2005-Present

     1994-2004

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Systems Engineers’ Role in Biomedical Research. Convection-Enhanced Drug Delivery
DR Esfahani, K Tangen, M Sadeh, A Seksenyan, BL Neisewander, AI Mehta, AA Linninger. In Computer Aided Chemical Engineering: Quantitative Systems Pharmacology Models and Model-Based Systems with Applications, Ed D. Manca, Elsevier, ISBN: 978-0-444-63964-6, 42, 271-295, 2018.
Validation of parametric mesh generation for subject-specific cerebroarterial trees using modified Hausdorff distance metrics
M Ghaffari, L Sanchez, G Xu, A Alaraj, XJ Zhou, FT Charbel, AA Linninger. Computers in Biology and Medicine, DOI: 10.1016/j.compbiomed.2018.07.004, 2018.
Quantification of near‐wall hemodynamic risk factors in large‐scale cerebral arterial trees
M Ghaffari, A Alaraj, X Du, XJ Zhou, FT Charbel, AA Linninger. International Journal for Numerical Methods in Biomedical Engineering 34, e2987, DOI: 10.1002/cnm.2987, 2018.
TMIC-45 Diffusion of D-2-hydroxygluterate From IDH1 Mutant Gliomas in the Brain
A Linninger, G Hartung, B Liu, S Mirkov, K Tangen, R Lukas, D Unruh, CD James, JN Sarkaria, C Horbinski. Neuro-Oncology, 19 (6), 2018.
Cerebrospinal Fluid Dynamics and Intrathecal Delivery
K Tangen, A Mehta, A Linninger. Neuromodulation (Second Edition), Comprehensive Textbook of Principles, Technologies, and Therapies, 2, 829-846, 2018.
Cellular obstruction clearance in proximal ventricular catheters using low-voltage Joule heating
A Sane, K Tangen, D Frim, M Singh, A Linninger. IEEE Transactions on Biomedical Engineering, 0, 000-000, 2018.
Starling forces drive intracranial water exchange during normal and pathological states
A Linninger, C Xu, K Tangen, G Hartung. Croat Med Journal, 58, 384-394, 2017.
Large-scale subject-specific cerebral arterial tree modeling using automated parametric mesh generation for blood flow simulation
M Ghaffari, K Tangen, A Alaraj, X Du, F Charbel, A Linninger. Computers in Biology and Medicine, 91, 353-365, 2017.
Contrast time-density time on digital subtraction angiography correlates with cerebral arteriovenous malformation flow measured by quantitative magnetic resonance angiography, angioarchitecture, and hemorrhage
D Brunozzi, AE Hussein, SF Shakur, A Linninger, CY Hsu, FT Charbel, A Alaraj. Neurosurgery, 2017.
Computational and in-vitro experimental investigation of intrathecal drug distribution – parametric study of the effect of injection volume, cerebrospinal fluid pulsatility, and drug uptake
K Tangen, R Leval, AI Mehta, A Linninger, Anesthesia & Analgesia, 124(5), 1686-1696, 2017.

This article was featured as the cover of Anesthesia & Analgesia and the focus of an Infographic in the May issue of 2017.
The research is discussed in an editorial by leading experts and featured in an editorial video.



Backflow-free catheters for efficient and safe convection-enhanced delivery of therapeutics
E Lueshen, K Tangen, AI Mehta, A Linninger, Medical Engineering & Physics, 45, 15-24, 2017.
Intrathecal magnetic drug targeting for localized delivery of therapeutics in the central nervous system
I Venugopal, N Habib and A Linninger, Nanomedicine, 12(8), 865-877, 2017.
Validation of cerebral arteriovenous malformation hemodynamics assessed by DSA using quantitative magnetic resonance angiography: preliminary study
SF Shakur, D Brunozzi, AE Hussein, A Linninger, CY Hsu , FT Charbel, A Alaraj, Journal of NeuroInterventional Surgery, 2017.
Gap-free segmentation of vascular networks with automatic image processing pipeline
C Hsu, M Ghaffari, A Alaraj, M Flannery, X J Zhou, A Linninger, Computers in Biology and Medicine, 82, 29-39, 2017. [Download Code][Instructions] [SampleOriginalDataset][SampleFilteredDataset]
The capillary bed offers the largest hemodynamic resistance to the cortical blood supply
I Gould, P Tsai, D Kleinfeld, and A Linninger, Journal of Cerebral Blood Flow & Metabolism, 37(1), 52-68, 2017.

