The Scientist's Toolbox

"To succeed in a given task, must take advantage of the tools." - a Chinese proverb recounted by Raphael Tsu in his book "Superlattice to Nanoelectronics."

Scroll down through the following topics:

Research ethics and work environment

How to research?

Environmental Health and Safety

Science in Sweden

Experimental techniques 

Software

Writing 

Proposal-writing

Presentations 

Databases 

Applets 

Website-building 

Open access 

Crystallography and structure

Physics (classical, quantum)

Online seminar series 

Motivation and resilience

Research ethics, work environment, and mental health

• "On Being a Scientist", A short guide to the responsible conduct of research (a free pdf is available at the link after registration);

• NIH Research Ethics Course, a brief (~1 hr) online course that covers the basics of research ethics such as data acquisition and management, publication and authorship, etc.;

• "Who Are Corresponding Authors?" editorial by P. S. Weiss, ACS Nano, 2012, 6, 4, 2861; 

• CRediT - Contributor Roles Taxonomy, a taxonomy to assist with assigning author contributions in multi-author publications; 

• "Personal Responsibility under Dictatorship", 1964 essay by Hannah Arendt about choices and moral responsibility;

• "Words Matter: On the Debate over Free Speech, Inclusivity, and Academic Excellence", by Herbert et al., J. Phys. Chem. 2022 (Open Access);

• "The Social Dimension of Scientific Knowledge," an illuminating entry in the Stanford Encyclopedia of Philosophy, that discusses topics like big science, trust, authority, repeatability, and reputation (Open Access); 

• "Best Practices for Using AI When Writing Scientific Manuscripts," an editorial by Jillian M. Buriak et al., ACS Nano 2023; also see a segment on "Artificial Intelligence" from HBO's Last Week Tonight with John Oliver, February 27, 2023)

• "How Bullying Manifests at Work — and How to Stop It" by Ludmila N. Praslova, Ron Carucci, and Caroline Stokes, Harvard Business Review, Nov. 4, 2022;

• "Out in Inorganic Chemistry: A Celebration of LGBTQIAPN+ Inorganic Chemists" by Abhik Ghosh and William B. Tolman, Inorg. Chem., 61, 14, 5435-5441, 2022;

• "An Exploration of Lived Experiences of Sexually and Gender Diverse Staff Members in Higher Education: A Case Study" by Panagiotis Pentaris et al., Journal of Homosexuality, 1-22, 2024; (Open Access)

• "How well-intentioned white male physicists maintain ignorance of inequity and justify inaction" by Melissa Dancy and Apriel K. Hodari, arXiv:2210.03522, 2022; and a news article discussing it, "See No Bias, Hear No Bias, Speak for No Change" by Katherine Wright, Physics, 16, 33, 2023;

• "Why Everyone Feels Like They’re Faking It" by Leslie Jamison, The New Yorker, February 6, 2023;

• "Values Are More Than Statements: Connecting Actions to Values to Build Inclusive Cultures in Chemistry Research Groups", by Pallai, Hoffman, and Schlau-Cohen, J. Chem. Ed. 2024;

• "A framework for understanding effective allyship", by Pietri et al., Nature Reviews Psychology, 3, 686–700, 2024;

Specific to Doctoral Education:

• "Program Elements’ Impact on Chemistry Doctoral Students’ Professional Development: A Longitudinal Study" by Busby and Harshman, Chem. Ed. Res. Practice., 2023;

• "The Influence of Challenge Research Stressors on Research Creativity Among Chinese Doctoral Students: A Mediated Moderation Model" by Liu, Wu, and Gao, Frontiers in Psychology, 2023;

• "Abuse and Exploitation of Doctoral Students: A Conceptual Model for Traversing a Long and Winding Road to Academia" by Cohen and Baruch, J. Business Ethics, 2021;

How to research?

How does one learn how to conduct research? It has been a sum of lived experiences, pursued passions, interactions with teachers, mentors, and collaborators, observations of role models from close and afar, memorized bits and pieces of wisdom, and experiences of others shared through the books and articles here and there. Nevertheless, the mind seeks a structured narration that captures that experience, reminds, and guides through the surrounding noise and information. No single resource captures all of the aspects of how to research, but the ones that have been most helpful from my experience are listed below.

• "The Effective, Efficient Professor: Teaching Scholarship and Service" by Philip C. Wankat, 2002;

• "An Introduction to Scientific Research" by E. Bright Wilson, 1952; 

• "The Art of Doing Science and Engineering: Learning to Learn" by Richard C. Hamming, 1997; (Also see: "You and Your Research" - a seminar given by Hamming at Bell Communications Research Colloquia Series, on March 7, 1986);

• "How to become a successful physicist" by Carl Wieman, Physics Today, 2022;

• "Where Research Begins" by Thomas S. Mullaney and Christopher Rea, 2022;

• "The Burden of Disproof" by Susannah L. Scott, ACS Catalysis, 9, 5, 4706-4708, 2019;

• "To Err is Human; To Reproduce Takes Time" by Susannah L. Scott et al., ACS Catalysis, 12, 6, 3644-3650, 2022;

• "Report on Reproducibility in Condensed Matter Physics", by Akrap et al., arXiv, [2501.18631], 2025;

• ... and a corresponding documentary, "Reproducibility in Condensed Matter Physics" on YouTube;

Environmental Health and Safety

• ECHA Guidance on the compilation of safety data sheets (December 16, 2020);

• "Hydrazine and Aqueous Hydrazine Solutions: Evaluating Safety in Chemical Processes" by Niemeier and Kjell, Org. Process Res. Dev., 17, 12, 1580–1590, 2013;

• "Current best practices for handling inorganic nanoparticle waste in a laboratory setting" by Mattox et al., JSM Chemistry, 5, 2, 1045, 2017; (Open Access)

