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Publications.html
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<h3>This page contains</h3>
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<li>Provisional patents/published/submitted papers</li>
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<li>Preprints and technical reports</li>
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<h4>Provisional patents</h4>
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<ol type = "1">
<li>Systems and methods for removal of extra-column band broadening in chromatographic peaks, <b><i> US Provisional Patent, </i> ID:63/506,895, </b>2023 (Daniel W. Armstrong, M. Farooq Wahab, Troy T. Handlovic, and S. Roy). </li>
</ol>
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<br>
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<div class="col-md-12">
<h4>Peer reviewed published journal articles</h4>
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<div class="col-md-7">
<ol type = "1">
<li> Solving advanced task-specific problems in measurement sciences with generative AI (ChatGPT-4), <b><i> Analytical Chemistry, </i> </b> 2024 (M. Farooq Wahab, Troy Handlovic, S. Roy, Ryan Jacob Burk, Daniel Armstrong). <a href="https://pubs.acs.org/doi/abs/10.1021/acs.analchem.4c01734">[journal]</a> </li>
<li> An evolutionary differential game for regulating the role of monoclonal antibodies in treating signaling pathways in esophageal cancer, <b><i> Royal Society Open Science, </i> </b> 2024 (Mesfer Alajmi and S. Roy). <a href="https://royalsocietypublishing.org/doi/10.1098/rsos.240347">[journal]</a></li>
<li>Second-order modified nonstandard explicit Euler and explicit Runge-Kutta methods for n-dimensional autonomous differential equations, <b><i> Computation, </i> </b> 2024 (Fawaz Alalhareth, Madhu Gupta, Hristo Kojouharov and S. Roy). <a href="https://www.mdpi.com/2079-3197/12/9/183">[journal]</a> </li>
<li> Liouville optimal control framework in prostate cancer, <b><i> Applied Mathematical Modeling, </i>134:417-433,</b> 2024 (Hussein Edduweh and S. Roy). <a href="https://www.sciencedirect.com/science/article/abs/pii/S0307904X24002981">[journal]</a></li>
<li> A new approach to high contrast and resolution reconstruction in quantitative photoacoustic tomography, <b><i> Journal of Computational and Applied Mathematics, </i> 451:116065, </b> 2024 (Anwesa Dey, Alfio Borzi and S. Roy). <a href="https://www.sciencedirect.com/science/article/pii/S0377042724003157">[journal]</a></li>
<li> Numerical approximation of kinetic Fokker-Planck equations with
specular reflection boundary conditions, <b><i> Journal of Computational Physics, </i> 503:112841, </b>2024 (S. Roy and Alfio Borzi). <a href="https://www.sciencedirect.com/science/article/pii/S0021999124000901?via%3Dihub">[journal]</a></li>
<li> A robust optimal control framework for controlling aberrant RTK signaling pathways in esophageal cancer, <b><i> Journal of Mathematical Biology, </i> 88(14), </b>2023 (S. Roy, Zui Pan, Naif Abu Qarnayn, Mesfer Alajmi, Ali Alatwi, Asma Alghamdi, Ibrahem Alshaoosh, Zahra Asiri, Berlinda Batista, Shreshtha Chaturvedi, Olusola Dehinsilu, Hussein Edduweh, Rodina El-Adawy, Emran Hossen, Bardia Mojra, Jashmon Rana) <b>(with all students of my MATH 5392 class)</b>. <a href="https://link.springer.com/article/10.1007/s00285-023-02033-0">[journal]</a> </li>
<li>Radon transform with Gaussian beam: Theoretical and numerical reconstruction scheme, <b><i> Applied Mathematics and Computation, </i> 452:128024, </b>2023 (S. Roy, Gihyeon Jeon and Sunghwan Moon). <a href="https://www.sciencedirect.com/science/article/abs/pii/S0096300323001935">[journal]</a> </li>
<li> Automated regularized deconvolution for eliminating extra-column effects in fast high-efficiency
separations, <b><i> Analytical Chemistry, </i> 95(29):11028-11036, </b>2023 (Troy T. Handlovic, M. Farooq Wahab, S. Roy, Ronald E. Brown and Daniel W. Armstrong). <a href="https://pubs.acs.org/doi/10.1021/acs.analchem.3c01279">[journal]</a> </li>
