Research

The research rotation was an option before 2019 for residents who were interested in participating in the clinical research and development projects during the residency. Since 2019, the research rotation has been an integral part of the Yale Medical Physics Residency Training Program.

The goal of the research rotation is to help residents further developing their critical thinking and problem-solving skills. These skills are not only helpful for residents to become good clinical medical physicists but also essential for them to become future leaders in medical physics. The research rotation has the following characteristics:

• Research rotation is fully funded by the program
• Total duration is one year
• Timing for the research rotation is flexible and can be taken between any clinical rotations
• Research mentors are selected through discussion and mutual agreement
• Research projects are selected by the resident and mentors
• Peer-reviewed publication is highly encouraged but not required for graduation

(Names in bold are residents)

• PJ Jensen, Z Chen, “Comparison of PTV Contouring Methods for 3D Conformal Breast Cancer Treatment Planning”, AAPM Annual Meeting (2022).
• W Donahue, E Draeger, D Han, Z Chen, “Results of Using An Automated Tool for the Verification of TPS and OIS Database Consistency Following Treatment Plan Transfer”, AAPM Spring Clinical Meeting (2022).
• PJ Jensen, C Tien, Z Chen, “The Effect of Quantum Noise on Multilateration for HDR Source Position Localization”, Brachytherapy 21, S25–S26 (2022).
• C Tien, W Donahue, DM Giles, Z Chen, “The Impact of Sublethal Damage Repair on Biological Dose for a Stepping-Source Brachytherapy Delivery in a Single-Fraction Prostate Treatment” Brachytherapy 21, S32–S33 (2022).
• S Shrestha, W Newhauser, W Donahue, A Perez-Andujar, “Stray Neutron Radiation Exposures From Proton Therapy: Physics-Based Analytical Models of Neutron Spectral Fluence, Kerma and Absorbed Dose”, AAPM Annual Meeting (2022)
• E Draeger, Z Chen, R Decker, CJ Tien, “Utilizing Tumor Control Probability to Aid in Selection of Multi-Dwell or Single-Dwell Methodology for Leipzig-Style Applicators: A Preliminary Study”, Brachytherapy 20, S28–S29 (2021)
• W Donahue, E Draeger, D Han, Z Chen, “Automated Verification of Treatment Parameter Transfer Between TPS and OIS Databases Via Direct Value Comparison”, Med Phys. 48, e117-635 (2021)
• P. James Jensen, W Donahue, Z Chen, “An Improved Statistical Model for Gamma Index Pass Rates in Intensity Modulated Radiation Therapy Patient-Specific Quality Assurance”, Med Phys. 48, e117-635 (2021)
• P. James Jensen, AAPM SLAM competition at Chapter (CAMPS) and Annual Meeting, 2021
• W Donahue, AAPM SLAM competition at Chapter (CAMPS), 2021
• E Draeger, W Donahue, Z Chen, “On the Feasibility of Angle-Resolved Portal Dosimetry for Patient Specific Quality Assurance of VMAT Plans”, Med Phys. 47, e820 (2020)
• E Draeger, Z Chen, X Tang, “Validation of OSLD In-Vivo Dosimetry for Total Body Irradiation”, Med Phys. 47, e877 (2020)
• W Donahue, H Chen, M Lazea, Z Chen, B Wang, “Verification of MV Radiation Isocenter Using the CIRS ISO Phantom Model 23A”, Med Phys. 47, e878 (2020)
• H Chen, K Morley, R Rodriguez, E Draeger, M Shafiq ul Hassan, Z Chen, “A Small Footprint Couch-Top Support Device for Image-Guided Radiotherapy of Heavy Patients”, Med Phys. 47, e690 (2020)
• E Draeger, D Pinkham, Z Chen, C Tien, “Development of Multiple Dwell Techniques in Horizontally-Oriented Leipzig-Style Applicators for Surface Brachytherapy Guided by a Model-Based Dose Calculation Algorithm”, Med Phys. 47, e745 (2020)
• M Shafiq ul Hassan, H Chen, J Bond, D Allen, Z Chen, “Evaluation of a Commercial Tungsten Eye Shield for Orthovoltage Beams Using Gafchromic Film”, Med Phys. 47, e769 (2020)
• E. Draeger, D Carlson, et al., “Using electron paramagnetic resonance for in vivo biodosimetry in radiotherapy patients” Med Phys. 46 (2019)
