Wiley & Sons, Ltd.}, number={4}, journal={OPTIMAL CONTROL APPLICATIONS & METHODS}, author={Kepler, GM and Tran, HT and Banks, HT}, year={2000}, pages={143–160} }
 @article{batzel_tran_2000, title={Stability of the human respiratory control system I. Analysis of a two-dimensional delay state-space model}, volume={41}, ISSN={["1432-1416"]}, DOI={10.1007/s002850000044}, abstractNote={A number of mathematical models of the human respiratory control system have been developed since 1940 to study a wide range of features of this complex system. Among them, periodic breathing (including Cheyne-Stokes respiration and apneustic breathing) is a collection of regular but involuntary breathing patterns that have important medical implications. The hypothesis that periodic breathing is the result of delay in the feedback signals to the respiratory control system has been studied since the work of Grodins et al. in the early 1950's [12]. The purpose of this paper is to study the stability characteristics of a feedback control system of five differential equations with delays in both the state and control variables presented by Khoo et al. [17] in 1991 for modeling human respiration. The paper is divided in two parts. Part I studies a simplified mathematical model of two nonlinear state equations modeling arterial partial pressures of O2 and CO2 and a peripheral controller. Analysis was done on this model to illuminate the effect of delay on the stability. It shows that delay dependent stability is affected by the controller gain, compartmental volumes and the manner in which changes in the ventilation rate is produced (i.e., by deeper breathing or faster breathing). In addition, numerical simulations were performed to validate analytical results. Part II extends the model in Part I to include both peripheral and central controllers. This, however, necessitates the introduction of a third state equation modeling CO2 levels in the brain. In addition to analytical studies on delay dependent stability, it shows that the decreased cardiac output (and hence increased delay) resulting from the congestive heart condition can induce instability at certain control gain levels. These analytical results were also confirmed by numerical simulations.}, number={1}, journal={JOURNAL OF MATHEMATICAL BIOLOGY}, author={Batzel, JJ and Tran, HT}, year={2000}, month={Jul}, pages={45–79} }
 @article{batzel_tran_2000, title={Stability of the human respiratory control system II. Analysis of a three-dimensional delay state-space model}, volume={41}, ISSN={["0303-6812"]}, DOI={10.1007/s002850000045}, abstractNote={A number of mathematical models of the human respiratory control system have been developed since 1940 to study a wide range of features of this complex system. Among them, periodic breathing (including Cheyne-Stokes respiration and apneustic breathing) is a collection of regular but involuntary breathing patterns that have important medical implications. The hypothesis that periodic breathing is the result of delay in the feedback signals to the respiratory control system has been studied since the work of Grodins et al. in the early 1950's [1]. The purpose of this paper is to study the stability characteristics of a feedback control system of five differential equations with delays in both the state and control variables presented by Khoo et al. [4] in 1991 for modeling human respiration. The paper is divided in two parts. Part I studies a simplified mathematical model of two nonlinear state equations modeling arterial partial pressures of O2 and CO2 and a peripheral controller. Analysis was done on this model to illuminate the effect of delay on the stability. It shows that delay dependent stability is affected by the controller gain, compartmental volumes and the manner in which changes in the ventilation rate is produced (i.e., by deeper breathing or faster breathing). In addition, numerical simulations were performed to validate analytical results. Part II extends the model in Part I to include both peripheral and central controllers. This, however, necessitates the introduction of a third state equation modeling CO2 levels in the brain. In addition to analytical studies on delay dependent stability, it shows that the decreased cardiac output (and hence increased delay) resulting from the congestive heart condition can induce instability at certain control gain levels. These analytical results were also confirmed by numerical simulations.}, number={1}, journal={JOURNAL OF MATHEMATICAL BIOLOGY}, author={Batzel, JJ and Tran, HT}, year={2000}, month={Jul}, pages={80–102} }
