Biomedical physics program launches

A new PhD program, hosted by the departments of radiology and radiation oncology, trains students in technologies used for therapy and diagnostics.

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Lewei Zhao

Affiliate, Department Funds Fellow in Graduate Medical Education

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Dr.Lewei Zhao is medical physics resident in Department of Radiation Oncology, Stanford University. He graduated from Wuhan University, China, 2014 with a BS in Pure Mathematics. He got his PhD from Wayne State University, 2019 in Computational Mathematics. He was a postdoc in Beaumont Proton Therapy Center, Michigan from 2019 to 2023. During his postdoc, he took a medical physics certificate program from Wayne State University 2021-2022. His research interest is mathematical application s in medical physics.

Clinical Focus

  • radiation therapy
  • Mathematical Computing
  • Mathematical Model

Professional Education

  • BS, School of Mathematics and Statistics, Wuhan University, Pure Mathematics (2014)
  • PhD, Department of Mathematics, Wayne State University, Applied and Computational Mathematics (2019)
  • CAMPEP Certificate, Department of Radiation Oncology, Wayne State University, Medical Physics (2022)

Research Interests

  • Data Sciences

Current Research and Scholarly Interests

Mathematical applications in medical physics

All Publications

Spot-scanning Proton Arc (SPArc) has been of significant interest in recent years because of its superior plan quality. Currently, the primary focus of research and development is on deliverability and treatment efficiency.To address the challenges in generating a deliverable and efficient SPArc plan for a proton therapy system with a massive gantry, we developed a novel SPArc optimization algorithm (SPArcDMPO ) by directly incorporating the machine-specific parameters such as gantry mechanical constraints and proton delivery sequence.SPArc delivery sequence model (DSMarc ) was built based on the machine-specific parameters of the prototype arc delivery system, IBA ProteusONE®, including mechanical constraint (maximum gantry speed, acceleration, and deceleration) and proton delivery sequence (energy and spot delivery sequence, and irradiation time). SPArcDMPO resamples and adjusts each control point's delivery speed based on the DSMarc calculation through the iterative approach. In SPArcDMPO, users could set a reasonable arc delivery time during the plan optimization, which aims to minimize the gantry momentum changes and improve the delivery efficiency. Ten cases were selected to test SPArcDMPO . Two kinds of SPArc plans were generated using the same planning objective functions: (1) original SPArc plan (SPArcoriginal ); (2) SPArcDMPO plan with a user-pre-defined delivery time. Additionally, arc delivery sequence was simulated based on the DSMarc and was compared. Treatment delivery time was compared between SPArcoriginal and SPArcDMPO . Dynamic arc delivery time, the static irradiation time, and its corresponding time differential (time differential = dynamic arc delivery time-static irradiation time) were analyzed, respectively. The total gantry velocity change was accumulated throughout the treatment delivery.With a similar plan quality, objective value, number of energy layers, and spots, both SPArcoriginal and SPArcDMPO plans could be delivered continuously within the ± 1 degree tolerance window. However, compared to the SPArcoriginal , the strategy of SPArcDMPO is able to reduce the time differential from 30.55 ± 11.42%(90 ± 32 s) to 14.67 ± 6.97%(42 ± 20 s), p < 0.01. Furthermore, the corresponding total variations of gantry velocity during dynamic arc delivery are mitigated (SPArcoriginal vs. SPArcDMPO ) from 14.73 ± 9.14 degree/s to 4.28 ± 2.42 degree/s, p < 0.01. Consequently, the SPArcDMPO plans could minimize the gantry momentum change based on the clinical user's input compared to the SPArcoriginal plans, which could help relieve the mechanical challenge of accelerating or decelerating the massive proton gantry.For the first time, clinical users not only could generate a SPArc plan meeting the mechanical constraint of their proton system but also directly control the arc treatment speed and momentum changes of the gantry during the plan optimization process. This work paved the way for the routine clinical implementation of proton arc therapy in the treatment planning system.

