Jackson Lab Manual

CONTENTS:

1. Introduction 2. Workplace Expectations 3. Personal Well-Being 4. Group Operations 5. Conflict Resolution 6. Getting Started in the Group 7. Exit policy

I. INTRODUCTION

Mission Statement: Our lab integrates molecular quantum mechanics, computational statistical mechanics, and machine learning to describe soft materials at multiple length scales. We are particularly interested in soft materials with electronic, ionic, and reactive functionalities. We pride ourselves on scientific communication and strong mentorship within the group. We believe that great scientists come from anywhere on the planet.

Diversity Statement: The Jackson group is committed to social justice and strives to maintain a positive research and learning environment based on open communication, mutual respect, and non- discrimination. The Jackson group will not discriminate on the basis of race, sex, age, gender, economic class, disability, veteran status, religion, sexual orientation, color, or national origin. Diversity of thought and background forms the backbone for impactful scientific work and is fundamental to the work that we do on a daily basis.

What are some scientific topics we get excited about? Multiscale theory and computation, bioelectronics, static electricity, how to derive electronic structure from coarse-grained representations, systematic coarse-graining, reactive models, network analysis and graph theory, experimental collaborations, sequence-defined polymers, electron and ion transport in soft materials, sustainable polymer design, thermal and chemical degradation, flexible electronics, molecular and polymeric interfaces, complex macromolecular architectures, data-driven computational techniques and machine learning, advanced sampling algorithms and inverse design of chemical and polymeric structures.

What kind of a theory group are we? Our research is focused on the multiscale understanding of soft material chemistries. As multiscale soft materials design exists at the frontier of computational and theoretical methods, many problems we work on necessitate the development of new methods. With that said, if adequate theoretical and computational methods exist to tackle the problems of interest, we will use them. We are not a traditional theoretical chemistry group focusing in a single area (e.g. electronic structure theory, quantum dynamics, or statistical mechanics) – the problems we work on are highly interdisciplinary and will expose group members to a broad array of theoretical and computational techniques.

While we are housed in a Chemistry department, we could find comfortable homes and collaborations in Chemical Engineering, Materials Science, or Physics departments. If you are interested in a group that will expose you to a broad array of interdisciplinary problems and theoretical/computational methodologies, this is the lab for you!

II. WORKPLACE EXPECTATIONS

Responsibilities of the PI: Generally speaking, my plan is to coach you intensively for the first two years. This is critical because I want to make sure that the fundamentals of theory and computation are ingrained in a correct and rigorous fashion, such that the remainder of your work throughout your career is rock-solid and reliable. My aim is that, following your candidacy, you will take on more independence and develop and execute your own scientific ideas within the context of your project(s). With this in mind, I aim to become more hands-off as you progress through your Ph.D. – you have the fundamentals, you have demonstrated competency, and now the goal is to develop independence in your research. In the last year of your Ph.D., my role will become more of a delegator – I will be assigning you projects, trusting in your technical competency and ability to creatively problem solve, and becoming your cheerleader and advocate as you progress towards your next career stage. To be concrete – whatever future career (industry, academia, government) you are interested in, I will support you to the absolute best of my ability. Lab members may contact me via email, phone, or text as well as come by the office whenever the door is open.

Nick’s contact information: Office: 350E Noyes Email: [email protected] Office Phone: TBD

How much am I expected to work? The focus is on progress in your project(s) rather than the number of hours worked. I’ve seen people work 40 hours/week and make great progress, and I’ve seen people work 80 hours/week and get nothing done. On average, I generally see people that work ~50-60 hours/week having strong success.

With this said, some of the best advice I can give about being successful in graduate school is to have a regular schedule. Be in the office 9-5 on weekdays. Being present 9-5 ensures that both I, and other lab members, can interact with you, which is an absolutely critical part of your (and my) continued scientific development. To be clear: this is NOT me saying that you only need to work 40 hours per week to be successful.

