Biomedical & Healthcare Engineering

Operations Research for Disease Prediction, Prevention, and Control

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Associated Faculty

Chaitra Gopalappa

Engineering Thematic Area:

Laboratory for Multiscale Bioengineering and Mechanobiology

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Our research applies and integrates fundamental engineering principles, such as manufacturing, biomechanics, materials science, and micro/nanoengineering, to understand and harness the mechanobiology of stem cells for modeling currently incurable human diseases and for applications in regenerative medicine. Current research interests include:

Stem cell bioengineering
System mechanobiology
Microengineering
Active biomaterials
Lab-on-chip
Tissue biomechanics

Engineering Thematic Area:

Biomedical & Healthcare Engineering

Biofluids & Vascular Biology Laboratory

Engineering Thematic Area:

Biomedical & Healthcare Engineering

Yubing Sun

Assistant Professor

317 Engineering Laboratory

University of Massachusetts
160 Governors Drive
Amherst, MA 01003-2210

ybsun@umass.edu

(413) 545-4543

(413) 545-1027

Laboratory for Multiscale Bioengineering and Mechanobiology

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Education

B.S., University of Science and Technology of China, 2010
Ph.D., University of Michigan, Ann Arbor, 2015

Research

Stem cell bioengineering
System mechanobiology
Microengineering
Active biomaterials
Lab-on-chip
Tissue biomechanics

Program Area:

Mechanical Engineering

Research Area:

Publications

Koh Meng Aw Yong, Yubing Sun, Sofia D. Merajver, and Jianping Fu. Mechanotransduction-induced reversible phenotypic switching in prostate cancer cells. Biophysical Journal, vol.112, pp. 1236-1245, 2017.
Xin Cui, Weijin Guo, Yubing Sun, Baoce Sun, Shuhuan Hu, Dong Sun, Raymond HW Lam. A microfluidic device for isolation and characterization of transendothelial migrating cancer cells. Biomicrofluidics, vol. 11, 014105, 2017.
Tianfa Xie, Jamar Hawkins, Yubing Sun. Traction force measurement using deformable microposts. Methods in Molecular Biology, invited contribution, in press, 2017.
Di Chen*, Yubing Sun*, Cheri X. Deng, and Jianping Fu. Improving survival of disassociated human embryonic stem cells by mechanical stimulation using acoustic tweezing cytometry. Biophysical Journal (Biophysical Letter), vol. 108, pp. 1315-1317, 2015.
Yubing Sun, Koh Meng Aw Yong, Luis G. Villa-Diaz, Xiaoli Zhang, Weiqiang Chen, Renee Philson, Shinuo Weng, Haoxing Xu, Paul H. Krebsbach and Jianping Fu. Hippo/YAP-mediated rigidity-dependent motor neuron differentiation of human pluripotent stem cells. Nature Materials, vol. 13, pp. 599-604, 2014.
Zhenzhen Fan*, Yubing Sun*, Di Chen*, Weiqiang Chen, Cheri Deng, and Jianping Fu. Acoustic tweezing cytometry for live-cell subcellular control of intracellular cytoskeleton contractility. Scientific Reports, vol. 3, 2176, 2013.
Yubing Sun, Christopher S. Chen, and Jianping Fu. Forcing stem cells to behave: A biophysical perspective of cellular microenvironment. Annual Review of Biophysics, vol. 41, pp. 519-542, 2012.
Yubing Sun, Luis G. Villa-Diaz, Raymond Hiu-Wai Lam, Weiqiang Chen, Paul H. Krebsbach, and Jianping Fu. Matrix mechanics regulates fate decisions of human embryonic stem cells. PLoS ONE, vol. 7, e37178, 2012.
Weiqiang Chen, Luis G. Villa-Diaz, Yubing Sun, Shinuo Weng, Raymond Hiu-Wai Lam, Paul H. Krebsbach, and Jianping Fu. Nanotopography influences adhesion, spreading, and self-renewal of human embryonic stem cells. ACS Nano, vol. 6, pp. 4094-4103, 2012.
Raymond Hiu-Wai Lam, Yubing Sun, Weiqiang Chen, and Jianping Fu. Elastomeric microposts integrated into microfluidics for flow-mediated endothelial mechanotransduction analysis. Lab on a Chip, vol. 12, pp. 1865-1873, 2012.