 @article{kottler_tran_wessell_1999, title={A complete steady state model of solute and water transport in the kidney}, volume={29}, ISSN={["1872-9479"]}, DOI={10.1016/S0895-7177(99)00055-2}, abstractNote={The purpose of this paper is to incorporate a detailed model, along with an optimized set of parameters for the proximal tubule, into J. L. Stephenson's current central core model of the nephron. In this model a set of equations for the proximal tubule are combined with Stephenson's equations for the remaining four tubules and interstitium, to form a complete nonlinear system of 34 ordinary differential and algebraic equations governing fluid and solute flow in the kidney. These equations are then discretized by the Crank-Nicholson scheme to form an algebraic system of nonlinear equations for the unknown concentrations, flows, hydrostatic pressure, and potentials. The resulting system is solved via factored secant update with a finite-difference approximation to the Jacobian. Finally, numerical simulations performed on the model showed that the modeled behavior approximates, in a general way, the physiological mechanisms of solvent and solute flow in the kidney.}, number={6}, journal={MATHEMATICAL AND COMPUTER MODELLING}, author={Kottler, NE and Tran, HT and Wessell, DE}, year={1999}, month={Mar}, pages={63–82} }
 @article{beeler_tran_dietz_1999, title={Representation of GaP formation by a reduced order surface kinetics model using p-polarized reflectance measurements}, volume={86}, ISSN={["1089-7550"]}, DOI={10.1063/1.370783}, abstractNote={This contribution presents results on the parameter estimation of rate constants and optical response factors in a reduced order surface kinetics (ROSK) model, which has been developed to describe the decomposition kinetics of the organometallic precursors involved and their incorporation into the film deposition. As a real-time characterization technique, we applied p-polarized reflectance spectroscopy (PRS) during low temperature growth of epitaxial GaP heterostructures on Si(001) substrates by pulsed chemical beam epitaxy. The high surface sensitivity of PRS allows us to follow alterations in the composition and thickness of the surface reaction layer as they are encountered during periodic precursor supply. Linkage of the PRS response to the ROSK model provides the base for the parameter estimation of the reduced order surface kinetics model, giving insights into the organometallic precursor decomposition and growth kinetics.}, number={1}, journal={JOURNAL OF APPLIED PHYSICS}, author={Beeler, S and Tran, HT and Dietz, N}, year={1999}, month={Jul}, pages={674–682} }
 @article{banks_musante_tran_1998, title={A dispersion model for the hepatic uptake and elimination of 2,3,7,8-tetrachlorodibenzo-p-dioxin}, volume={28}, ISSN={["0895-7177"]}, DOI={10.1016/S0895-7177(98)00077-6}, abstractNote={A convection-dispersion model for the uptake and elimination of 2,3,7,8-tetrachlorodibenzo- p -dioxin (TCDD) in the liver is presented. The model is adapted from the general dispersion model of Roberts and Rowland and includes the dynamics of TCDD interaction with two intracellular proteins, the Ah receptor and cytochrome P450 IA2. A “well-mixed” compartment was added to describe the venous blood concentration of TCDD. The result is a nonlinear system of seven coupled partial and ordinary differential equations with time delays.}, number={1}, journal={MATHEMATICAL AND COMPUTER MODELLING}, author={Banks, HT and Musante, CJ and Tran, HT}, year={1998}, month={Jul}, pages={9–29} }