My schedule: I aim to be in the office 8 am - 6 pm daily. I work Saturdays but split my weekends between UIUC and Chicago to spend time with my wife. I am available for meetings on Saturdays (in person or skype). I typically take Sundays off. Barring exceptional circumstances, I do not answer emails between the hours of 9 pm and 6 am.

What thematically constitutes a Ph.D. in the Jackson Lab? The criteria I set for students graduating from my lab are motivated by a single goal: that students are best prepared to obtain their job of choice following graduation. This outcome is optimal for me as well as students because I am a firm believer that the quality of a scientific lab is dictated by the quality of the scientists that graduate from the lab. To this end, here are my expectations of Ph.D.’s in my lab:

• The ability to independently design, and rigorously execute, original scientific research. • A technical expertise that you can sell in your future job applications (e.g. network analysis, polymer physics, machine learning, high performance computing, etc). • Excellent scientific communication skills (speaking, writing, and listening).

What practically constitutes a Ph.D. in the Jackson Lab:

• A minimum of three 1st author publications = (evidence of expertise and ability to execute projects). • One oral and one poster presentation at a professional conference = (practice in scientific communication). • Collaboration and interaction with an experimental group = (practice in scientific communication).

How do I make sure I have a successful Ph.D.?

Rule 1: Take ownership of your project. Know the background information and caveats of your research thoroughly. Frequently re-evaluate where YOU think your project should be headed and devise potential paths for moving forward in those directions. I encourage you to communicate these ideas with me so that I can give you feedback – it is more than likely that some of your ideas will be fantastic avenues to pursue and I want you (eventually) working on ideas related to your project that YOU came up with.

Rule 2: Learn from others and understand what you are learning. It’s OK to initially use software packages and theories as black boxes for exploratory calculations, but you will not be publishing any results until you thoroughly understand every technique or theory that you are using to generate data.

Rule 3: Get the help you need both within the group and outside of it: group meetings, seminars, other lab members, your committee, and other faculty in the department. There is an expert at UIUC in almost any topic of interest – take advantage of that.

Rule 4: Don’t lose yourself in your project. Science is a constant exercise in finding the deepest minimum in a potential energy surface that provides the best rewards. Digging down into your project from a single perspective is key to making advancements – however, don’t forget to broadly educate yourself (seminars, literature) in areas outside of your immediate expertise. The history of science (theory in particular) is often one of people taking ideas from other fields and applying them to their interest areas (look at how polymer theory developed by simply applying frameworks from quantum mechanics for a beautiful example). Exposing yourself to many different ideas is a key element of making progress in your own specialization.

Rule 5: Learn how to train people. A Ph.D. enables one to lead research teams (industry, government, academia) – you can’t lead research teams without a Ph.D. Take the time to show others within the group how to do things (undergraduates, graduates, postdocs, me!).

Time away from the Laboratory:

• Vacation policy: 30 total vacation days (note: major holidays such as Christmas and New Years and University holidays are to be counted as vacation days). Students can use these days whenever they want. If you will be absent for 1-2 days, please give me a day’s notice (if possible). Please provide several weeks’ notice about an upcoming vacation that lasts more than one week (this is to ensure that if I need a result provided or a poster presented during your absence, I can adapt various members’ schedules to accommodate this in advance). • Sick days: If illness or mental health are interfering with your research, time off is expected and this does not count as vacation days. Please do not come to lab if you have cold or flu-like symptoms. If overall health is significantly affecting your research progress, a leave of absence should be discussed with the PI. • Mental health: I am passionate about student mental health. Should you be suffering from mental health issues, please let me know and I will be happy to work with you to develop a more accommodating schedule. If you feel that you need a mental health day, please take one and let me or someone in the group know that you will be doing so. Also, please avail yourself of the University’s mental health resources (https://www.counselingcenter.illinois.edu). • Emergency situations: Family emergencies are covered as the same policy of illness. Please notify me if you will be out for a family emergency. • International students: It is understood that international students may take less frequent but extended vacation time. • Adverse weather: If classes are cancelled, or the temperature is below 10 degrees Fahrenheit, students may elect to work from home. • Conferences: Do not count as days off. • If you are considering maternity/paternity leave, please contact me directly to develop a schedule that supports you and is consistent with University policies.