• E. Draeger, AAPM SLAM competition at Chapter (CAMPS) and Annual Meetings, 2019
• M. Butkus, R. Stewart, D. Carlson, “Mechanisms of Particle Relative Biological Effectiveness (RBE) –Effects of DSB Clustering on the Nanometer Scale”, Particle Therapy Co-Operative Group (PTCOG) 58th Annual Meeting (2019)
• M Petrongolo, C Tien, Z Chen, “Dosimetric implications of air within channels of brachytherapy applicators”, Brachytherapy. 17, S127 (2018)
• C Tien, F Guo, M Petrongolo, JE Bond, Z Chen, “Achievable Image Quality Metrics From Initial Institutional Experience with Leksell Gamma Knife Icon”, Med Phys. 45, e547 (2018)
• M Butkus, R Stewart, Z Chen, D Carlson, “Double Strand Break (DSB) Complexity and Proximity Effects Within the Repair-Misrepair Fixation (RMF) Model for Improved Predictions of Cell Survival From Heavy Ions”, Med Phys. 45, e532 (2018)
• M. Scholz*, R. Stewart, R. Hawkins, T. Friedrich, D. Carlson, M. Butkus, “A Comparison of Biophysical Models Predicting the Relative Biological Effectiveness (RBE) for Treatment Planning in Ion Beam Therapy”, 25th International Conference on Application of Accelerators in Research and Industry (CAARI), August 2018.
• RD Stewart, DJ Carlson, M Butkus, R Hawkins, T Friedrich, M Scholz, “A comparison of mechanism inspired models for particle relative biological effectiveness (RBE)”, Med Phys. 45, (2018)
• M. Butkus, T. Palmer, “Multi-Ion Analysis of RBE using the Microdosimetic Kinetic Model”, Council on Ionizing Radiation Measurements and Standards (CIRMS) 25th Annual Meeting, March 2017.
• M. Petrongolo, T. Niu, and L. Zhu, “Improved single-scan dual-energy CT using primary modulation”, Med Phys. 44, (2017).
• C. J. Tien, M Butkus, J Stahl, J Qian, Z. Chen, S Damast, “Does variable 192Ir dose rate affect vaginal toxicity in high-dose-rate brachytherapy?”, Brachytherapy, 16, S76-77 (2017).
• H Chen, F Guo, D Carlson, J Deng, R Nath, Z Chen, “Commissioning and Potential Clinical Implementation and Advantages of a 2.5 MV Photon Beam for Selected Radiotherapy Cases”, Med Phys. 44, 3206 (2017)
• H Chen, J Kim, D Carlson, J Deng, R Nath, Z Chen, “A Simple Predictor for V105 in Breast Tangential Treatment Planning”, Med Phys. 44, 3000 (2017)
• M. Butkus. “How Yale Streamlines Daily Clinical Workflow with Delta4 Phantom+”. Presentation for Scandidos, December 7th and 8th, 2016. [Webinar]
• M Butkus, T Palmer, “Impact of Radial Fluctuations in RBE for Therapeutic Proton Beams”, Med Phys. 43, (2016)
• M Butkus, T Palmer, “Application of a Modified Microdosimetric‐Kinetic Model to Analyze Relative Biological Effectiveness of Ions Relevant to Light Ion Therapy Using the Particle Heavy Ion Transport System”, Med Phys. 43, (2016)
• M. Butkus. “Patient-Specific QA with Delta4 Phantom and Phantom+. Presentation for Scandidos”, ASTRO Annual Meeting, September 2016
• S Geneser, M. Butkus. “A Method for Evaluating the Direct Impact of Failed IMRT QAs on Patient Dose”, AAPM 58th Annual Meeting, July 2016
• H Chen, Z Chen, R Nath, F Guo, “Quality Assurance of 4DCT Process Using ET Gating Phantom System”, Med Phys. 42, 3302 (2015)
• W. Liu, C. MacDonald, H. Abbas, R. Nath, Z. Chen, “Nanoparticle Enhanced Focused Kv X-ray Radiation Therapy”, Int J Radiat Oncol Biol Phys. 93, S146-147 (2015)
• R Abolfath, F Guo, Z Chen, R Nath, “First principle calculation of quantum yield in photodynamic therapy”, Med Phys. 41, 266 (2014)
• H Abbas, R Abolfath, R Nath, Z Chen, “Dosimetric impact of patient positioning uncertainty in SBRT treatments”, Med Phys. 41, 346 (2014)
• H Abbas, D Carlson, J Deng, R Nath, and Z Chen, “On the use of onboard portal dosimetry for patient-specific QA of RadioArc plans”, Med Phys. 40, 297 (2013)
• R Abolfath, D Carlson, Z Chen, and R Nath, “Molecular dynamics simulation of DNA damage induction by ionizing radiation”, Med Phys. 40, 552 (2013)