Juan Jiménez

Assistant Professor

111 Engineering Lab I

160 Governors Drive
University of Massachusetts
Amherst, MA 01003-2210

email: juanjimenez at umass.edu

Jiménez Research Group

UMass IALS

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Education

BS, Michigan State University, 1999
MS, Princeton University, 2002
PhD, Princeton University, 2007
Postdoctoral Fellowship, University of Pennsylvania, 2011

Research

Biomedical Engineering
Biofluids
Fluid Dynamics
Cardiovascular Engineering
Medical Devices
Vascular Biology
Cell Motility & Dynamics

Program Area:

Mechanical Engineering

Research Area:

Publications

Davies PF, Manduchi E, Jiménez JM, Jiang YZ 2017. Biofluids, cell mechanics and epigenetics: Flow-induced epigenetic mechanisms of endothelial gene expression. Journal of Biomechanics 50, 3-10
Sweet DT, Jiménez JM, Chang J, Hess PR, Mericko-Ishizuka P, et al. 2015. Lymph flow regulates collecting lymphatic vessel maturation in vivo. J Clin Invest
Jiang YZ, Manduchi E, Jiménez JM, Davies PF. 2015. Endothelial epigenetics in biomechanical stress: Disturbed flow-mediated epigenomic plasticity in vivo and in vitro. Arteriosclerosis, Thrombosis, and Vascular Biology
Jiménez JM, Prasad V, Yu MD, Kampmeyer CP, Kaakour AH, et al. 2014. Macro- and microscale variables regulate stent haemodynamics, fibrin deposition and thrombomodulin expression. J R Soc Interface 11:20131079
Jiang YZ, Jiménez JM, Ou K, McCormick ME, Zhang LD, Davies PF. 2014. Hemodynamic disturbed flow induces differential DNA methylation of endothelial kruppel-like factor 4 promoter in vitro and in vivo. Circ Res 115:32-43
Davies PF, Manduchi E, Stoeckert CJ, Jiménez JM, Jiang YZ. 2014. Emerging topic: flow-related epigenetic regulation of endothelial phenotype through DNA methylation. Vascul Pharmacol 62:88-93
Jiménez JM, Smits AJ. 2011. Tip and Junction Vortices Generated by the Sail of a Yawed Submarine Model at Low Reynolds Numbers. Journal of Fluids Engineering-Transactions of the Asme 133:-
Jiménez JM, Reynolds RT, Smits AJ. 2010. The Effects of Fins on the Intermediate Wake of a Submarine Model. Journal of Fluids Engineering-Transactions of the ASME 132
Jiménez JM, Hultmark M, Smits AJ. 2010. The intermediate wake of a body of revolution at high Reynolds numbers. J Fluid Mech 659:516-39
Jiménez JM, Davies PF. 2009. Hemodynamically driven stent strut design. Ann Biomed Eng 37:1483-94

Honors

2016 BMES Innovation and Career Development Award
2013 Poster Presentation Prize - 42nd Annual Philadelphia Workshop on Hemostasis, Thrombosis and Atherosclerosis
2011 - 2016 Mentored Quantitative Research Development Award - NIH
2007-2010 Ruth L. Kirschstein Institutional National Research Service Award – NIH

Lynch Research Group

The Lynch Lab

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Lynch Research Group

Associated Faculty

Maureen Lynch, Assistant Professor

Engineering Thematic Area:

Biomedical & Healthcare Engineering

Maureen Lynch

Assistant Professor

LSL N575

LSL N575
University of Massachusetts
160 Governors Drive
Amherst, MA 01003-2210

maureenlynch@umass.edu

413-545-6689

413-545-1027

Lynch Research Group

Institute for Applied Life Sciences

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Education

B.S., Clemson University, Mechanical Engineering, 2005
M.S./Ph.D., Cornell University, Mechanical Engineering, 2010
Postdoctoral Fellow, Cornell University, Biomedical Engineering