External Funding: When a graduate student is accepted into the group, I maintain full responsibility for funding that person through either RA or TA appointments throughout the course of their Ph.D., consistent with departmental standards. However, I strongly encourage any students interested in applying for external funding opportunities (NSF GRFP, NDSEG, etc) to mention this interest to me in meetings so that we can work towards creating a strong application to one or more funding opportunities.

When a postdoctoral researcher is accepted into the group, the term of their appointment and potential for renewal will be negotiated and made clear in the offer letter. If current or potential postdoctoral researchers are interested in applying for an external fellowship, they should contact me directly by email to discuss such opportunities.

Rules for Meetings:

• If my door is open, I am happy to chat at any time. If my door is closed, it is intentional and I need to concentrate on other tasks, so please only knock if it is an emergency. • Come into meetings with a specific list of topics you would like to discuss – this way I can be most helpful to you. • Bring paper and a pen to take notes with during the meeting.

Communication is Key: The best way that both you and I can get the most out of your Ph.D. is by having open lines of communication. I will do my best to constantly communicate my thoughts and expectations to you, and you should do the same for me. Small regular adjustments are much more effective (and less stressful!) than a single massive course correction down the road. I am a firm believer that happy and motivated people do the most creative science, and communication is critical to this.

Expectation of Conduct: Students are expected to uphold the highest level of ethical conduct in accordance with the policies of the University of Illinois. Unethical conduct such as fabrication of results can seriously jeopardize one’s career and goes against what we stand for as scientists.

The Jackson group is committed to maintain a safe and welcoming environment for all, regardless of race, gender, sexual orientation, disability, physical appearance, religion, and other identifiers. All students are expected to maintain an environment free from harassment and discrimination, in accordance with the policies set out by the University of Illinois. If you witness, or are the target of, harassment or discrimination, please consider reporting it to Prof. Jackson, to the Assistant Director of Graduate Diversity & Program Climate, or to your Title IX coordinator.

III. PERSONAL WELL-BEING

Happiness: You are here to do a Ph.D. at one of the top research institutions in the world. You were admitted under the premise that becoming an outstanding and productive scientist is what you want to do with your life, and of course there are expectations associated with this. However, life is more than only what you do in your Ph.D. and you should never forget this. Work hard, be proud of what you do, push yourself intellectually and creatively, but nothing comes before your health and wellness. One thing that I firmly believe is that happy and relaxed people do the best science.

Group Care Activities:

• If you notice a person in the group is out for several days, check in with that person (not calling them out to others). • No judgement, just checking in (e.g. “Just wanted to make sure you are doing okay” or “Do you need help with anything?”) • Going to the doctor, going to counseling, working out, going to yoga, going to a meditation class, going for a walk – these are all activities that are strongly encouraged. There is no need to report these activities. Of course, we agree as a group to not abuse this policy. • RSO database (https://union.illinois.edu/get-involved/office-of-registered-organizations) • ARC group fitness schedule (https://campusrec.illinois.edu/programs/group-fitness/group-fitness- class-schedule/) • Counseling Center (https://counselingcenter.illinois.edu/) • McKinley Health Center (https://mckinley.illinois.edu/) • Women’s Resource Center (https://oiir.illinois.edu/womens-center) • Cultural Houses (https://oiir.illinois.edu/our-centers)

IV. GROUP OPERATIONS

We are a very new and small group, so this section will evolve as the group grows!

V. CONFLICT RESOLUTION

Authorship: Authorship should be discussed at the beginning of projects with all potential authors and should be agreed upon unanimously. Frequently, authorship can change as projects progress, but any changes should be discussed with all authors. The order of authorship is impacted by many factors, but the final order should be determined by PI. Students cannot promise authorship orders (e.g., “If you do this, you’ll be second author.”)

