PoSM Lab Github
Physics of Soft Matter Lab at Harvey Mudd College
PosMLab Training & Onboarding
Welcome to PoSMLab! Here you will find an introduction to our group and useful onboarding information.
Onboarding Logistics
Logistical details if you want to get started in PoSMLab (expand/collapse)
General Logistics
MATLAB
Most of our analysis and simulation code is written in MATLAB. If you don’t have MATLAB installed, please follow the HMC Instructions for Installing MATLAB on your computer
If you are relatively new to MATLAB, a good place to start is the two-hour MATLAB onramp course. If you’re looking for some more advanced topics, you could also check out the MATLAB ordinary differential equation course that is helpful for some of our simulation work.
Discord
We use Discord to communicate as a whole team in the summer when we are working full time. During the academic year, email is a bettter way to communicate because the team is usually working asyncrhonously. But when you are actively working on a posmlab project, try to get in the habit of logging into Discord.
Here’s a link to join the posmlab Discord server.
Google Drive
The posmlab Shared Google Drive
posmlab Google Drive folder is a place to store large files/data.
The “poslmab/Papers” folder is currently where we store pdf files of relevant literature. Please add any new papers here with the naming convention below and place copies of relevant literature in that folder.
| Number of authors | Filename Format | Example |
|---|---|---|
| 1 | Authorlastname Journalname Year.pdf | Doe Phys Rev Lett 2015.pdf |
| 2 | Firstauthorlastname and Secondauthorlastname Journalname Year.pdf | Lee and Doe Science 2018 |
| 3+ | Firstauthorlastname et al Journalname Year.pdf | Lee et al Nature 2017 |
Once saved in Google Drive, you can right click on the document and “Get shareable link” to provide easy access from other sources (e.g. Github repository readme file).
Other logistics
When starting remind Mark that he needs to:
- Enable swipe access to the Lab in Galileo B101 (he needs your Student ID Number so he can fill out this form
- give you passwords to group accounts
- give you a lab notebook if you prefer a physical notebook
- add you to the posmlab Google Group (which gives access to the posmlab Google Drive)
- to add you to the posmlab Github organization (he needs your Github username to do this)
Group Accounts:
| Service | Name |
|---|---|
| Gmail | physicsofsoftmatter@gmail.com |
| posm_lab | |
| Squarespace (managed by Mark) | posmlab.org |
| Google Drive | posmlab shared drive |
| Slack | posmlab.slack.com |
| Github | github.com/posmlab |
Group Culture
To get a sense of some of the dynamics research we are doing, please watch this video on the Rockwell Retro Encabulator.
Did you watch the video? (expand/collapse)
A common reaction to that video is going from an initial curiosity, to confusion, then finally amusement. But what does this have to do with doing research as an undergrad?
Entering a new area of research is difficult for anyone! You are about to be confronted with a lot of new information, and a lot of it you won’t understand right away. That’s part of the process and totally okay.
Our group culture is one where not knowing and seeking clarification is a strength. Even questions that you feel you should know the answer to already, or seem obvious to others are important to ask. If you don’t understand something, it’s probably because it wasn’t explained well! Here’s what we ideally do in posmlab if we don’t fully understand:
- ask for clarification - any question is a good question that arises from curiosity or a desire to understand!
- document our new understanding along with any sticking points for future group members
Also note that in posmlab, Mark is a teammate/collaborator/advisor not a boss/supervisor. Openly questioning his advice is encouraged! To promote an open and equal discussion please refer to Mark on a first-name basis in our research group (rather than Prof. Ilton).
Generally, our group culture has been one where we are supportive of one another, take interest in what others in the group are doing, and are willing to put our work aside momentarily to help someone else out!
Scientific Papers
Part of the process of doing science is reading scientific papers related to our work. Reading a scientific paper can be a fairly daunting task. A good resource is How to Read a Paper - The Three Pass Approach. Depending on what you are trying to get from a paper (a high-level overview? the main ideas?), you may only need to perform one or two passes of the paper. The key idea is to start with a bird’s eye view on your first reading, and then zooming in to more granular details on subsequent passes.
We will often use a “Journal Club” as a format for sharing and discussing scientific papers. Aptly described as a “nerdy book club” by Prof. Mendelson in Engineering, Journal Clubs are a great way to ensure that you are sharpening your ability to read primary literature. If you haven’t done this before, check out 5 quick tips for your first JC.
At some point, it will come time for you to write-up your work. Remember that the main product of academic research is a scientific paper. If you think about (and actively work on) writing a paper based on your work, it can more effectively direct your efforts. Although it is written about chemistry research, this guide to Writing a Paper is a good read. The paper Ten simple rules for structuring papers has some helpful tips as well.
Introduction to PoSMLab Research
Introduction to the physics of ultra-fast elastic movements (expand/collapse)
With the logistics out of the way, let’s dig into the research topics we study! Below is a step-by-step guide to getting acquainted with the research we do in posmlab.
Common steps for all students
1) Watch this short PoSMLab Introduction video
2) Read more examples of ultra-fast organisms that use elastic energy to drive movement. Contribute to that document by adding more information from a primary literature source for one organism (your first contribution to a posmlab Github repository!).
3) Read more examples of engineered microrobotic devices inspired by nature. Contribute to that document by adding more information from a primary literature source for one device.
4) Look at Fig. 1 of Roberts and Azizi JEB 2011:
What are the three main functions of biological springs? Which one are we focused on in our research?
Optional: skim the full paper Roberts and Azizi JEB 2011.
5) Do a careful reading of Longo et al JEB 2019 which lays out a framework for Latch-mediated Spring-actuated (LaMSA) systems. Come up with three questions that you would like answered (could be clarifying questions, conceptual questions, research questions, or even just highlighting places that are confusing).
6) Watch the video when does a spring beat a motor?.
Your next steps depend on what are of posmlab you are joining (ask Mark if you’re unsure!)
Lab Subgroups
Each subgroup represents a different facet of our lab. It’s common for students to move between subgroups over the course of their time in the lab. Take a look at whatever you’re interested in!