 @article{bachmann_sukidi_hopfner_harris_dietz_tran_beeler_ito_banks_1998, title={Real-time monitoring of steady-state pulsed chemical beam epitaxy by p-polarized reflectance}, volume={183}, ISSN={["0022-0248"]}, DOI={10.1016/s0022-0248(97)00410-7}, abstractNote={The structure in the p-polarized reflectance (PR) intensity Rp4(t) - observed under conditions of pulsed chemical beam epitaxy (PCBE) - is modeled on the basis of the four-layer stack: ambient/surface reaction layer (SRL)/epilayer/substrate. Linearization of the PR intensity with regard to the phase factor associated with the SRL results in a good approximation that can be expressed as Rp4 = Rp3 + ΔRp.Rp3 is the reflectivity of the three-layer stack ambient-epilayer-substrate. ΔRp describes the properties of the SRL. An explicit relation is derived between ΔRp(t) and the time-dependent surface concentrations ch(t) (h = 1, 2, …, N) of the constituents of the SRL, which holds for conditions of submonolayer coverage of the surface by source vapor molecules. Under conditions of low temperature PCBE at high flux, the SRL is expected to exhibit nonideal behavior, mandating replacement of the surface concentrations by activities. Also, in this case, the thickness of the SRL must be represented in terms of partial molar volumina Vh. Since the relation between ΔRp(t) and the activities of reactants, intermediates and products of the chemical reactions driving heteroepitaxial growth is non-linear, the extraction of kinetic parameters from the measured time dependence of the PR signal generally requires numerical modeling.}, number={3}, journal={JOURNAL OF CRYSTAL GROWTH}, author={Bachmann, KJ and Sukidi, N and Hopfner, C and Harris, C and Dietz, N and Tran, HT and Beeler, S and Ito, K and Banks, HT}, year={1998}, month={Jan}, pages={323–337} }
 @article{bachmann_hopfner_sukidi_miller_harris_aspnes_dietz_tran_beeler_ito_et al._1997, title={Molecular layer epitaxy by real-time optical process monitoring}, volume={112}, DOI={10.1016/S0169-4332(96)00975-0}, abstractNote={In this paper we consider modern methods of optical process monitoring and control in the context of atomic layer epitaxy. One specific method, p-polarized reflectance spectroscopy (PRS), is chosen to assess details of layer-by-layer growth. We show that PRS monitoring under conditions of steady-state growth by pulsed chemical beam epitaxy (PCBE) can achieve the deposition of molecular layers of GaP on silicon (100) deposited with a precision of 5%, which can be improved by reducing the growth rate and increasing the period of time averaging of the reflectance data. Since in the nucleation period prior to formation of a contiguous heteroepitaxial film inhomogeneous surface chemistry and roughening complicates the modeling of the overgrowth process, advances in both experimental methods and theory are required for extending the control to non-steady-state growth conditions. Results of simultaneous single-wavelength PR monitoring and laser light scattering measurements in conjunction with atomic force microscopy studies of short period heteroepitaxial overgrowth processes are presented. The extension of PRS to the monitoring of organometallic chemical vapor deposition at higher pressures is also discussed.}, number={1997 Mar.}, journal={Applied Surface Science}, author={Bachmann, K. J. and Hopfner, C. and Sukidi, N. and Miller, A. E. and Harris, C. J. and Aspnes, D. E. and Dietz, N. A. and Tran, Hien and Beeler, S. C. and Ito, K. and et al.}, year={1997}, pages={38–47} }
 @inproceedings{fiechter_castleberry_dietz_bachmann_banks_ito_scroggs_tran_1995, place={Warrendale, PA}, title={High Pressure Vapor Transport of ZnGeP 2 : I, Parameter Evaluation}, booktitle={7th International Symposium on Experimental Methods for Microgravity Materials Science : proceedings of the Seventh International Conference on Experimental Methods for Microgravity Materials Science}, publisher={Minerals, Metals and Materials Society,}, author={Fiechter, S. and Castleberry, R.H. and Dietz, N. and Bachmann, K.J. and Banks, H.T. and Ito, K. and Scroggs, J.S. and Tran, H.}, editor={Schiffman, R.A.Editor}, year={1995}, pages={57–66} }
 @inproceedings{scroggs_banks_ito_ravindran_tran_bachmann_castleberry_dietz_1995, place={Warrendale, PA}, title={High Pressure Vapor Transport of ZnGeP 2 : II, Three-Dimensional Simulation of Gas-dynamics under Microgravity Conditions}, booktitle={7th International Symposium on Experimental Methods for Microgravity Materials Science : proceedings of the Seventh International Conference on Experimental Methods for Microgravity Materials Science}, publisher={Minerals, Metals and Materials Society,}, author={Scroggs, J.S. and Banks, H.T. and Ito, K. and Ravindran, S. and Tran, H.T. and Bachmann, K.J. and Castleberry, R.H. and Dietz, N.}, editor={Schiffman, R.Editor}, year={1995}, pages={67–72} }