Student-to-Student Conflicts: Start person-to-person – attempt to resolve the conflict in a gentle, non- accusatory tone. If the conflict escalates beyond what can be solved between the people involved, the conflict should be taken up with Nick. If required, Nick will contact Justin M. Brown in the Office for Student Conflict Resolution in order to help resolve the matter. If the conflict is threatening to one’s life, call 911 and then notify Nick. All ethics and scientific integrity issues should be reported to Nick.

Student-to-PI Conflicts: We recognize that there is a power difference involved in the resolution of such a conflict. It is preferred that a student would first manage the conflict informally in-house without involving administrators (if possible) via an email to Nick, another graduate student’s mediation, or a meeting with the Nick. Students should let Nick know if they feel that his response was inadequate and could do so via email. If the student still feels that the conflict has not been resolved, the student should let Nick know and address the issue with another mediator. Mediators/resources for graduate students include the departmental Assistant Director of Diversity and Climate Dr. Lloyd Munjanja, the Director of Graduate Studies Dr. Wilfred van der Donk, and Morris Mosley in the Faculty Staff Assistance Office.

Group Conflict: To avoid group issues, group members should clean up after themselves ASAP, particularly within shared spaces. Instruments should be reserved on the instruments calendar (Google calendar) and that reservation should be respected. Group members should handle equipment as instructed, turning off and cleaning whatever necessary and reporting any issues to the point person for that instrument. All the equipment in Z-group are assigned to at least one student for maintenance. Most equipment require training before using. Otherwise, students take turns to do cleaning within labs and the group room.

VI. GETTING STARTED IN THE GROUP

Is a Coding Background Required? Any previous experience is fantastic, but not required. All that is required is a strong background in physical chemistry and mathematics, and a passion to do science!

Get a laptop or desktop that has a Unix interface. Graduate students and postdocs will be provided with a laptop or desktop, as well as an external hard drive for data storage. All Linux machines and Macs have this functionality built into them. Windows 10 and above has recently established this functionality with Powershell. If you have a pre-Windows 10 machine, you will need to install a Unix environment (e.g. Cygwin). However, I would strongly advising using either Linux machines or Macs – it will make your life much easier.

Computational resources? We have a small group cluster named Scruggs run out of SCS, and also can use the SCS cluster lop as is needed. To request an account, discuss requesting access with Nick.

Learn a text editor: A text editor allows you to write code and edit documents within a UNIX environment. VIM and Emacs are two of the most common. I personally use emacs but am not remotely particular about this.

Attend Departmental Physical Chemistry Seminars: All graduate students and postdocs are expected to attend departmental physical chemistry seminars. This provides significant exposure to a broad diversity of research topics, as well as to successful (and unsuccessful) presentation styles.

Do a UNIX tutorial: There are thousands of these. Here is a reasonable one: http://www.ee.surrey.ac.uk/Teaching/Unix/unixintro.html

Start to Learn a Programming Language: In this group we primarily use a combination of Python and C/C++. If you have not programmed before, I would suggest starting with Python and learning how to do object-oriented programming. If speed is really of primary interest, writing in straight C/C++ is going to be ~10x faster. There are thousands of tutorials for these languages online, so find one that best suits you. A long time ago I used a website/book called “Learn Python the Hard Way” that I found to be very good.

As far as getting Python or C/C++ installed appropriately on your laptop or desktop (basic installations on computing clusters will generally be taken care of by staff), I would suggest using the Anaconda (Python 3) installation, and making sure numpy, scipy, cython, matplotlib, pandas, sklearn, keras, pytorch, jupyter notebooks are installed.

Computational Notebooks: For a long time theory and computational scientists were excused from having to keep track of their results in notebooks. This is not the policy in the Jackson Group. You may certainly keep a regular paper lab notebook, but I find that Jupyter notebooks (https://jupyter.org/) are an incredibly powerful tool and recommend their use. Keeping good lab notebooks is absolutely critical for scientific reproducibility. If you need to store large amounts of data, I have an unlimited number of external hard drives available for data storage. It is expected that for each published paper, there is a notebook and data storage source that can be easily accessed.