This article was featured on the cover page of Journal of Cerebral Blood Flow & Metabolism in the January issue of 2017.



This article was also featured in Obesity, Fitness & Wellness Week in week of January 14, 2017.

Changes in contrast transit times on digital subtraction angiography post pipeline embolization device deployment
A Alaraj, A Hussein, A Linninger, F Charbel II, C Hsu, F Charbel, V Aletich, Interventional Neuroradiology, 23(2), 137-142 2017.
Image-guidance technology and the surgical resection of spinal column tumors
B Desai, J Hobbs, G Hartung, G Xu, ZL Gokaslan, A Linninger, A Mehta, Journal of Neuro-Oncology, 131(3), 425-435, 2017.
Walk-In Brain: virtual reality environment for immersive exploration and simulation of brain metabolism and function
G Hartung, A Alaraj, A Linninger, Tools for Chemical Product Design, 649-658, 2016.
Additive Manufacturing of Subject-Specific Spine Model for In-Vitro Intrathecal Drug Delivery Study
L Lu, K Tangen, T Gabor, Y Pan, A Linninger, N Purandare, ASME 2016 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC 2016, Aug. 21-24, 2016.
Digital Manufacturing and in silico Modeling for rational design of drug delivery to the central nervous system
K Tangen, T Gabor, L Lu, Y Pan, A Linninger, Summer Biomechanics, 2016 Bioengineering and Biotransport Conference, 2016.
Magnetic field-enhanced cellular uptake of doxorubicin loaded magnetic nanoparticles for tumor treatment
I Venugopal, S Pernal, A Duproz, J Bentley, H Engelhard, and A Linninger, Materials Research Express, 3(9), 2016.
Hydrocephalus: the role of cerebral aquaporin-4 channels and computational modeling considerations of cerebrospinal fluid
B Desai, Y Hsu, B Schneller, J Hobbs, A Mehta, and A Linninger, Neurosurgical Focus, 41(3), E8, 2016.

This article was featured on the cover page of Neurosurgical Focus in the September issue of 2016.