 @inproceedings{batzel_tran_1995, place={College Station, Texas}, title={Human Respiratory Control System and Periodic Breathing}, booktitle={SES' 95 : Society of Engineering Science 32nd annual technical meeting, October 29 - November 2, 1995, New Orleans, LA}, author={Batzel, J.J. and Tran, H.T.}, year={1995}, pages={623–624} }
 @inbook{ito_tran_scroggs_1995, place={New York}, series={The IMA Volumes in Mathematics and its Applications}, title={Mathematical Issues in Optimal Design of a Vapor Transport Reactor}, ISBN={9781461275695, 9781461225263}, DOI={10.1007/978-1-4612-2526-3_9}, abstractNote={In this paper the optimal design of a vertical reactor for growing crystals and epitaxial layers by physical vapor transport technique is discussed. The transport phenomena involved in the deposition process is modeled by the gasdynamics equations and chemical kinematics. The problem is formulated as a shape optimization with respect to the geometry of the reactor and an optimal control problem by controlling the wall temperature. The material and shape derivatives of solutions to the so-called Boussinesq approximation are derived. Optimality condition and a numerical optimization method based on the augmented Lagrangian method are discussed for the boundary control of the Boussinesq flow. A numerical approximation based on the Jacobi polynomials for the axi-symmetric flow is developed along with a discussion of an iterative method based on GMRES for solving the resulting system of nonlinear equations.}, booktitle={Flow Control}, publisher={Springer}, author={Ito, K. and Tran, H.T. and Scroggs, J.S.}, editor={Gunzburger, Max D.Editor}, year={1995}, pages={197–218}, collection={The IMA Volumes in Mathematics and its Applications} }
 @inbook{ito_scroggs_tran_1995, title={Optimal Control of Thermally Coupled Navier Stokes Equations}, ISBN={9781461269168 9781461208396}, url={http://dx.doi.org/10.1007/978-1-4612-0839-6_13}, DOI={10.1007/978-1-4612-0839-6_13}, abstractNote={The optimal boundary temperature control of the stationary thermally coupled incompressible Navier- Stokes equation is considered. Well-posedness and existence of the optimal control and a necessary optimality condition are obtained. Optimization algorithms based on the augmented Lagrangian method with second order update are discussed. A test example motivated by control of transport process in the high pressure vapor transport (HPVT) reactor is presented to demonstrate the applicability of our theoretical results and proposed algorithm.}, booktitle={Optimal Design and Control}, publisher={Birkhäuser Boston}, author={Ito, Kazufumi and Scroggs, Jeffrey S. and Tran, Hien T.}, year={1995}, pages={199–214} }
 @inproceedings{banks_ito_scroggs_tran_bachmann_castleberry_fiechter_1994, place={New York}, title={Gasdynamics and Transport in a High-Pressure Reactor Under Microgravity Conditions}, booktitle={Proceedings of the 2nd IEEE Mediterranean Symposium on New Directions in Control and Automation (MED '94)}, publisher={IEEE Publications}, author={Banks, H.T. and Ito, K. and Scroggs, J.S. and Tran, H.T. and Bachmann, K.J. and Castleberry, H. and Fiechter, S.}, year={1994}, pages={427–433} }
 @inproceedings{fiechter_castleberry_wood_bachmann_tran_ito_scroggs_1994, place={Warrendale, PA}, title={High Pressure Vapour Transport of Binary and Ternary Compound Semiconductors}, booktitle={6th International Symposium on Experimental Methods for Microgravity Materials Science : proceedings of the Sixth International Symposium on Experimental Methods for Microgravity Materials Science}, publisher={Minerals, Metals and Materials Society}, author={Fiechter, S. and Castleberry, R.H. and Wood, G. and Bachmann, K.J. and Tran, H.T. and Ito, K. and Scroggs, J.S.}, editor={Schiffman, R.A. and Andrews, J.B.Editors}, year={1994}, pages={93–100} }