Cutting Your Teeth on Molecular Simulation: For getting started, I generally recommend the following three references as introductions to learning how to program in the context of physical chemistry and molecular simulation.

• Introduction to Computational Physical Chemistry – Schrier (the examples are coded in Mathematica – I suggest you do them in Python, C/C++, or FORTRAN). • Computer Simulations of Liquids – Allen and Tildesley (the examples are coded in FORTRAN but they have adapted the majority of them to Python in their online database). • Scott Shell (UCSB) posts an excellent set of molecular simulation course notes online that many people find useful (https://sites.engineering.ucsb.edu/~shell/che210d/assignments.html).

Mathematica: A good resource for checking your analytic integrals, plotting things quickly, visualization, and a variety of other easy to access features.

Avogadro: A very useful graphical user interface for 3-dimensional molecular structures, optimizing their geometries, and preparing them for quantum-chemical calculations by other programs (http://avogadro.cc/).

Molecular Visualization: VMD and Ovito are two common molecular simulation visualization codes used to examine and analyze molecular dynamics simulations.

For very high quality images, we will use Blender (https://docs.blender.org/manual/en/latest/addons/import_export/mesh_atomic.html), though this is often significantly more work than making images in VMD or Ovito, so should only be done when really necessary.

Learn to Search and Read the Literature:

Google Scholar: Google scholar has evolved to be a useful means of following the literature. Get yourself an account and sign up to receive publication notifications from researchers in your field.

ISI Web of Science

RSS Feeds: Use a service to aggregate the latest articles published in journals via their RSS feeds function. Feedly and RSSOwl are two RSS feed aggregators that I have had success with in the past.

What Journals Should I Read? 10-20 years ago this would be a much easier question to answer. In recent years, the number of new journals has exploded. With that said, here is a good list to get you started:

ACS Central Science, Accounts of Chemical Research, ACS Applied Materials & Interfaces, ACS Energy Letters, ACS Macro Letters, ACS Nano, Chemical Reviews, Chemistry of Materials, Journal of the American Chemical Society, Journal of Chemical Information and Modeling, Journal of Chemical Theory and Computation, The Journal of Physical Chemistry (A/B/C/Letters), Macromolecules, Nano Letters, Chemical Science, Chemical Society Reviews, Physical Chemistry Chemical Physics, Soft Matter, Journal of Materials Chemistry (A/B/C), Advanced Materials, Advanced Energy Materials, Advanced Functional Materials, Journal of Polymer Science Part A/B, Nature Materials, Nature Chemistry, Nature Physics, Nature, Science, Science Advances, Angewandte Chemie International Edition, Journal of Chemical Physics, npj Computational Materials, PNAS, Energy & Environmental Science, Current Opinions in Chemical Engineering.

Structure of Your First Project: Ideally, my personal goal is to have your first project be one in which you can learn as much fundamental knowledge as possible, is publishable as new and exciting science, and motivates future directions for your Ph.D.

Resources for Learning More in Materials Computation and Theory:

Below is a long list of textbooks I have found useful throughout my career as references for a broad variety of topics. If you find yourself needing to understand a particular topic in more depth, you are more than welcome to borrow my copies of these books.

Quantum Mechanics, Quantum Chemistry, and Electronic Structure Theory:

• Quantum Chemistry - McQuarrie • Introduction to Quantum Mechanics - Griffiths • Modern Quantum Mechanics – Sakurai • Quantum Mechanics in Chemistry – Ratner and Schatz • Modern Quantum Chemistry – Szabo and Ostlund • Introduction to Computational Chemistry – Jensen • Introduction to Computational Physical Chemistry – Schrier

Quantum Dynamics: • Quantum Dynamics: Applications in Biological and Materials Systems - Bittner • Chemical Dynamics in Condensed Phases – Nitzan • Introduction to Quantum Mechanics A Time-Dependent Perspective - Tannor