<li> A numerical scheme to solve Fokker-Planck control collective-motion problem, <b><i> Mathematics and Computers in Simulation, </i> 225:1056-1071, </b> 2023 (Muhammad Munir Butt and S. Roy). <a href="https://www.sciencedirect.com/science/article/abs/pii/S0378475423004317">[journal]</a> </li>
<li> On the parameter estimation of Box-Cox transformation cure model, <b><i> Statistics in Medicine, </i> 1-19, </b>2023 (Suvra Pal and S. Roy). <a href="https://onlinelibrary.wiley.com/doi/10.1002/sim.9739">[journal]</a> </li>
<li> Second-order modified positive and elementary stable nonstandard numerical methods for n-dimensional autonomous
differential equations, <b><i> Mathematical Methods in the Applied Sciences, </i> </b>2023 (Fawaz Alalhareth, Madhu Gupta, S. Roy and Hristo Kojouharov). <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/mma.9560">[journal]</a> </li>
<li> A new nonlinear sparse optimization framework in ultrasound-modulated optical tomography, <b><i> IEEE Transactions on Computational Imaging, </i> 8:1-11, </b>2022 (S. Roy). <a href="https://ieeexplore.ieee.org/document/9661298">[journal]</a> </li>
<li> Geometric characterization of polymeric capillaries, <b><i> Analytica Chimica Acta, </i> 1229:340345, </b>2022 (Enas N. Yousef, Purnendu K. Dasgupta, Seth A Horn, Phillip Shelor and S. Roy). <a href="https://www.sciencedirect.com/science/article/pii/S0003267022009163?dgcid=author">[journal]</a> </li>
<li>A Fokker-Planck feedback control framework for optimal personalized therapies in colon cancer-induced angiogenesis, <b><i> Journal of Mathematical Biology, </i> 84:23, </b> 2022 (S. Roy, Zui Pan and Suvra Pal). <a href="https://link.springer.com/article/10.1007/s00285-022-01725-3">[journal]</a></li>
<li> Developing a mathematical model of intracellular calcium dynamics for evaluating combined
anticancer effects of Afatinib and RP4010 in esophageal cancer, <b><i> International Journal of Molecular Sciences, </i> 23(3):1763, </b> 2022 (Yan Chang, Marah Funk, S. Roy, Elizabeth Stephenson, Sangyong Choi, Hristo Kojouharov, Benito Chen and Zui Pan). <a href="https://doi.org/10.3390/ijms23031763">[journal]</a></li>
<li> A numerical investigation of Brockett's ensemble optimal control problems,
<b><i> Numersiche Mathematik, </i> 149:1-42, </b>2021
(Jan Bartsch, Alfio Borzi, Francesco Fanelli and S. Roy).
<a href="https://doi.org/10.1007/s00211-021-01223-6">[journal]</a></li>
<li> Numerical inversion and uniqueness of a spherical radon transform restricted with a fixed angular span,
<b><i> Applied Mathematics and Computation, </i> 408:126338, </b>2021
(Rim Gouia-Zarrad, S. Roy and Sunghwan Moon).
<a href="https://www.sciencedirect.com/science/article/pii/S0096300321004276">[journal]</a></li>
<li>Second-order modified nonstandard Runge-Kutta and theta methods for one-dimensional autonomous differential equations,
<b><i> Applications and Applied Mathematics, </i> 16(2):788-803, </b>
2021 (Madhu Gupta, John M. Slezak, Fawaz Alalhareth, S. Roy and Hristo Kojouharov). <a href="https://digitalcommons.pvamu.edu/aam/vol16/iss2/1">[journal] </a></li>
<li> Store-operated calcium channels as drug target in gastroesophageal cancers,
<b><i> Frontiers in Pharmacology, </i> 12:944, </b>2021
(Yan Chang, S. Roy and Zui Pan).
<a href="https://www.frontiersin.org/articles/10.3389/fphar.2021.668730/full">[journal]</a></li>
<li> On the estimation of destructive cure rate model: A new study with exponentially weighted Poisson competing risks,
<b><i> Statistica Neerlandica, </i> 75(3):324-342, </b>2021
(Suvra Pal and S. Roy).
<a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/stan.12237">[journal]</a></li>
<li> Sparsity-based nonlinear reconstruction of optical parameters in two-photon photoacoustic computed tomography,
<b><i> Inverse Problems, </i> 37:044001, </b>2021
(Madhu Gupta, Rohit Kumar Mishra and S. Roy).