View details for DOI 10.1002/mp.16985

View details for PubMedID 38340368

Spot-scanning proton arc (SPArc) has been drawing significant interests in recent years because of its capability of continuous proton irradiation during the gantry rotation. Previous studies demonstrated SPArc plans were delivered on a prototype of the DynamicARC solution, IBA ProteusONE.We built a novel delivery sequence model through an independent experimental approach: the first SPArc delivery sequence model (DSMSPArc ). Based on the model, we investigated SPArc treatment efficiency improvement in the routine proton clinical operation.SPArc test plans were generated and delivered on a prototype of the DynamicARC solution, IBA ProteusONE. An independent gantry inclinometer and the machine logfiles were used to derive the DSMSPArc. Seventeen SPArc plans were used to validate the model's accuracy independently. Two random clinical operation dates (6th January and 22nd March, 2021) from a single-room proton therapy center (PTC) were selected to quantitatively assess the improvement of treatment efficiency compared to the IMPT.The difference between the logfile and DSMSPArc is about 3.2 ± 4.8%. SPArc reduced 58.1% of the average treatment delivery time per patient compared to IMPT (p < 0.01). Daily treatment throughput could be increased by 30% using SPArc using a single-room proton therapy system.The first model of dynamic arc therapy is established in this study through an independent experimental approach using logfiles and measurements which allows clinical users and investigators to simulate the dynamic treatment delivery and assess the daily treatment throughput improvement.

View details for DOI 10.1002/mp.16879

View details for PubMedID 38064634

Objective. To investigate the impact of various delivery tolerance window settings on the treatment delivery time and dosimetric accuracy of spot-scanning proton arc (SPArc) therapy.Approach. SPArc plans were generated for three representative disease sites (brain, lung, and liver cancer) with an angle sampling frequency of 2.5°. An in-house dynamic arc controller was used to simulate the arc treatment delivery with various tolerance windows (±0.25, ±0.5, ±1, and ±1.25°). The controller generates virtual logfiles during the arc delivery simulation, such as gantry speed, acceleration and deceleration, spot position, and delivery sequence, similar to machine logfiles. The virtual logfile was then imported to the treatment planning system to reconstruct the delivered dose distribution and compare it to the initial SPArc nominal plan. A three-dimensional gamma index was used to quantitatively assess delivery accuracy. Total treatment delivery time and relative lost time (dynamic arc delivery time-fix beam delivery time)/fix beam delivery time) were reported.Main Results. The 3D gamma passing rate (GPR) was greater than 99% for all cases when using 3%/3 mm and 2%/2 mm criteria and the GPR (1%/1 mm criteria) degraded as the tolerance window opens. The total delivery time for dynamic arc delivery increased with the decreasing delivery tolerance window length. The average delivery time and the relative lost time (%) were 630 ± 212 s (253% ± 68%), 322 ± 101 s (81% ± 31%), 225 ± 60 s (27% ± 16%), 196 ± 41 s (11% ± 6%), 187 ± 29 s (6% ± 1%) for tolerance windows ±0.25, ±0.5, ±1, and ±1.25° respectively.Significance. The study quantitatively analyzed the dynamic SPArc delivery time and accuracy with different delivery tolerance window settings, which offer a critical reference in the future SPArc plan optimization and delivery controller design.