 @article{manitius_tran_1994, title={Numerical Approximations for Hereditary Systems with Input and Output Delays: Convergence Results and Convergence Rates}, volume={32}, ISSN={0363-0129 1095-7138}, url={http://dx.doi.org/10.1137/s0363012989161699}, DOI={10.1137/s0363012989161699}, abstractNote={In this paper, the averaging approximation scheme for linear retarded functional differential equations with delays in control and observation is considered in the context of the state space theory developed by Pritchard and Salamon [SIAM J. Control Optim., 25 (1987), pp.~121--144]. Using known results from linear semigroup theory, convergence and estimate of convergence rate of the approximating semigroups are established. These extend results due to Banks and Burns [SIAM J. Control Optim., 16 (1978), pp.~169--208] and Lasiecka and Manitius [SIAM J. Numer. Anal., 25 (1988), pp.~883--907] on hereditary systems with delays in state, to the case when delays in control and observation are included. The main difference from the case when delays in input and output are excluded is that unbounded input and output operators must be dealt with in the abstract formulation. Moreover, in the presence of the unboundedness of the input and output operators, new convergence results of the state solutions and the output are also obtained.}, number={5}, journal={SIAM Journal on Control and Optimization}, publisher={Society for Industrial & Applied Mathematics (SIAM)}, author={Manitius, A. and Tran, H. T.}, year={1994}, month={Sep}, pages={1332–1363} }
 @article{banks_tran_woodward_1993, title={Estimation of Variable Cefficients in the Fokker–Planck Quations Using Moving Node Finite Elements}, volume={30}, ISSN={0036-1429 1095-7170}, url={http://dx.doi.org/10.1137/0730082}, DOI={10.1137/0730082}, abstractNote={Inverse problems are considered for the estimation of temporally and spatially varying coefficients in the Fokker–Planck or forward Kolmogorov equation that often arise in size/age structured population models. These are difficult problems even for simulation studies since they share certain numerical difficulties with transport-dominated diffusion-convection problems of fluid dynamics. These difficulties stem from the fact that when the convection is large compared to the diffusion, both traditional finite difference or finite element methods produce erroneous oscillatory solutions. In this paper, computational techniques are presented that combine a variation of the moving finite element method with spline approximations for the parameter estimation problems. Computational details of our numerical algorithm along with theoretical convergence results are presented. Several numerical examples illustrating the effectiveness of the method are also given.}, number={6}, journal={SIAM Journal on Numerical Analysis}, publisher={Society for Industrial & Applied Mathematics (SIAM)}, author={Banks, H. T. and Tran, H. T. and Woodward, D. E.}, year={1993}, month={Dec}, pages={1574–1602} }
 @article{bachmann_xing_scroggs_tran_ito_castleberry_wood_1993, title={Heteroepitaxy of Wide Bandgap Ternary Semiconductors}, volume={32}, ISSN={0021-4922 1347-4065}, url={http://dx.doi.org/10.7567/jjaps.32s3.133}, DOI={10.7567/jjaps.32s3.133}, number={S3}, journal={Japanese Journal of Applied Physics}, publisher={IOP Publishing}, author={Bachmann, K. J. and Xing, G. -C. and Scroggs, J. S. and Tran, H. T. and Ito, K. and Castleberry, H. and Wood, G.}, year={1993}, month={Jan}, pages={133} }
 @article{tran_scroggs_bachmann_1993, place={Philadelphia, PA}, title={Modeling of Flow Dynamics and its Impact on the Optimal Reactor Design Problem}, journal={Proceeding of 1992 AMS-IMS-SIAM Summer Research Conference on Control and Identification of Partial Differential Equations}, publisher={SIAM Publications}, author={Tran, H. and Scroggs, J.S. and Bachmann, K.J.}, year={1993}, pages={1–13} }
 @article{heinkenschloss_kelley_tran_1992, title={Fast Algorithms for Nonsmooth Compact Fixed-Point Problems}, volume={29}, ISSN={0036-1429 1095-7170}, url={http://dx.doi.org/10.1137/0729099}, DOI={10.1137/0729099}, abstractNote={A fast algorithm for compact fixed-point problems with nonsmooth nonlinearities is designed and analyzed. The algorithm is a combination of an extension of the Atkinson–Brakhage–Nystrom algorithm for smooth problems and a generalization of work by Yamamoto and Chen for nonsmooth problems. A critical structural hypothesis in the general theory is explicitly verified in the context of problems that can be expressed as integral equations with certain types of nonsmoothness. The work is motivated by problems in combat modeling. In particular, we consider the solution of an optimality system that arises in control of competitive systems.}, number={6}, journal={SIAM Journal on Numerical Analysis}, publisher={Society for Industrial & Applied Mathematics (SIAM)}, author={Heinkenschloss, M. and Kelley, C. T. and Tran, H. T.}, year={1992}, month={Dec}, pages={1769–1792} }