Clearance of subarachnoid hemorrhage from the cerebrospinal fluid in computational and in vitro models
K Tangen, N S Narasimhan, K Sierzega, T Preden, A Alaraj, A Linninger, Annals of Biomedical Engineering, 44(12), 3478-3498, 2016.
Quantum dot conjugated magnetic nanoparticles for targeted drug delivery and imaging
I Venugopal, S Pernal, F Davalos, D Ashkenaz, A Linninger, Nano Biomedicine & Engineering 8(1), 24-38, 2016.
Simulation-free estimation of reaction propensities in cellular reactions and gene signaling networks
KM Yenkie, UM Diwekar , A Linninger, Computers & Chemical Engineering, 87, 154-163, 2016.
Prototype biosensor for detection of myelin basic protein biomarker in hydrocephalus diagnosis
I Venugopal, R Sirhan, S Basati, A Linninger, Sensor Letters 14 (1), 84-92, 2016.
Automatic recognition of subject-specific cerebrovascular trees
CY Hsu, B Schneller, A Alaraj A, M Flannery, XJ Zhou, A Linninger, Magnetic Resonance in Medicine, 77, 398–410 2016.
Cerebrospinal fluid mechanics and its coupling to cerebrovascular dynamics
A Linninger, K Tangen, C Hsu, D Frim, Annual Review of Fluid Mechanics, 48, 219-257, 2016.
Correlation between angiographic transit times and neurological status on admission in patients with aneurysmal subarachnoid hemorrhage
A Ivanov, A Linninger, C-Y Hsu, S Amin-Hanjani, V A. Aletich, F T. Charbel, and A Alaraj, Journal of Neurosurgery, 124, 1093-1099, 2016.
Dynamic regulation of aquaporin-4 water channels in neurological disorders
Y Hsu, M Tran, A Linninger, Croat Med Journal, 56(5), 401–421, 2015.
CNS wide simulation of flow resistance and drug transport due to spinal microanatomy
K Tangen, Y Hsu, D Zhu, A Linninger, Journal of Biomechanics, 48, 2144-2154, 2015. [Download Fourier Tables]
Intermedullary spinal cord tumors: a review of current and future treatment strategies
M Tobin, J Geraghty, H Engelhard, A Linninger, A Mehta, Journal of Neurosurgery, 39, 1-10, 2015./td>
Hematocrit distribution and tissue oxygenation in large microcirculatory networks
I Gould, A Linninger, Microcirculation, 22, 1-18, 2015.
Implant-assisted intrathecal magnetic drug targeting to aid in therapeutic nanoparticle localization for potential treatment of central nervous system disorders
E Lueshen, I Venugopal, T Soni, A Alaraj and A Linninger, Journal of Biomedical Nanotechnology, 11, 253-261, 2015.
Interpretation of cellular imaging and AQP4 quantification data in a single cell simulators
S Kim, Y Hsu and A Linninger, Processes, 2, 218-237, 2014.
A computational model of cerebrospinal fluid production and reabsorption driven by starling forces
J Buishas, I Gould and A Linninger, Croat Med Journal, 55(5), 481-497, 2014.
Impedance changes indicate proximal ventriculoperitoneal shunt obstruction in-vitro
S Basati, K Tangen, Y Hsu, H Lin, D Frim and A Linninger, IEEE Transactions on Biomedical Engineering, 62(12), 2787-2793, 2014.
Elected best paper of the year 2014 in Computers and Chemical Engineering.
A computer-aided framework for development, identification and management of physiologically-based pharmacokinetic models
M Heitzig, A Linninger, G Sina, R Gania, Computers & Chemical Engineering, 71, 677–698, 2014.
First principles pharmacokinetic modeling: a quantitative study on cyclosporin
A Mosat, E Lueshen, M Heitzig, C Hall, A Linninger, G. Sin, R. Gani, Computers & Chemical Engineering, 54, 97-110, 2013.
Cerebral microcirculation and oxygen tension in the human secondary cortex
A Linninger, I Gould, T Marinnan, C Hsu, M Chojecki, and A Alaraj, Annals of Biomedical Engineering, 41, 2264-2284, 2013.
Quantitative integration of biological, pharmacokinetic, and medical imaging data for organ-wide dose-response predictions
Y Hsu, A Linninger, IEEE Transaction on Biomedical Engineering, (60) 3, 625-632, 2013.
Intrathecal magnetic drug targeting using gold-coated magnetite nanoparticles in a human spine model
E Lueschen, I Venugopal, J Kanikunnel, T Soni, A Alaraj, and A Linninger, Nanomedicine, 9(8), 1155-1169, 2012.