View details for DOI 10.1088/1361-6560/acfec5

View details for PubMedID 37774715

Objective. Proton dosimetric uncertainties resulting from the patient's daily setup errors in rotational directions exist even with advanced image-guided radiotherapy techniques. Thus, we developed a new rotational robust optimization SPArc algorithm (SPArcrot) to mitigate the dosimetric impact of the rotational setup error in Raystation ver. 6.02 (RaySearch Laboratory AB, Stockholm, Sweden).Approach.The initial planning CT was rotated ±5° simulating the worst-case setup error in the roll direction. The SPArcrotuses a multi-CT robust optimization framework by taking into account of such rotational setup errors. Five cases representing different disease sites were evaluated. Both SPArcoriginaland SPArcrotplans were generated using the same translational robust optimized parameters. To quantitatively investigate the mitigation effect from the rotational setup errors, all plans were recalculated using a series of pseudo-CT with rotational setup error (±1°/±2°/±3°/±5°). Dosimetric metrics such as D98% of CTV, and 3D gamma analysis were used to assess the dose distribution changes in the target and OARs.Main results.The magnitudes of dosimetric changes in the targets due to rotational setup error were significantly reduced by the SPArcrotcompared to SPArc in all cases. The uncertainties of the max dose to the OARs, such as brainstem, spinal cord and esophagus were significantly reduced using SPArcrot. The uncertainties of the mean dose to the OARs such as liver and oral cavity, parotid were comparable between the two planning techniques. The gamma passing rate (3%/3 mm) was significantly improved for CTV of all tumor sites through SPArcrot.Significance.Rotational setup error is one of the major issues which could lead to significant dose perturbations. SPArcrotplanning approach can consider such rotational error from patient setup or gantry rotation error by effectively mitigating the dose uncertainties to the target and in the adjunct series OARs.

View details for DOI 10.1088/1361-6560/aca874

View details for Web of Science ID 000902410500001

View details for PubMedID 36546347

Objective. Proton arc therapy (PAT) is a new delivery technique that exploits the continuous rotation of the gantry to distribute the therapeutic dose over many angular windows instead of using a few static fields, as in conventional (intensity-modulated) proton therapy. Although coming along with many potential clinical and dosimetric benefits, PAT has also raised a new optimization challenge. In addition to the dosimetric goals, the beam delivery time (BDT) needs to be considered in the objective function. Considering this bi-objective formulation, the task of finding a good compromise with appropriate weighting factors can turn out to be cumbersome.Approach. We have computed Pareto-optimal plans for three disease sites: a brain, a lung, and a liver, following a method of iteratively choosing weight vectors to approximate the Pareto front with few points. Mixed-integer programming (MIP) was selected to state the bi-criteria PAT problem and to find Pareto optimal points with a suited solver.Main results. The trade-offs between plan quality and beam irradiation time (staticBDT) are investigated by inspecting three plans from the Pareto front. The latter are carefully picked to demonstrate significant differences in dose distribution and delivery time depending on their location on the frontier. The results were benchmarked against IMPT and SPArc plans showing the strength of degrees of freedom coming along with MIP optimization.Significance. This paper presents for the first time the application of bi-criteria optimization to the PAT problem, which eventually permits the planners to select the best treatment strategy according to the patient conditions and clinical resources available.

View details for DOI 10.1088/1361-6560/aca5e9

View details for Web of Science ID 000897929700001

View details for PubMedID 36541505

Applied Physics

Ph.D. program

The Applied Physics Department offers a Ph.D. degree program; see  Admissions Overview  for how to apply.  

1.  Courses . Current listings of Applied Physics (and Physics) courses are available via  Explore Courses . Courses are available in Physics and Mathematics to overcome deficiencies, if any, in undergraduate preparation. It is expected the specific course requirements are completed by the  end of the 3rd year  at Stanford.

Required Basic Graduate Courses.   30 units (quarter hours) including:

  • Basic graduate courses in advanced mechanics, statistical physics, electrodynamics, quantum mechanics, and an advanced laboratory course. In cases where students feel they have already covered the materials in one of the required basic graduate courses, a petition for waiver of the course may be submitted and is subject to approval by a faculty committee.
  • 18 units of advanced coursework in science and/or engineering to fit the particular interests of the individual student. Such courses typically are in Applied Physics, Physics, or Electrical Engineering, but courses may also be taken in other departments, e.g., Biology, Materials Science and Engineering, Mathematics, Chemistry. The purpose of this requirement is to provide training in a specialized field of research and to encourage students to cover material beyond their own special research interests.​

​ Required Additional Courses .  Additional courses needed to meet the minimum residency requirement of 135 units of completed course work. Directed study and research units as well as 1-unit seminar courses can be included. Courses are sometimes given on special topics, and there are several seminars that meet weekly to discuss current research activities at Stanford and elsewhere. All graduate students are encouraged to participate in the special topics courses and seminars. A limited number of courses are offered during the Summer Quarter. Most students stay in residence during the summer and engage in independent study or research programs.