Research

The current standard of care for bone metastasis is therapies targeting the cells that degrade bone. These cells are directed by cancer cells to degrade bone in order to release pro-tumorigenic growth factors stored within the skeletal extracellular matrix. These therapies are not curative and do not halt metastasis-mediated bone degradation, indicating additional factors contribute to bone degradation. My research program focuses on the skeletal mechanical environment and its regulation of cancer. Specifically, I will investigate 1) the skeleton’s mechanical environment and its regulation of the remodeling process, and 2) the role of osteoblastic cells, which comprise the principal sensor and effector cells of mechanical cues, in metastatic processes. My long-term goal is to identify novel therapeutic targets for treating and preventing bone metastases as well as cancer-associated reductions in bone strength. My experimental approach uses novel in vivo and in vitro mechanical loading model systems to correlate cellular function with cancer pathogenesis, tissue-level changes in tumor burden, and skeletal tissue strength.

Program Area:

Mechanical Engineering

Research Area:

Publications

Lynch ME and Fischbach C. “Biomechanical forces in the skeleton and their relevance to bone metastasis: biology and engineering considerations.” Advanced Drug Delivery Reviews, 79-80: 119-34, 2014. doi: 10.1016/j.addr.2014.08.009.
Main RP, Lynch ME, van der Meulen MCH. “Load-induced changes in bone stiffness and cancellous and cortical bone mass following tibial compression diminish with age in female mice.” The Journal of Experimental Biology, 217: 1775-83, 2014. doi: 10.1242/jeb.085522.
Lynch ME, Brooks DJ, Mohanan S, Lee MJ, Polamraju P, Dent KC, Bonassar L, van der Meulen MCH, Fischbach C. “In Vivo Tibial Compression Decreases Osteolysis and Tumor Formation in a Human Breast Cancer Metastasis Model.” Journal of Bone and Mineral Research, 28: 2357-2367, 2013. doi: 10.1002/jbmr.1966.
Infanger DW, Lynch ME, Fischbach C. “Engineered Culture Models for Studies of Tumor-Microenvironment Interactions.” Annual Review of Biomedical Engineering, 15: 29-53, 2013. doi: 10.1146/annurev-bioeng-071811-150028.
Lynch ME, Main RP, Xu Q, Schmicker TL, Schaffler MB, Wright TM, van der Meulen MCH. “Tibial Compression increases Cortical and Cancellous Bone Mass in Adult Female Mice.” Bone, 49: 439-46, 2010. doi: 10.1016/j.bone.2011.05.017.
Lynch ME, Main RP, Walsh DJ, Xu Q, Schaffler MB, Wright TM, van der Meulen MCH. “Cancellous bone adaptation to tibial compression is not sex-dependent in growing mice.” Journal of Applied Physiology, 109:685-691, 2010. doi: 10.1152/japplphysiol.00210.2010.
Main RP, Lynch ME, van der Meulen MCH. “In vivo tibial stiffness is maintained by whole bone morphology and cross-sectional geometry in growing female mice.” Journal of Biomechanics, 43:2689-2694, 2010. doi: 10.1016/j.jbiomech.2010.06.019.

Links

Lab Affiliation:

Lynch Research Group

Institute for Applied Life Sciences

Chaitra Gopalappa

Assistant Professor

120D Marston Hall

160 Governors Drive

University of Massachusetts

Amherst, MA 01003-2210

chaitrag@umass.edu

(413) 545-2306

(413) 545-1027

Academic Website

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Education

B.E. in Industrial Engineering, Bangalore Institute of Technology, 2002

Masters in Industrial Engineering, University of South Florida, 2006

Ph.D. in Industrial Engineering, University of South Florida, 2010

Research

Systems simulation modeling, applied probability modeling, and economic analysis in public health, such as: projecting future cases of HIV and other STIs and analyzing impact and cost-effectiveness of national intervention strategies; and estimating transition parameters for modeling natural history of cancer and projecting disease burden.