<a href="https://doi.org/10.1088/1361-6420/abdd0f">[journal]</a></li>
<li> A second-order nonstandard theta method for autonomous differential equations,
<b><i> Applied Mathematics Letters, </i>112:106775, </b>2020
(Hristo Kojouharov, S. Roy, Madhu Gupta, Fawaz Alalhareth and John M Slezak).
<a href="https://www.sciencedirect.com/science/article/abs/pii/S0893965920303931">[journal]</a>
</li>
<li> Sparse reconstruction of log-conductivity in current density impedance tomography,
<b><i> Journal of Mathematical Imaging and Vision, </i> 62:189-205, </b>2020
(Madhu Gupta, Rohit Kumar Mishra and S. Roy).
<a href="https://doi.org/10.1007/s10851-019-00929-5">[journal]</a></li>
<li> A new non-linear conjugate gradient algorithm for destructive cure rate model and a
simulation study: illustration with negative binomial competing risks,
<b><i> Communications in Statistics - Simulation and Computation, </i> </b>2020
(Suvra Pal and S. Roy).
<a href="https://www.tandfonline.com/doi/full/10.1080/03610918.2020.1819321">[journal]</a></li>
<li>How to place an obstacle having a dihedral symmetry centered at a given point inside
a disk so as to optimize the fundamental Dirichlet eigenvalue,
<b><i> Journal of Optimization Theory and Applications, </i> 184(1):162-187, </b>2020
(Anisa M. H. Chorwadwala and S. Roy).
<a href="https://doi.org/10.1007/s10957-019-01483-1">[journal]</a></li>
<li>A theoretical investigation of Brockett's ensemble optimal control problems,
<b><i> Calculus of Variation and Partial Differential Equations, </i> 58:162, </b>2019
(Jan Bartsch, Alfio Borzi, Francesco Fanelli and S. Roy).
<a href="https://doi.org/10.1007/s00526-019-1604-2">[journal]</a></li>
<li>A Fokker-Planck approach to control collective motion,
<b><i> Computational Optimization and Applications, </i> 69(2):423--459, </b>2018
(S. Roy, Mario Annunziato, Alfio Borzi and Christian Klingenberg).
<a href="https://doi.org/10.1007/s10589-017-9944-3">[journal]</a></li>
<li>Image reconstruction from radially incomplete spherical Radon data,
<b><i> European Journal of Applied Mathematics, </i> 29(3): 470--493, </b>2018
( Gaik Ambartsoumian, Rim-Gouia-Zarrad, Venkateswaran P. Krishnan and S. Roy).
<a href="https://doi.org/10.1017/S0956792517000250">[journal]</a></li>
<li>A new optimisation approach to sparse reconstruction of log-conductivity in acousto-electric tomography,
<b><i> SIAM Journal of Imaging Sciences, </i> 1(2):1759--1784, </b>2018
(S. Roy and Alfio Borzi).
<a href="https://epubs.siam.org/doi/abs/10.1137/17M1148451">[journal]</a></li>
<li>A fully non-linear optimization approach to acousto-electric tomography,
<b><i> Inverse Problems, </i> 34:104004, </b>2018
(Bolaji Adesokan, Kim Knudsen, Venkateswaran P. Krishnan and S. Roy).
<a href="https://doi.org/10.1088/1361-6420/aad6b1">[journal]</a></li>
<li>Pedestrian motion constrained by FP-constrained Nash games,
<b><i> Royal Society Open Science, </i> 4(9):170648, </b>2017
(S. Roy, Alfio Borzi and Abderrahmane Habbal).
<a href="http://rsos.royalsocietypublishing.org/content/4/9/170648">[journal]</a></li>
<li>Numerical investigation of a class of Liouville control problems, <b> <i> Journal of Scientific Computing,
</i> 73(1):178-202 </b>, 2017 (S. Roy and Alfio Borzi).
<a href="http://dx.doi.org/10.1007/s10915-017-0410-2">[journal]</a> </li>
<li> A variational approach to estimate incompressible fluid flows, <b><i> Proceedings of Mathematical Sciences, Springer,
</i> 127(1):175-201</b>, 2017
(Praveen C., S. Roy and A. S. Vasudeva Murthy).