(Names in bold are residents; *indicates publications by residents during the residency with projects originated outside the residency)

• Guan F, Chen H, Draeger E, Li Y, Aydin R, Tien C, Chen Z. “Characterization of GafchromicTM EBT4 film with clinical kV/MV photons and MeV electrons”. Precision Radiation Oncology 2023, 7: 84-91. DOI: 10.1002/pro6.1204.
• Guan F, Wang X, Yang M, Draeger E, Han D, Iga K, Guo F, Perles L, Li Y, Sahoo N, Mohan R, Chen Z. “Dosimetric response of Gafchromic™ EBT‐XD film to therapeutic protons”. Precision Radiation Oncology 2023, 7: 15-26. DOI: 10.1002/pro6.1187.
• WP Donahue, E Draeger, DY Han, Z Chen, “Frequency of errors in the transfer of treatment parameters from the treatment planning system to the oncology information system in a multi-vendor environment. J Appl Clin Med Phys. 2022;e13868. https://doi.org/10.1002/acm2.13868
• H Chen, K Morley, R Rodriguez, E Draeger, M Shafiq ul Hassan, Z Chen, “A Small Footprint Couch-Top Support Device for Image-Guided Radiotherapy of Heavy Patients”, J. Applied Clinical Med Phys. 2022;e13788. https://doi.org/10.1002/acm2.13788
• Jensen PJ, Torok JA, Goodwin CR, Floyd SR, Wu Q, Wu QJ, Kirkpatrick JP. “Purposeful irradiation of the epidural space to enhance local control without compromising cord sparing in spine radiosurgery.” J Radiosurg SBRT, 2022; 8:21-26. PMID: 35387408*
• Mairani A, Mein S, Blakely EA, Debus J, Durante M, Ferrari A, Fuchs H, Georg D, Grosshans DR, Guan F, Haberer T, Harrabi SB, Horst F, Inaniwa T, Karger CP, Mohan R, Paganetti H, Parodi K, Sala PR, Schuy C, Tessonnier T, Titt U, Weber U. Roadmap: helium ion therapy. Phys Med Biol 2022 PMID: 35395649*
• Yang M, Wang X, Guan F, Titt U, Iga K, Jiang D, Takaoka T, Totake S, Katayose T, Umezawa M, Schüler E, Frank SJ, Lin SH, Sahoo N, Koong AC, Mohan R, Zhu XR. Adaptation and dosimetric commissioning of a synchrotron-based proton beamline for FLASH experiments. Phys Med Biol 2022 PMID: 35853442*
• Wang Q, Titt U, Mohan R, Guan F, Zhao Y, Yang M, Yepes P. Optimization of FLASH Proton Beams Using a Track-Repeating Algorithm. Med Phys 2022 PMID: 35900902*
• McNerlin C, Guan F, Bronk L, Lei K, Grosshans D, Young DW, Gaber MW, Maletic-Savatic M. Targeting hippocampal neurogenesis to protect astronauts’ cognition and mood from decline due to space radiation effects. Life Sciences in Space Research. 2022 Jul 29.*
• Shrestha S, Newhauser WD, Donahue WP, Pérez-Andújar A. “Stray neutron radiation exposures from proton therapy: physics-based analytical models of neutron spectral fluence, kerma and absorbed dose.” Phys Med Biol. 2022 Jun 15;67(12). doi: 10.1088/1361-6560/ac7377. PMID: 35613603*
• E Draeger, DW Pinkham, Z Chen, CJ Tien. “A set of directly implementable template plans for users of multiple-dwell methodology in 192Ir brachytherapy using Leipzig-style applicators.” Brachytherapy. 2021 20(2):401-409.
• Jensen PJ, Zhang J, Koontz BF, Wu QJ. “A Novel Machine Learning Model for Dose Prediction in Prostate Volumetric Modulated Arc Therapy Using Output Initialization and Optimization Priorities.” Front Artif Intell. 2021 4:624038. doi: 10.3389/frai.2021.624038. PMID: 33969289*