Program Area:

Industrial Engineering

Research Area:

Publications

Stover, J., Gopalappa, C., Mahy, M., Doherty, M.C., Easterbrook, P.J., Weiler, G., and Ghys, P.D., The impact and cost of the 2013 WHO recommendations on eligibility for antiretroviral therapy, AIDS, 28 Suppl. 2:S225-30, 2014
Gopalappa, C., Stover, J., Shaffer, N., and Mahy, M., The Costs and Benefits of Option B+ for the Prevention of Mother-to-Child Transmission of HIV, AIDS, 28 Suppl. 1:S5-14, 2014
Gopalappa, C., Huang, Y., Melanie, T., Kwame, O., and Gift, T., Cost-effectiveness of screening and treating men for chlamydia and gonorrhea in Maricopa correctional facilities to prevent possible pelvic inflammatory disease in women from transmissions, STD, 40 (10):776-783, 2013
Farnham, P., Gopalappa, C., Sansom, S., Costs and effectiveness of early versus late treatment in view of recent guidelines for starting treatment at an earlier HIV stage, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, JAIDS, 64(2):183-189, 2013.
Farnham, P.G., Holtgrave, D. R., Gopalappa, C., Angela B. Hutchinson, Stephanie L. Sansom, Lifetime Costs and QALYs Saved from HIV Prevention in the Test and Treat Era, Letter to the Editor, JAIDS, 64(2):e15-e18, 2013
Gopalappa, C., Farnham, P., Hutchinson, A., and Sansom, S., Cost-effectiveness of the National HIV/AIDS Strategy (NHAS) goal of increasing the proportion linking to care at diagnosis, JAIDS, 61 (1):99-105, 2012.
Gopalappa, C., Cremaschi, S., Das, T., Orcun, S., Applied Probability Models for Estimating Progression Rates between Colorectal Cancer Stages, Health Care Management Science 14(1), March 2011: Pg 1-21
Gopalappa, C., Das, T., Enkemann, S., and Eschrich, S., Removal of Hybridization and Scanning Noise from Microarrays, IEEE Transactions on Nanobioscience, 8(3), 2009

Honors

Registration:

Steven M. Teutsch Prevention Effectiveness Post-doctoral Fellowship, Centers for Disease Control and Prevention, 2010- 12
Pritsker Doctoral Dissertation Award, Institute of Industrial Engineers, 3rd Place, 2011

Links

Homepage:

Academic Website

Frank Sup

Associate Professor

Marston 120E

120 E Marston Hall
University of Massachusetts
160 Governor's Drive
Amherst, MA 01003-2210

sup@ecs.umass.edu

(413) 545-2946

(413) 545-1027

Mechatronics and Robotics Research Laboratory

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Education

B.S., University of Illinois, Urbana-Champaign, 2001
M.S., Vanderbilt University, 2006
Ph.D., Vanderbilt University, 2009

Research

Design, modeling and control of electromechanical systems with a focus on rehabilitation engineering.

Program Area:

Mechanical Engineering

Research Area:

Publications

Please see my Google Scholar page

Honors

2009 IEEE International Conference on Rehabilitation Robotics Best Paper Award
2014 Paul Winske Access Award - Stavros Center for Independent Living for exceptional service to persons with disabilities

Blair Perot

Professor

Marston 210A

210A Marston Hall
University of Massachusetts
160 Governors Drive
Amherst, MA 01003-2210

perot@ecs.umass.edu

(413) 545-3925

(413) 545-1027

Research Laboratory

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Education

B.S.E., Princeton University, 1987;
M.S., Stanford University, 1989;
Ph.D., Stanford University, 1994

Research

Turbulence Modeling; Computational Fluid Dynamics; Numerical Methods; Supercomputers & Parallel Computation; Droplets, Hydrophobic Surfaces, and Micro Flows

Program Area:

Mechanical Engineering

Research Area:

Publications

Y. Song and J. B. Perot, CFD Simulation of the NREL Phase VI Rotor , Wind Engineering, 39 (3), 299–310, 2015. doi: 10.1260/0309-524X.39.3.299
T. P. Eiting, J. B. Perot, E. R. Dumont, How much does nasal cavity morphology matter? Patters and rates of olfactory airflow in phyllostomid bats, Proceedings of the Royal Society B – Biological Sciences, 7:282 (1800) :20142161, 2015. doi: 10.1098/rspb.2014.2161.
B. Koren, R. Abgrall, P. Bochev, J. Frank and J. B. Perot Physics-compatible Numerical Methods, Journal of Computational Physics, 257 B, 1039-1526, 2014, doi: 10.1016/j.jcp.2013.10.015
C. J. Zusi and J. B. Perot, Simulation and Modeling of Turbulence Subjected to a Periods of Axisymmetric Contraction or Expansion, Physics of Fluids, 26, 115103, 2014; http://dx.doi.org/10.1063/1.4901188
T.P. Eiting, T. D. Smith, J. B. Perot and E. R. Dumont, The Role of the Olfactory Recess in Olfactory Airflow, Journal of Experimental Biology, 217 (10), 1799-1803, 2014, doi:10.1242/jeb.097402
J. B. Perot and C. J. Zusi, Differential Forms for Scientists/Engineers, Journal of Computational Physics, 257B, 1373–1393, 2014. DOI: 10.1016/j.jcp.2013.08.007
C. J. Zusi and J. B. Perot, Simulation and Modeling of Turbulence Subjected to a Period of Uniform Plane Strain, Physics of Fluids, 25, 110819, 2013, DOI: 10.1063/1.4821450
S.V. Kathuria, A. Chan, R. Graceffa, R. Nobrega, C. R.Matthews, T. C. Irving, J. B. Perot, O. Bilsel, Advances in turbulent mixing techniques to study microsecond protein folding reactions. Biopolymers, 99 (11), 888-896, 2013. DOI: 10.1002/bip.22355
A. Khajeh-Saeed, and J. B. Perot, Direct Numerical Simulation of Turbulence Using GPU Accelerated Supercomputers, Journal of Computational Physics, 235, 241-257, 2013.
M. B. Martell and J. B. Perot, The Oriented-Eddy Collision Model, Flow Turbulence and Combustion, 89 (3), 335-359, 2012.
A. Khajeh-Saeed, and J. B. Perot, Computational Fluid Dynamics Simulations using Many Graphics Processors, Computing in Science and Engineering, 14 (3), 10-19, 2012.
J. B. Perot, Determination of the Decay Exponent in Mechanically Stirred Isotropic Turbulence, Advances in Physics, 1, 022104, 2011.
J. B. Perot, Discrete Conservation Properties of Unstructured Mesh Schemes, Annual Reviews of Fluid Mechanics, 43, 299–318, 2011.
A. Khajeh-Saeed and J. B. Perot, Chapter 13: GPU-Supercomputer Acceleration of Pattern Matching, GPU Computing Gems, Emerald Edition, Wen-mei Hwu editor, Elsevier Inc, pp 185-198, 2011.

Honors

N.W.O.Visiting Professor, Delft University of Technology, 2010-2011
Professor of the Year, ASME Student Society, 2008, 2010.
J.M. Burgers Visiting Professor, Delft University of Technology, Netherlands, 2003-2004
Lilly Fellowship, Center for Teaching, 2002-2003.
Joseph Goldstein Award for Outstanding Junior Faculty, University of Massachusetts, 2002.
College Outstanding Teacher Award, University of Massachusetts, 2002.
STEMTEC Fellow, Five Colleges, 2002.
College Outstanding Advisor Award, University of Massachusetts, 2000.
Terman Graduate Fellowship, Stanford University, 1988-1989.
Summa Cum Laude (Highest Honors), Princeton University, 1987.
Phi Beta Kappa, National Honor Society, Princeton University, 1987.
Tau Beta Pi, Engineering Honor Society, Princeton University, 1986.

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