 @inproceedings{tran_scroggs_1992, place={New York}, title={Optimal Control of Fluid Flow in a Vertical Chemical Vapor Deposition Reactor}, booktitle={Proceedings of the 31st IEEE Conference on Decision and Control : December 16-18, 1992, Westin La Paloma, Tucson, Arizona, USA}, publisher={IEEE Control Systems Society}, author={Tran, H. and Scroggs, J.S.}, year={1992}, pages={3405–3409} }
 @article{ito_tran_manitius_1991, title={A Fully-Discrete Spectral Method for Delay-Differential Equations}, volume={28}, ISSN={0036-1429 1095-7170}, url={http://dx.doi.org/10.1137/0728060}, DOI={10.1137/0728060}, abstractNote={In this paper a new Lanczos-tau method for solving linear functional differential equations is introduced. The scheme has infinite order of accuracy both in time and in the delayed argument. The high accuracy in time is obtained without increasing the computational work and memory space which is needed for a one-step explicit difference scheme. The article demonstrates how to implement the algorithm in a robust and efficient manner and to treat problems with piecewise continuous initial function. Numerical results illustrating the behavior of the method when faced with difficult problems are presented and the numerical results are compared to those obtained by using two other methods.}, number={4}, journal={SIAM Journal on Numerical Analysis}, publisher={Society for Industrial & Applied Mathematics (SIAM)}, author={Ito, K. and Tran, H. T. and Manitius, A.}, year={1991}, month={Aug}, pages={1121–1140} }
 @inbook{tran_1991, title={Numerical Studies of the Linear Quadratic Control Problem for Retarded Systems with Delay in Control}, ISBN={9780817636111 9781461204275}, url={http://dx.doi.org/10.1007/978-1-4612-0427-5_21}, DOI={10.1007/978-1-4612-0427-5_21}, abstractNote={In this paper we report on the results of our continuing efforts on using the averaging approximation scheme for retarded functional differential equations. The central focus of this paper is our numerical studies of constructing feedback soLutions to linear quadratic regulator (LQR) problems for retarded systems with delay in control. For completeness, we shall also give a brief summary and discussion of an abstract approximation framework and convergence theory developed previously by Ito and Tran in[9]. In [9]we presented an approximation framework for the numerical treatment of algebraic Riccati equations for a class of linear infinite dimensional systems with unbounded input and output operators studied by Pritchard and Salamon in[19] In this paper we will call it the Pritchard-Salamon clans. This approximation theory which yields convergence of the approximating Riccati operators as well as convergence of the approximating gain operators extends earlier results developed in[7][2][8]in which the input and output operators are assumed to be bounded to the unbounded cases. The main features which distinguish the work in [9]from other work existing in the literature, see e.g.[11][14][15] are the assumptions on the smoothness of the underlined semigroup and the observation map. Because of the smoothness assumptions, the algebraic Riccati soLution has a smoothing property which in turn implies boundedness of the feedback gain operator. Although the theory developed in[9]does not cover many important boundary control problems studied by Lasiecka and Triggiani in [13] and Flandoli, Lasiecka, and Triggiani in[6] for example, it does enable us to treat the control problem governed by delay differential equations with delays in control and observation.}, booktitle={Computation and Control II}, publisher={Birkhäuser Boston}, author={Tran, Hien T.}, year={1991}, pages={307–324} }
 @inproceedings{manitius_tran_1990, title={Finite dimensional approximations for functional differential equations with input and output delays}, url={http://dx.doi.org/10.1109/cdc.1990.203893}, DOI={10.1109/cdc.1990.203893}, abstractNote={The authors present some results on the numerical approximations for linear retarded functional differential equations with delays in control and observation. Specifically, they consider the averaging approximation scheme for such systems treated as evolution equations with unbounded input and output operators in the state space set-up developed by A.J. Pritchard and D. Salamon (Technical Report no.2624, Mathematics Research Center, University of Wisconsin, Madison, WI, 1984).<<ETX>>}, booktitle={29th IEEE Conference on Decision and Control}, publisher={IEEE}, author={Manitius, A. and Tran, H.T.}, year={1990} }
