A PhD is a long journey full of ups and downs. Sounds cliché (big warning, this blog will be full of them), but in my opinion, it is the ultimate example of the expression “it’s not a sprint, it's a marathon.” As a fifth year and, hopefully, finishing my grad school journey during this school year, I tend to talk with a lot of younger students who are just starting or are at the middle of their PhD about the entire experience and some of the expectations I had, or the good and bad things I’ve faced. As I look back at this entire process, I had one big realization I want to share with you guys through this blog. I concluded that “a PhD can be summarized in the fact that every school year has one clear goal.” It’s a very simple and very loose way to describe it, and yes, I’m skipping a lot of the small details that happen throughout the process, but if we step back and look at the big picture, I think you’ll get what I mean.
For the rest of this blog, I’ll go through each of the five years (or so) that it takes to complete a PhD and explain what I think is the objective of every year. My goal is to help those students that are currently anxious about the future years, those who are a bit lost and lack the motivation of what to do next, and/or those students who are looking for a broad idea of what the PhD journey is by answering some of their questions or helping them focus on what they should be focusing right now, and even planning for the future. With that long-winded intro, let’s continue with the series and talk about year two.
Big clarification, I’m a Chemistry PhD student, so my journey and the way each year works is based on that premise and can be easily applied to most of the STEM PhDs. For other areas, the process might be quite different, but I hope this at least can give some idea of how this works for those in other areas.
Year two
Goal: QE/Dissertation Proposal
We’ll start with the summer between year one and year two.
This summer will be the first time you can focus completely on research. You won’t have classes, TA duties, or seminars, leaving all your time to make progress on your project. It’s a great opportunity to get trained on the instruments you’ll need, practice using them, and start analyzing your samples as much as you can.
The main goal, and the big deadline, of this year is your Qualifying Exam (QE) or Dissertation Proposal (depending on your program). Whichever the case, they work in a very similar way.
The QE has two parts:
- A written document containing the full proposal for your project (I’ll go deeper into this in a moment).
- A presentation in front of a committee made up of faculty from your department.
Because of this, summer is the perfect time to lay the foundations for your project. That means having a clear sense of your overall goal and the plan you’ll follow to achieve it. Once you have that vision, you can break it down into short-, medium-, and long-term goals that will guide you step by step.
During this summer and the entire fall semester, your focus should be on completing as many short-term goals as possible. The most important part is achieving “proof of concept.” In other words, generating results that show your plan of action is feasible and that your proposed research can realistically lead to your final goal. A strong foundation here will help you immensely when it’s time for your QE.
Fall Semester: Pre-QE Preparation
In Chemistry, you’ll also have another departmental presentation this semester, just like the one you gave at the end of year one. Think of this as a dress rehearsal for your QE: Prepare your slides and structure your talk in a way that mirrors how you’ll eventually present at the QE. Doing this saves time later and gives you a chance to practice your flow, polish your presentation style, and even get feedback on potential questions you might face. Take this presentation seriously as pre-QE preparation. As the semester ends, I highly recommend taking a proper winter break. Rest as much as possible, you’ll need it, because the spring semester will be intense.
Spring Semester: QE Season
Right at the start of the spring semester, you’ll have a meeting where your QE committee is assigned. From that point, you’ll have until the end of the semester (exact dates vary and are announced at the meeting) to schedule your QE presentation. Your committee typically consists of three faculty members, one of whom serves as chair and manages the official documentation. As of 2025, the written document is due two weeks before your presentation, but deadlines have changed in recent years, so keep an eye on updates.
Since the QE document and presentation would require an individual blog for each, I won’t go too deep into them, but I’ll give a summary of what is expected in both. Your QE revolves around the research you’ve done, the work you’re currently doing, and the future research you propose. That’s why it’s so important to have a clear understanding of your overall project goal before you start writing. You’ll need to present three aims that, if completed, lead to your final objective:
- Aim 1: Base work you’ve already completed.
- Aim 2: Current work with some data, but not yet finished.
- Aim 3: Fully proposed future work, with maybe a little preliminary data as proof of concept.
Alongside these aims, you’ll include a timeline covering your entire PhD, from year one through your expected graduation in year five. This gives the committee a clear picture of your project’s scope and feasibility.
The Day of the QE
On the day of your exam, you’ll give a 40 to 45-minute presentation. Committee members (and sometimes the audience) can ask questions at any point. After your talk, the public audience leaves, and you’ll have a closed session with just the committee. Here, you’ll continue answering questions, discussing potential challenges, and sometimes even receiving advice on new directions. There’s no strict time limit; it depends on the committee. Once that’s over, you’ll step out while the committee deliberates. Then you’ll be called back in to hear the result and receive their feedback.
After the QE
Once you pass, you officially become a PhD candidate and are eligible to request a Master of Arts degree. I highly recommend taking a few days off to relax and recover, mentally and emotionally, from the stress of the QE.
Depending on your timing, you may still need to finish other semester requirements (seminars, TA duties, etc.), but nothing will be as big as the QE. And with that, year two comes to an end.
In the next chapter of this series, I’ll cover the summer after year two and the journey through year three.
Stay tuned, and I hope this was useful for you.
About the author:
Manuel Carmona Pichardo is from Pachuca Hidalgo, Mexico and is a current Ph.D. student in Chemistry. He got his B.S. in Chemistry at Universidad Autónoma del Estado de Hidalgo in 2016 and his MSc in Chemistry from Cologne University in Cologne Germany. Read More
Further Reading:
PhD Retrospective: Each semester, One objective. Year One
Advice from a 6th Year PhD student