<a href="https://doi.org/10.1007/s12044-016-0317-0">[journal]</a></li>
<li> Numerical inversion of a broken ray transform arising in single scattering optical tomography, <b><i>IEEE Transactions on Computational Imaging, </i>
2(2):166-173</b>, 2016 (Gaik Ambartsoumian and S. Roy).
<a href="https://doi.org/10.1109/TCI.2016.2531581">[journal]</a></li>
<li> A Fokker-Planck feedback control-constrained approach for modelling crowd motion, <b> <i> Journal of Computational and Theoretical
Transport, </i> 45(6):442-458</b>, 2016 (S. Roy, Mario Annunziato and Alfio Borzi).
<a href="http://dx.doi.org/10.1080/23324309.2016.1189435">[journal]</a> </li>
<li>A variational approach to optical flow estimation of unsteady incompressible flows,<b> <i>International Journal of Advances in Engineering
Sciences and Applied Mathematics, Springer,</i> 7(3):149-167</b>, 2015 (S. Roy, Praveen C. and A. S. Vasudeva Murthy).
<a href="http://link.springer.com/article/10.1007%2Fs12572-015-0147-9">[journal]</a></li>
<li> An efficient numerical algorithm for Radon transform inversion with applications in ultrasound imaging.
<b> <i>Journal of Mathematical Imaging and Vision,</i> 53:78-91</b>, 2015 (S. Roy, Venkateswaran P. Krishnan, Praveen C. and A. S. Vasudeva Murthy).
<a href="http://link.springer.com/article/10.1007%2Fs10851-014-0550-z">[journal]</a></li>
<li> Reconstruction of a class of fluid flows by variational methods and inversion of integral transforms in tomography,
<b><i>Ph.D. thesis, Tata Institute of Fundamental Research,</i></b> 2015
<a href="Souvik_phd_thesis_compressed.pdf">[pdf]</a></li>
</ol>
</div>
</div>
<br>
<div class="row">
<div class="col-md-12">
<h4>Peer reviewed book chapters</h4>
</div>
</div>
<div class="row">
<div class="col-md-7">
<ol type = "1">
<li> Higher-order modified nonstandard finite difference methods for autonomous dynamical systems,
<b><i> Contemporary
Mathematics (CONM) book series: Mathematical and Computational Modeling of Phenomena
Arising in Population Biology and Nonlinear Oscillations, </i> (in print), </b>2023
(Fawaz Alalhareth, Madhu Gupta, Hristo Kojouharov and S. Roy).</a>
</li>
<li> Optimal personalized therapies in colon-cancer induced immune response using a Fokker-Planck framework,
<b><i> Mathematics and Computer Science Volume 2: Industrial Applications, Sharmistha Ghosh, Niranjanamurthy M, Krishanu Deyasi, Biswadip Basu Mallik, Santanu Das Editors., Wiley-Scrivener, </i> 33-48, </b>2023
(S. Roy and Suvra Pal).<a href="https://doi.org/10.1002/9781119896715.ch3">[journal]</a>
</li>
<li> Placement of an obstacle for optimizing the fundamental eigenvalue of divergence form elliptic operators,
<b><i> Variational Views in Mechanics, P. M. Mariano Editors., series "Advances in Continuum Mechanics", Birkhauser-Springer, Boston, </i> 123:157-183, </b>2021
(Anisa M. H. Chorwadwala and S. Roy).
<a href="https://doi.org/10.1007/978-3-030-90051-9_6">[journal]</a></li>
</ol>
</div>
</div>
<br>
<div class="row">
<div class="col-md-12">
<h4>Submitted articles</h4>
</div>
</div>
<br>
<div class="row">
<div class="col-md-7">
<ol type = "1">
<li> A SIMPL model of phage-bacteria interactions accounting for mutation and competition, 2024 (Carli Peterson, Darsh Gandhi, Austin Carlson, Aaron Lubkemann, Emma Richardson, John Serralta, Michael S Allen, S. Roy, Christopher M Kribs and Hristo V Kojouharov). </li>
<li> Optimal control of the damped viscous wave equation, 2024 (Alfio Borzi and S. Roy). </li>
<li> A robust optimal control framework for controlling the viral load in HIV, 2024 (Asma Alghamdi and S. Roy). </li>
<li> A differential game framework for modeling and control of colon
cancer, 2024 (Mesfer Alajmi and S. Roy). </li>
<li> Learning end-to-end inversion of circular Radon transforms in the partial radial setup, 2024 (Deep Ray and S. Roy). <a href="https://arxiv.org/pdf/2308.14144">[arxiv]</a></li>
</ol>
</div>
</div>
<div class="row">
<div class="col-md-12">
<h4>Conference Proceedings (Peer-reviewed)</h4>
</div>
</div>
<br>
<div class="row">
<div class="col-md-7">
<ol type = "1">
<li>Higher-order modified
nonstandard finite difference methods for autonomous dynamical systems,
<b><i>BIOMATH 2023 </i>
</b> 2023 (Fawaz Alalhareth, Madhu Gupta, Hristo Kojouharov and S. Roy).