The list of the PhD degree core coursework is listed in the bulletin here:  https://bulletin.stanford.edu/programs/APLPH-PHD .

3.  Dissertation Research.   Research is frequently supervised by an Applied Physics faculty member, but an approved program of research may be supervised by a faculty member from another department.

4.  Research Progress Report.   Students give an oral research progress report to their dissertation reading committee during the winter quarter of the 4th year.

5.  Dissertation.

6.  University Oral Examination .  The examination includes a public seminar in defense of the dissertation and questioning by a faculty committee on the research and related fields.

Most students continue their studies and research during the summer quarter, principally in independent study projects or dissertation research. The length of time required for the completion of the dissertation depends upon the student and upon the dissertation advisor. In addition, the University residency requirement of 135 graded units must be met.

Rotation Program

We offer an optional rotation program for 1st-year Ph.D. students where students may spend one quarter (10 weeks) each in up to three research groups in the first year. This helps students gain research experience and exposure to various labs, fields, and/or projects before determining a permanent group to complete their dissertation work. 

Sponsoring faculty members may be in the Applied Physics department, SLAC, or any other science or engineering department, as long as they are members of the Academic Council (including all tenure-line faculty). Rotations are optional and students may join a group without the rotation system by making an arrangement directly with the faculty advisor. 

During the first year, research assistantships (RAs) are fully funded by the department for the fall quarter; in the winter and spring quarters, RAs are funded 50/50 by the department and the research group hosting the student. RAs after the third quarter are, in general, not subsidized by the rotation program or the department and should be arranged directly by the student with their research advisor.

How to arrange a rotation

Rotation positions in faculty members’ groups are secured by the student by directly contacting and coordinating with faculty some time between the student’s acceptance into the Ph.D. program and the start of the rotation quarter. It is recommended that the student’s fall quarter rotation be finalized no later than Orientation Week before the academic year begins. A rotation with a different faculty member can be arranged for the subsequent quarters at any time. Most students join a permanent lab by the spring quarter of their first year after one or two rotations.  When coordinating a rotation, the student and the sponsoring faculty should discuss expectations for the rotation (e.g. project timeline or deliverables) and the availability of continued funding and permanent positions in the group. It is very important that the student and the faculty advisor have a clear understanding about expectations going forward.

What do current students say about rotations?

Advice from current ap students, setting up a rotation:.

  • If you have a specific professor or group in mind, you should contact them as early as possible, as they may have a limited number of rotation spots.
  • You can prepare a 1-page CV or resume to send to professors to summarize your research experiences and interest.
  • Try to tour the lab/working areas, talk to senior graduate students, or attend group meeting to get a feel for how the group operates.
  • If you don't receive a response from a professor, you can send a polite reminder, stop by their office, or contact their administrative assistant. If you receive a negative response, you shouldn't take it personally as rotation availability can depend year-to-year on funding and personnel availability.
  • Don't feel limited to subfields that you have prior experience in. Rotations are for learning and for discovering what type of work and work environment suit you best, and you will have several years to develop into a fully-formed researcher!

You and your rotation advisor should coordinate early on about things like: 

  • What project will you be working on and who will you be working with?
  • What resources (e.g. equipment access and training, coursework) will you need to enable this work?
  • How closely will you work with other members of the group? 
  • How frequently will you and your rotation advisor meet?
  • What other obligations (e.g. coursework, TAing) are you balancing alongside research?
  • How will your progress be evaluated?
  • Is there funding available to support you and this project beyond the rotation quarter?
  • Will the rotation advisor take on new students into the group in the quarter following the rotation?

About a month before the end of the quarter, you should have a conversation with your advisor about things like:

  • Will you remain in the current group or will you rotate elsewhere?
  • If you choose to rotate elsewhere, does the option remain open to return to the present group later?
  • If you choose to rotate elsewhere, will another rotation student be taken on for the same project?
  • You don't have to rotate just for the sake of rotating! If you've found a group that suits you well in many aspects, it makes sense to continue your research momentum with that group.