Frequency and magnitude of cerebrospinal fluid pulsations influence intrathecal drug distribution: key factors for interpatient variability
Y Hsu, M H D M Hettiarachchi, D Zhu and A Linninger, Anesthesia & Analgesia, 115 (2) , 386-394, 2012.
Cerebrospinal fluid volume measurements in hydrocephalic rats
S Basati, B Desai, A Alaraj, F Charbel, and A Linninger, Journal of Neurosurgery, 10, 347-354, 2012.
Interspecies scaling in pharmacokinetics: a novel whole-body physiologically based modeling framework to discover drug biodistribution mechanisms in vivo
C Hall, A Mošat, E Lueshen, and A Linninger, Journal of Pharmaceutical Sciences, 101(3), 1221–1241, 2012.
Biomedical systems research - new perspectives opened by quantitative medical imaging
A Linninger, Position paper in Comp. Chem. Eng, 36, 1-9, 2012.
Exact solution of the diffusion-convection equation in cylindrical geometry
O Ivanchenko, O N Sindhwani, and A Linninger, AICHE J, 58(4), 1299-1302, 2012.
Integrated design and control under uncertainty: embedded control optimization for plantwide processes
J Moon, S Kim, and A Linninger, Comp. Chem. Eng, 35, 1718– 1724, 2011.
The effect of pulsatile flow on intrathecal drug delivery in the spinal canal
H D M Herriarachchi, Y Hsu, T Harris, and A Linninger, A. Biom. Eng., 39(10), 2592-2602, 2011.
Ventricular wall movements and cerebrospinal fluid flow in hydrocephalus
R D Penn, S Basati, B Sweetman, X Gou, A Linninger, J. Neurosurg., 115, 159-164, 2011.
Three-dimensional computational prediction of cerebrospinal fluid flow in the human brain
B Sweetman, M Xenos, L Zitella, A Linninger, Computer in Biology and Medicine, 41, 67-75, 2011.
Rigorous synthesis and simulation of complex distillation networks
G Ruiz, S Kim, L Moes, A Linninger, AIChE Journal, 57(1), 136-148, 2011.
Dynamic brain phantom for intracranial volume measurements
S Basati, T Harris, A Linninger, IEEE Transactions on Biomedical Engineering, 58(5), 1450-1455, 2011.
Methods for determining agent concentration profiles in agarose gel during convection-enhanced delivery
N Sindhwani, O Ivanchenko, E Lueshen, K Prem, A Linninger, IEEE Transactions on Biomedical Engineering, 58(3), 626-632, 2011.
Cerebrospinal fluid flow dynamics in the central nervous system
B Sweetman, and A Linninger, A. Biom. Eng., 39(1), 484-496, 2011.
Experimental techniques for studying poroelasticity in brain phantom gels under high flow microinfusion
O Ivanchenko, N Sindhwani, and A Linninger, J. of Biomechanical Eng., 132(5), 051008, 2010.
Pinch point calculation and its implication on robust distillation design
D Beneke, S Kim, and A Linninger, Chinese Journal of Chemical Engineering, 19(6), 911-925, 2011.
Graphical design and analysis of thermally coupled sidestream columns using column profile maps and temperature collocation
D Beneke and A LinningerAICHE J, 57(9), 2406-2420, 2011.
Rigorous separation design. 1. multicomponent mixtures, nonideal mixtures, and prefractionating column networks
S Kim, G Ruiz, and A Linninger, Industrial & Engineering Chemistry Reasearch, 49(14), 6499-6513, 2010.
Rigorous separation design. 2. network design solutions for mixtures with various volatility differences and feed compositions
S Kim and A Linninger, Industrial & Engineering Chemistry Reasearch, 49(18), 8670-8684, 2010. 
A mathematical model of blood, cerebrospinal fluid and brain dynamics
A Linninger, M Xenos, B Sweetman, S Ponkshe, X Guo, and R Penn. Journal of Mathematical Biology, 59(6), 729-759, 2009.
Normal and hydrocephalic brain dynamics; reduced cerebrospinal fluid reabsorption and ventricular enlargement
A Linninger, B Sweetman and R Penn, Annals of Biomedical Engineering.37(7), 1434-1447, 2009.
Design and optimization of energy efficient complex separation networks
G Ruiz, S Kim, J Moon, L Zhang, and A Linninger, Comp. Chem. Eng., 34(9), 1556-1563, 2010.
Industry-wide energy saving by complex separation networks
A Linninger, Comp. Chem. Eng., 33(12), 2018-2027, 2009.
The physics of hydrocephalus-a review