 @inproceedings{ito_tran_1989, place={Basel}, series={International series of numerical mathematics}, title={Linear Quadratic Optimal Control Problem for Linear Systems with Unbounded Input and Output Operators: Numerical Approximations”}, ISBN={9783764323455, 9780817623456}, booktitle={Control and estimation of distributed parameter systems : 4th International Conference on Control of Distributed Parameter Systems, Vorau, July 10-16, 1988}, publisher={Birkhäuser Verlag}, author={Ito, K. and Tran, H.T.}, editor={Kappel, E. and Kunisch, K. and Schappacher, W.Editors}, year={1989}, pages={171–195}, collection={International series of numerical mathematics} }
 @inproceedings{tran_michelson_ito_leith_1989, place={Basel}, title={Stochastic Models of Subpopulation Emergence in Heterogeneous Tumors}, booktitle={Electrical and power systems : modelling and simulation}, publisher={J.C. Balzer AG}, author={Tran, H. and Michelson, S. and Ito, K. and Leith, J.T.}, editor={Robert, J. and Midvidy, W.Editors}, year={1989} }
 @article{michelson_ito_tran_leith_1989, title={Stochastic models for subpopulation emergence in heterogeneous tumors}, volume={51}, ISSN={0092-8240}, url={http://dx.doi.org/10.1016/s0092-8240(89)80060-6}, DOI={10.1016/s0092-8240(89)80060-6}, number={6}, journal={Bulletin of Mathematical Biology}, publisher={Springer Nature}, author={Michelson, S and Ito, K and Tran, H and Leith, J}, year={1989}, pages={731–747} }
 @inproceedings{ito_tran_1988, title={Linear quadratic regulator problem for infinite dimensional linear systems with delays in control}, url={http://dx.doi.org/10.1109/cdc.1988.194687}, DOI={10.1109/cdc.1988.194687}, abstractNote={The authors consider the linear quadratic optimal control problem for linear control systems with delays in control defined on a Hilbert space H/sub 0/, and they develop a numerical approximation method for approximate Riccati operators. They show how to reformulate the problem as a boundary control problem, using the product space H/sub 0/*L/sub 2/ as the state space. They then present an approximation framework for computing the Riccati operators (in finite-dimensional spaces) that can be guaranteed to converge to the Riccati operators of the infinite-dimensional systems with unbounded input.<<ETX>>}, booktitle={Proceedings of the 27th IEEE Conference on Decision and Control}, publisher={IEEE}, author={Ito, K. and Tran, H.T.}, year={1988}, month={Jan}, pages={2012–2017} }
 @article{manitius_tran_payre_roy_1987, title={Computation of Eigenvalues Associated with Functional Differential Equations}, volume={8}, ISSN={0196-5204 2168-3417}, url={http://dx.doi.org/10.1137/0908032}, DOI={10.1137/0908032}, abstractNote={This paper describes a method for computing the eigenvalues associated with systems of linear retarded functional differential equations (RFDE's). The method finds the eigenvalues directly from a certain characteristic equation which is automatically determined from system matrices. The eigenvalues contained in some bounded region around the origin are approximately computed by a combinatorial algorithm suggested earlier by H. Kuhn [15] for approximations of zeros of ordinary polynomials. The eigenvalues of large modulus, which are distributed in some curvilinear strips, are computed from some asymptotic formulas obtained directly from the parameters of the characteristic equation. To verify that all the eigenvalues have been found, we use a highly reliable procedure proposed by Carpentier and Dos Santos, which evaluates the number of zeros of an analytic function in a given region. Numerical results are presented for several examples and compared with those obtained by a method based on finite-dimensional approximations of delay equations.}, number={3}, journal={SIAM Journal on Scientific and Statistical Computing}, publisher={Society for Industrial & Applied Mathematics (SIAM)}, author={Manitius, A. and Tran, H. and Payre, G. and Roy, R.}, year={1987}, month={May}, pages={222–247} }