Application process

View Admissions Overview View the Required Online Ph.D. Program Application  

Contact the Applied Physics Department Office at  [email protected]  if additional information on any of the above is needed.

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February 1, 2024

Dr. Ruijiang Li

Dr. Ruijiang Li was awarded an NIH R01 award from the National Cancer Institute (NCI) for research in MRI and blood biomarkers of neoadjuvant therapy response and outcomes in rectal cancer. Congratulations Ruijiang!

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5 Public Health Courses Premeds Should Take

Epidemiology and health policy are among courses that can help help aspiring medical students become physician leaders.

Premeds Take 5 Public Health Courses

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Studying health policy helps future doctors understand policies at local, national, and international levels, and teaches them to advocate for their patients.

As a premedical student, you can take public health courses that will allow you to better understand health at a population level. An understanding of public health can help you become a physician leader in the community.

The COVID-19 pandemic put a spotlight on the importance of public health . While not perfect, our local and national public health infrastructure allowed the public to understand the severity of the COVID-19 disease as well as create measures to protect the health of our communities.

While the COVID-19 pandemic highlighted the importance of public health, there are other diseases where doctors are called upon to promote population-level changes while taking care of patients.

Doctors serve as leaders in their communities by providing medical expertise and advocating for public health initiatives. They can translate their insights from patient care to create hospitalwide and communitywide policies to protect other individuals, and doctors who are trained in epidemiology and community health can study the transmission of the diseases. They can also spearhead community public health initiatives, including health education campaigns and community clinics, to expand access to medical care.

Dr. Rishi Mediratta graduated from Johns Hopkins University in Maryland with a bachelor’s in public health studies. That degree gave him a foundational understanding of global health issues, public health theories and statistics that enabled him to conduct research and create community health programs in Ethiopia focused on combatting child mortality.

"Throughout college and during my first gap year before medical school, I founded the Ethiopian Orphan Health Foundation, a nonprofit organization that provided community-based health care and education to 91 orphans near Gondar, Ethiopia," he says.

"I integrated lessons that I learned from my classes in epidemiology and public health to partner with community members to help orphaned children. For instance, I saw how Ethiopians bonded during traditional coffee ceremonies. I used coffee ceremonies to create a dialogue with the community about stigmatized child health topics.”

Mediratta then pursued a master’s of science in public health at the London School of Hygiene & Tropical Medicine as a British Marshall Scholar.

“Further public health studies showed me the various stakeholders involved in creating global health policies for newborns and children. I learned how health policies were created based on synergies from multiple perspectives. These insights were instrumental when I worked with policymakers at the World Bank and World Health Organization.”

Mediratta received his medical degree at Stanford University School of Medicine in California, where he continued to spearhead initiatives to improve population health, primary care and global health. Now he is a clinical associate professor of pediatrics at Stanford medical school and a faculty fellow at the Center for Innovation in Global Health.

These public health classes and topics will be helpful for premedic students :

• Biostatistics • Epidemiology • Health equity • Health policy • Community health and community-based classes

Biostatistics

Biostatistics is the application of statistics to life sciences, including public health. In a biostatics class, premeds learn quantitative and qualitative data collection methods as well as when to use different types of statistical analyses.

Premed students who take biostatistics will be able to better understand the role of evidence in public health research, policy and clinical practice, critically evaluate medical literature and tailor their treatment plans for patients based on rigorous scientific evidence, Mediratta says.

Epidemiology

Epidemiology is the study of diseases or disorders within groups of people and ways to prevent or control them. Premed students who take an epidemiology course will be able to understand the causes, prevalence and distribution of a disease in the community. Doctors who understand the epidemiology of a disease can help make informed decisions about prevention and treatment for their patients.