Statistical Mechanics and Classical Dynamics: • Statistical Mechanics: A Concise Introduction for Chemists – Widom • Introduction to Modern Statistical Mechanics – Chandler • Statistical Mechanics – McQuarrie • Understanding Molecular Simulation – Frenkel and Smit • A Guide to Monte Carlo Simulations in Statistical Mechanics – Landau and Binder • Theory of Simple Liquids with Applications to Soft Matter – Hansen and McDonald • Nonequilibrium Statistical Mechanics – Zwanzig • Statistical Mechanics: Theory and Molecular Simulation – Tuckerman • Classical Dynamics of Particles and Systems – Thornton and Marion • Nonlinear Dynamics and Chaos with Applications to Physics, Biology, Chemistry, and Engineering - Strogatz

Condensed Matter: • Principles of Condensed Matter Physics – Chaikin and Lubensky • Introduction to Solid State Physics – Kittel

Network Analysis: • A First Course in Network Theory – Estrada and Knight • Networks – Newman • Network Flows – Ahuja, Magnanti, and Orlin

Machine Learning: • Python Machine Learning – Sebastian Raschka • Deep Learning with Python - Chollet • Hands-On Machine Learning with Scikit-Learn & Tensorflow - Geron • Deep Learning – Goodfellow, Bengio, Courville

The Living Journal of Computational Molecular Science (https://www.livecomsjournal.org/) • Best Practices for Computing Transport Properties (https://www.livecomsjournal.org/article/6324- best-practices-for-computing-transport-properties-1-self-diffusivity-and-viscosity-from-equilibrium- molecular-dynamics-article-v1-0) • Best Practices for Foundations in Molecular Simulations (https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular- simulations-article-v1-0) • Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations (https://www.livecomsjournal.org/article/5067-best-practices-for-quantification-of-uncertainty-and- sampling-quality-in-molecular-simulations-article-v1-0)

VII. EXIT POLICIES

When a group member graduates, as a PhD or as a master, the group member’s contributions should be celebrated in a group event. The group social chair should take the initiative in organizing this event. The group event may be a shared meal, a potluck, a board games party or any other appropriate activity.

Regardless of how a group member exits the group, steps should be taken with cooperation from the departing group member to ensure that any useful skills or knowledge developed by said group member will remain available to the group.

❖ Before the group member physically leaves (ideally as soon as an exit is planned), the supervisor, the departing group member and any in house collaborator (e.g. co-authors on papers) should meet and agree on what needs to be documented in writing and what needs to be passed on in training. ❖ To ensure completeness, the written documents should be read and understood by the professor and continuing group members.

If graduating with a PhD is no longer an option or if a student no longer intends to continue in the PhD program, the student may consider graduating with a master’s degree.

❖ The requirements for a master’s degree by coursework are enumerated in Section 4.3.1 of the Dept. of Chemistry Graduate Manual. ❖ The coursework and documentation requirements for a thesis master’s degree are enumerated in Section 4.3.2 of the Dept. of Chemistry Graduate Manual. Research requirements should be determined through discussion between the student and the professor, possibly in consultation with the program coordinator.

If a student wishes to switch to a different research group, the student should follow the procedures described in Section 5.2.14 of the Dept. of Chemistry Graduate Manual. In addition, the student should ensure continuity of skills or knowledge (see point two) before exiting the group to the best of the student’s ability.

If the professor finds a student’s work performance unsatisfactory, the professor must provide a written, detailed account of 1) how the student is not meeting expectations and 2) what the student needs to change or start doing to meet expectations. Presenting this written account to the student will initiate a 90-day probationary period for the student to implement these changes. This probationary period is distinct from the post-termination 30-day period described in Section 5.2.14 of the Dept. of Chemistry Graduate Manual.

After this 90-day probationary period, if the professor wishes to seek the exit of a student from the group, the professor should notify the student in writing of the causes for which their exit is sought. The professor should proceed as described in Section 5.2.14 of the Dept. of Chemistry Graduate Manual.