 @article{manitius_tran_1986, title={Numerical simulation of a non-linear feedback controller for a wind tunnel model involving a time delay}, volume={7}, ISSN={0143-2087 1099-1514}, url={http://dx.doi.org/10.1002/oca.4660070103}, DOI={10.1002/oca.4660070103}, abstractNote={Abstract}, number={1}, journal={Optimal Control Applications and Methods}, publisher={Wiley}, author={Manitius, A. and Tran, H.}, year={1986}, month={Jan}, pages={19–39} }
 @article{manitius_tran_1985, title={Computation of closed-loop eigenvalues associated with the optimal regulator problem for functional differential equations}, volume={30}, ISSN={0018-9286}, url={http://dx.doi.org/10.1109/tac.1985.1103866}, DOI={10.1109/tac.1985.1103866}, abstractNote={A solution of the linear quadratic control problem involving functional differential equations gives a linear feedback control law which modifies the original system dynamics. Under certain assumptions, the eigenvalues of the modified linear system constitute a stable part of a spectrum of a hamiltonian operator associated with the optimization problem. These eigenvalues can be computed without solving the infinite dimensional Riccati equation. In this paper we present a method based on an earlier algorithm (constructed by A. Manitius, G. Payre and R. Roy) which solves directly the characteristic equation of the closed loop system, and compare it with a direct computation of eigenvalues of a symplectic hamiltonian matrix arising from a finite dimensional approximation of a functional differential equation.}, number={12}, journal={IEEE Transactions on Automatic Control}, publisher={Institute of Electrical and Electronics Engineers (IEEE)}, author={Manitius, A. and Tran, H.}, year={1985}, month={Dec}, pages={1245–1248} }
 @inproceedings{tran_manitius_1985, title={On the numerical approximations for linear functional differential equations with input and output delays}, url={http://dx.doi.org/10.1109/cdc.1985.268746}, DOI={10.1109/cdc.1985.268746}, abstractNote={In this paper we state some new results on the approximations for linear retarded functional differential equations with delays in control and observation. We consider the finite difference (i.e., averaging) approximation scheme for such systems treated as evolution equations in the state space setup, and we establish several basic properties of the approximation scheme. These results are extensions of recent results of Lasiecka and ManitiusL1 to the case of systems with input and output delays.}, booktitle={1985 24th IEEE Conference on Decision and Control}, publisher={IEEE}, author={Tran, Hien and Manitius, A.}, year={1985}, month={Dec} }
 @inproceedings{manitius_tran_1983, title={Computation of closed loop eigenvalues associated with the optimal regulator problem for functional differential equations}, url={http://dx.doi.org/10.1109/cdc.1983.269791}, DOI={10.1109/cdc.1983.269791}, abstractNote={A solution of the linear quadratic control problem involving functional differential equations gives a linear feedback control law which modifies the original system dynamics. Under certain assumptions, the eigenvalues of the modified linear system constitute a stable part of a spectrum of a hamiltonian operator associated with the optimization problem. These eigenvalues can be computed without solving the infinite dimensional Riccati equation. In this paper we present a method based on an earlier algorithm (constructed by A. Manitius, G. Payre and R. Roy) which solves directly the characteristic equation of the closed loop system, and compare it with a direct computation of eigenvalues of a symplectic hamiltonian matrix arising from a finite dimensional approximation of a functional differential equation.}, booktitle={The 22nd IEEE Conference on Decision and Control}, publisher={IEEE}, author={Manitius, A. and Tran, H.}, year={1983} }
 @inproceedings{manitius_tran_1983, place={Baltimore, MD}, title={Numerical Simulation of Linear and Nonlinear Feedback Controllers for a Wind Tunnel Model Involving a Time Delay”}, booktitle={Proceedings of the Seventeenth Annual Conference on Information Sciences and Systems : papers presented March 23, 24, and 25, 1983}, publisher={Johns Hopkins University}, author={Manitius, A. and Tran, H.}, editor={Weinert, H.L. and Melville, R.C.Editors}, year={1983} }