“Knowing epidemiology allows me to appreciate nuances in the distribution of clinical symptoms, risk factors, and diseases in populations," Mediratta says. "For example, I learned how newborns in low- and middle-income countries die from prematurity, complications from birth and sepsis. I developed and validated a Neonatal Mortality Score that predicts which newborns are likely to die when they are admitted to neonatal intensive care units in Ethiopia. I hope that one day, health care providers can use our research to more quickly identify newborns who are at risk of dying and provide them with monitoring and interventions that save their lives.”

Health Equity

Health equity courses teach premedical students about health care disparities – which vary by income, race/ethnicity, sexual orientation and disability status – and inequities within populations. These courses also give students ways to advocate for disadvantaged individuals and populations.

Premedical students can take a general health equity class or seminars focused on specific populations or health systems that incorporate health equity. “Doctors who are knowledgeable about health care disparities can advocate for equitable access to health care services," Mediratta says. "Through research, advocacy and community involvement, physicians can address the social determinants of health that contribute to health inequities.”

Health Policy

In a health policy class, premeds will learn about health care systems and the stakeholders influencing health care policies. Studying health policy helps future doctors understand policies at local, national, and international levels, and teaches them to advocate for their patients by supporting policies that promote better access to quality health care and decrease health care disparities.

Reflecting on his clinical practice, Mediratta says, “understanding the factors that influence health policies has allowed me to help my patients navigate our complex health care system, such as connecting patients to services covered by their medical insurance or accessing transportation services to and from hospitals.”

Community Health and Community-Based Classes

A community health course explores the multifaceted factors influencing health outcomes, including social determinants of health and environmental factors, and also examines public health interventions. Some courses include an experiential learning component so students can conduct projects that address community health needs.

Mediratta, for instance, taught an elective at Stanford University that allowed students to collaborate with community partners to creatively implement projects that address COVID-19-related challenges.

"One student produced a children’s book that combatted vaccine hesitancy and created read-aloud videos of the book. Even after the class ended, the student organized workshops in elementary schools to educate children about vaccine. Our class serves as a model for how universities can implement medical service-learning courses to empower students while simultaneously addressing the community’s needs.”

Taking public health courses during your premedical career will give you strong foundational knowledge to be a health care leader. As a doctor, you will be able to help your patients navigate through the challenges of health care systems, participate in policymaking that affects millions of individuals, and direct research projects that advance the health of our communities.

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  1. Biomedical Physics (BMP) PhD Program

    The Biomedical Physics (BMP) Graduate Program is a PhD training program hosted by the Departments of Radiology and Radiation Oncology within the Stanford University School of Medicine. The objective of the PhD in BMP is to train students in research focused on technology translatable to clinical medicine, including radiation therapy, image ...

  2. Biomedical Physics (BMP) PhD Program

    This new Stanford PhD program seeks to train future generations of leaders in medical physics, imaging science, molecular imaging and diagnostics, allowing them to translate these new tools to address critical challenges in clinical medicine. ... As the scope of medical physics has expanded, students pursuing careers in this field have been ...

  3. Med Physics

    Welcome to the Division of Medical Physics, a branch of the Department of Radiation Oncology at Stanford University. We are concerned with three areas of activity: clinical service and consultation, research and development, and teaching.Our vision is to be the world's premier program committed to excellence and innovation in clinical practice, scientific research, technological development ...

  4. Biophysics PhD Program

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  5. Graduate Admissions

    The GRE General and Physics exam scores will be accepted but are not required in the 2024-25 application cycle (2023-24 academic year). The Department of Physics welcomes graduate applications from individuals with a broad range of life experiences, perspectives, and backgrounds who would contribute to our community of scholars.

  6. Biomedical physics program launches

    A new PhD program, hosted by the departments of radiology and radiation oncology, trains students in technologies used for therapy and diagnostics.

  7. Radiation Oncology

    Our Mission. To bring the most advanced care to our patients by being at the cutting edge of research and technology. Using the most state-of-the-art imaging systems and radiation delivery platforms in the world, our highly integrated team of physicians, physicists, dosimetrists, nurses, and radiation therapists share a commitment to provide ...

  8. PDF Led by Quynh-Thu Le, MD, FACR, FASTRO The Stanford University Physics

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