</a> </li>
<li>A Fokker-Planck framework for parameter estimation and sensitivity analysis in colon cancer,
<b><i>AIP Conference Proceedings </i>
2522:070005 </b> 2022 (S. Roy, Suvra Pal, Achyuth Manoj, Susanth Kakarla, Juan Villegas and Mesfer Alajmi).
<a href="https://doi.org/10.1063/5.0100741"> [journal]
</a> </li>
<li>Second-order nonstandard explicit Euler method,
<b><i>AIP Conference Proceedings </i></b> 2020 (Madhu Gupta, John M. Slezak, Fawaz Alalhareth, S. Roy and Hristo Kojouharov).
<a href="https://aip.scitation.org/doi/abs/10.1063/5.0033534"> [journal],
</a> </li>
<li>A sparsity-based Fokker-Planck optimal control framework for modeling traffic flows,
<b><i>AIP Conference Proceedings </i></b> 2020 (S. Roy).
<a href="https://aip.scitation.org/doi/abs/10.1063/5.0033514"> [journal],
</a> </li>
</ol>
</div>
</div>
<br>
<div class="row">
<div class="col-md-12">
<h4>Conference Proceedings (Not peer-reviewed)</h4>
</div>
</div>
<br>
<div class="row">
<div class="col-md-7">
<ol type = "1">
<li>Automatic Segmentation and 3D Visualization of Pelvic Mesh Using Mathematical Modelling and Machine Learning Techniques in MRI,
<b><i>Journal of Urology
</i>203(Supplement 4): e605-e605</b> 2020 (Gaik Ambartsoumian, S. Roy, Gaurav Khatri and Philippe Zimmern). <a href="https://www.auajournals.org/doi/abs/10.1097/JU.0000000000000891.05"> [journal],
</a></li>
<li>Automatic Segmentation and 3D Visualization of Pelvic Mesh Using Mathematical Modelling and Machine Learning Techniques in MRI,
<b><i>ICS, Gothenberg </i></b> 2019 (Gaik Ambartsoumian, S. Roy, Gaurav Khatri and Philippe Zimmern).
<a href="https://www.ics.org/2019/abstract/27"> [website],
</a> </li>
<li>Bubble drag coefficient formulation and stability analysis for multiphase-turbomachinery problems (Shear flow/breakup GE2),
<b><i>Modeling week and study group meeting on industrial problems, Supercomputer education research center
58-73<a href="technical_report_2.pdf">
[pdf]</a></i></b>, 2011 (Gaurav Sharma and S. Roy). </li>
<li>Report on the problem of fish feeding.
<b><i>Modeling week and study group meeting on industrial problems, Supercomputer education research center, 32-55
<a href="technical_report_1.pdf">[pdf]</a></i></b>, 2011 ( S. Roy). </li>
</ol>
</div>
</div>
<br>
<div class="row">
<div class="col-md-12">
<h4>Technical reports</h4>
</div>
</div>
<br>
<div class="row">
<div class="col-md-7">
<ol type = "1">
<li>Personalized prediction of treatment response for peritoneal carcinomatosis via a hybrid mechanistic/AI approach, Technical Report,
<b><i>Advancing Cancer Biology at the Frontiers of Machine Learning and Mechanistic Modeling, NCI-NIH Innovation Lab</i></b>, 2020 (Carlos Chan, Mahsa Dabagh, Dave Fuller, Sara Gosline and S. Roy). </li>
<li>Review of Handbook of Numerical Methods for Hyperbolic Problems: Basic and Fundamental Issues (Remi Abgrall and Chi-Wang Shu),
<b><i>SIAM Reviews, 60(3):768-771, </b>, 2018 (S. Roy). </li>
</ol>
</div>
</div>
</div>
<br>
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