R Penn and A Linninger, Pediatric Neurosurgery, 45, 161-174, 2009.
An impedance sensor to monitor and control cerebral ventricular volume
A Linninger, S Basati and R Penn, Medical Engineering and Physics, 31(7), 838-45, 2009.
A hybrid sequential niche algorithm for optimal engineering design with solution multiplicity
J Moon and A Linninger, Computers and Chemical Engineering, 33(7), 1261-1271, 2009.
Computational methods for predicting drug transport in anisotropic and heterogeneous brain tissue
A Linninger, M Somayaji, X Guo, T Erickson, X Guo and R Penn, J of Biomechanics, 41, 2176-2187, 2008.
Assessing chronic liver toxicity based on relative gene expression data
K Kulkarni, P Larsen, and A Linninger, Journal of Theoretical Biology, 254, 308-318, 2008.
Rigorous mathematical modeling techniques for optimal delivery of macromolecules to the brain
A Linninger, M R Somayaji, L Zhang, M S Hariharan, and R. Penn, IEEE Transaction on Biomedical Engineering, 55 (9), 2303-2313, 2008.
Parallel hybrid algorithm for process flexibility analysis
J Moon, K Kulkarni, L Zhang, and A Linninger, Industrial and Engineering Chemistry Research, 47, 8324-8436, 2008.
Multi-scale modeling and solution multiplicity in catalytic pellet reactors
K Kulkarni, J Moon, L Zhang, A Lucia, and A Linninger,Industrial and Engineering Chemistry Research, 47(22), 8572-8581, 2008.
A barrier-terrain methodology for global optimization
A Lucia, R Gattupalli, K Kulkarni and A Linninger, Industrial and Engineering Chemistry Research, 47, 2666-2680, 2008.
Prediction of convection-enhanced drug delivery to the human brain
A Linninger, MR Somayaji, M Mekarski and L Zhang, Journal of Theoretical Biology, 250, 125-138,2008.
Elected best paper of the year 2008 in Computers and Chemical Engineering.
Systematic design of drug delivery therapies
M Somayaji, M Xenos, L Zhang, M Mekarski and A. Linninger, Computers and Chemical Engineering 32, 89–98, 2008.
Integrating systems design and control using dynamic flexibility analysis
A Malcolm, J Polan, L Zhang, B Oguannaike, A Linninger, AIChE Journal 53(8), 2048-2061, 2007.
Discovery of transport and reaction properties in distributed systems
L Zhang, K Kulkarni, MR Somayaji, M Xenos, A Linninger, AIChE Journal 53(2), 381-396, 2007.
Optimal regulation for sustainable drug manufacturing
A Malcolm, L Zhang and A Linninger, International J. of Environment and Pollution 29(1-3), 144-164, 2007.
Cerebrospinal fluid flow in the normal and hydrocephalic human brain
A Linninger, M Xenos, D Zhu, MR Somayaji and R Penn, IEEE Transactions on Biomedical Engineering 54(2), 291-302, 2006.
Distributed system design under uncertainty
L Zhang, C Xue, A Malcolm, K Kulkarni and A Linninger, Ind. Eng. Chem. Res., 45(25), 8252-8360, 2006.
Dynamics of lateral ventricle and cerebrospinal fluid in normal and hydrocephalic brains
D Zhu, M Xenos, A Linninger and R Penn, Journal of magnetic resonance imaging, 24, 756-770, 2006.
Model and parameter uncertainty in distributed systems
K Kulkarni, L Zhang and A Linninger, Ind. Eng. Chem. Res.,45(23), 7832-7840, 2006.
Design of environmental regulatory policies for sustainable emission reduction
A Malcolm, L Zhang and A Linninger, AIChE Journal, 52(8), 2792-2804, 2006.
Towards computer-aided separation synthesis
L Zhang and A Linninger, AIChE Journal, 52(4), 1392-1409, 2006.
Solving kinetic inversion problems via a physically bounded Gauss-Newton (PGN) method
W Tang, L Zhang, A Linninger, R Tranter and K Brezinsky, Ind. Eng. Chem. Res, 44(10), 3626-3637, 2005.
Pulsatile cerebrospinal fluid dynamics in the human brain
A Linninger, C Tsakiris, DC Zhu, M Xenos, P Roycewicz, Z Danziger and R.Penn, IEEE Transactions on Biomedical Engineering, 52(4), 557-565, 2005.
Pressure gradients in the brain: an experimental model of hydrocephalus
RD Penn, MC Lee, A Linninger, K Miesel, SN Lu and L Stylos, J. Neurosurgery, 1069-1075, 2005.
Data Repository for Papers Under Review
G Hartung, C Vesel, R Morley, A Alaraj, J Sled, D Kleinfeld, A Linninger