• Halloran A, Newhauser W, Chu C, Donahue W. “Personalized 3D-printed anthropomorphic phantoms for dosimetry in charged particle fields.” Phys Med Biol. 2021 Nov 18;66(22). doi: 10.1088/1361-6560/ac3047. PMID: 34654002*
• Donahue WP, Newhauser WD. “Computational feasibility of simulating whole-organ vascular networks.” Biomed Phys Eng Express. 2020 Oct 21;6(5):055028. doi: 10.1088/2057-1976/abaf5b. PMID: 33444259*
• Donahue WP, Newhauser WD, Li X, Chen F, Dey J. “Computational feasibility of simulating changes in blood flow through whole-organ vascular networks from radiation injury.” Biomed Phys Eng Express. 2020 Oct 21;6(5):055027. doi: 10.1088/2057-1976/abaf5c. PMID: 33444258*
• Donahue WP, Newhauser WD, Wong H, Moreno J, Dey J, Wilson VL. “Computational feasibility of calculating the steady-state blood flow rate through the vasculature of the entire human body.” Biomed Phys Eng Express. 2020 Sep 8;6(5):055026. doi: 10.1088/2057-1976/abaf5d. PMID: 33444257*
• Paul R, Shafiq-Ul Hassan M, Moros EG, Gillies RJ, Hall LO, Goldgof DB. “Deep Feature Stability Analysis Using CT Images of a Physical Phantom Across Scanner Manufacturers, Cartridges, Pixel Sizes, and Slice Thickness.” Tomography. 2020 Jun;6(2):250-260. doi: 10.18383/j.tom.2020.00003. PMID: 32548303*
• R. Stewart, D. Carlson, M. Butkus, R. Hawkins, T. Friedrich, M. Scholz. “A Comparison of Mechanism-Inspired Models for Particle Relative Biological Effectiveness (RBE)”, Med. Phys. 45 (11), 2018.
• H. Abbas, B. Chang, Z. Chen, “Motion management in gastrointestinal cancers”, J. Gastrointest Oncol, 2014, 5, 223-235.
• R. Abolfath, D Carlson, Z. Chen, R. Nath, “A molecular dynamics simulation of DNA damage induction by ionizing radiation”, Phys Med Biol, 2013, 58 7143-7157.
• E Draeger, A Sawant, C Johnstone, B Koger, S Becker, Z Vujaskovic, IL Jackson, Y Poirier, “A Dose of Reality: How 20 years of inconsistent physics and dosimetry reporting in radiobiology studies may have contributed to the reproducibility crisis”, Int J Radiat Oncol Biol Phys 2020, 106(2):243-252.*
• Y Poirier, S Becker, C Decesaris, W Culberson, E Draeger, et al.,“The Impact of Radiation Energy on Dose Homogeneity and Organ Dose in the Gottingen Minipig Total-Body Irradiation Model”, Rad Res 2020, 194(5):544-556*
• Y Poirier, C Prado, K Prado, E Draeger, IL Jackson, Z Vujaskovic, “Use of CT simulation and 3-D radiation therapy treatment planning system to develop and validate a total-body irradiation technique for the New Zealand White rabbit”, Int J Radiat Biol 2020, DOI: https://doi.org/10.1080/09553002.2019.1665215.*
• M Petrongolo, L Zhu, “Single-Scan Dual-Energy CT Using Primary Modulation. IEEE Trans Med Imaging”, 2018 Aug; 37(8):1799-1808. PMID: 29994601.*
• J Harms, T Wang, M Petrongolo, T Niu, L Zhu, “Noise suppression for dual-energy CT via penalized weighted least-square optimization with similarity-based regularization”, Med Phys. 2016 May; 43(5):2676.*

Faculty research and selected publications can be found from the department website under the “Research & Publications” tab of each program faculty member's profile.