• "Impact of Source Position and Obstructions on Fume Hood Releases" by Mattox et al., Annals of Work Exposures and Health, 63, 8, 937-949; 2019;

• "A review and critique of academic lab safety research" by Ménard and Trant, Nat. Chem., 12, 1, 17-25, 2020;

• "Safe Handling of Cannulas and Needles in Chemistry Laboratories" by Chandra, Zebrowski, Lenertz, ACS Chem. Health Saf., 29, 2, 175–183, 2022; 

• "How Dangerous Is Too Dangerous? A Perspective on Azide Chemistry" by Treitler and Leung, J. Org. Chem., 87, 17, 11293-11295, 2022; (Free to read)

• "Insights from a laboratory fire" by Jones et al., Nat. Chem., 15, 7, 885-889, 2023;

• "Hidden Perils of Lead in the Lab: Guidelines for Containing, Monitoring, and Decontaminating Lead in the Context of Perovskite Research" by Salvador, Motter, and McCulloch, Chem. Mater., 32, 17, 7141-7149, 2020;

Science in Sweden

• Book: A Beginner's Guide to Swedish Academia (September 2022);

Experimental techniques

• All You Wanted to Know about Nuclear Magnetic Resonance Spectroscopy (and more) - Prof. Hans J. Reich (1943-2020) Collection;

• The Schlenk Line Survival Guide by Dr. Andryj Borys (@AndryjBorys); see also "An Illustrated Guide to Schlenk Line Techniques" by A. M. Borys, Organometallics, 42, 3, 182–196, 2023 (Open Access);

• GISAXS guide and tutorials on grazing incidence diffraction by Dr. Detlef-M. Smilgies. Thoroughly referenced materials with a lot of examples;

• Best Practices for Using Microscopy Data in Manuscripts: From Pretty Pictures to Scientific Evidence, an editorial by Sara Bals at al., ACS Nano, 18, 21, 13453-13457, 2024; 

Software

• ImageJ and/or Fiji (I use it for analysis of transmission electron microscopy images of nanoparticles. For the description of the "thresholding method" of size determination using ImageJ see paper 1, and for the detailed examination of the method see paper 2 (open access));

• Feedly (RSS feed reader, I use it to keep up with the latest published articles in ACS, RSC, Wiley, etc.);

• MagicPlot (affordable alternative to OriginLab, thanks to Mike Brennan for pointing it out);

• WebPlotDigitizer (a tool to extract numerical data from the images of plots, thanks to Mike Brennan for pointing it out);

• EndNote (been using this reference manager since undergrad, it's not free but worth investment if you write your manuscripts and proposals in MS Word);

• NotePad++ (extremely versatile notepad software);

• Grammarly (As a non-native English speaker I find this software indispensable for proof-reading of the written text);

• UltraSearch by JamSoftware (to quickly find anything on your PC);

• Spectragryph software for opening spectra in manufacturer's file formats (e.g., *.dsw from Cary spectrometers, *.fs from Edinburgh Instruments, and so on), their motto "Free your spectral data from the spectrometer system. View & work your data wherever you want.";

• ProfilmOnline is a web-based application for surface imaging and analysis. The application supports a large variety of file formats from different profilometers and instruments and is straightforward to use.

• PowDLL a program for interconversion between various formats of powder X-ray diffraction data files.

Writing

• "The Craft of Science Writing" edited by Siri Carpenter, is a collection of very engaging pieces of scientific journalism and how to write about science;

• "Academic English: Writing" on Coursera is an online course from the University of California Irvine. I took parts of it when I was writing my Ph.D. thesis and can recommend it to anyone wanting to improve their writing skills;

• "Grammarly" is an indispensable proof-reading service;

• Regarding writing and publishing scientific papers, many good editorials appear from time to time across publishers and journals. Some that caught my attention and which I found reflective, fully or in part, of my experience as an author are listed here:

  • • "Beating the odds for journal acceptance" by Warren Warren, Sci. Adv. 2022;

    • "Increase Your Impact: Writing Tips to Reach a Broader Audience" by Ray Schaak, ACS Nanoscience Au 2022;

    • "Judging a manuscript by its cover (letter)" by Steve Cranford, Matter 2021;

    • "Revising Manuscripts: Trying to Make Everyone Happy" by Anastassia Alexandrova and Greg Hartland, J. Phys. Chem. C 2021;

• "Hype kills your story" editorial, Nat. Nanotech., 19, 715, 2024; (Note: Ironically, the editorial is written in a hyped style);

• Coursera free online courses on writing in English:

  • •  "Getting Started with Essay Writing" (University of California, Irvine), is an excellent and very practical introduction to different types of essays, that are essential building blocks for more complex writings in research.

    • "Writing in English at University" (Lund University), is a more comprehensive course about writing, summarized in a free e-textbook.

Proposal-writing

• How to Write a Competitive MSCA IF Proposal (pdf slides by Dr. Juliane Sauer, OxygenEUm);

• Survivor's Guide to MSCA-IF (by Net4Mobility+); 

• My (successful) ERC Starting Grant Proposal by Sylvain Deville;

• Another example of successful ERC Starting Grant Proposal by Franco Vazza;

• Marie Curie Fellows Network (a Facebook group for connecting with other MSCA fellows and applicants for sharing questions and discussions about anything related to MSCA);

Presentations

Arguably, presenting the results of one's work is one of the most important parts of being a scientist. Clear and effective communication is essential if you aim to convince an audience (generally speaking) of the value of what you do as well as of yourself. Given how much time, effort, and passion the scientists put into their work that is virtually hidden, it is only logical that presentation should get serious attention, thought, and preparation. 

• "The Craft of Scientific Presentations: Critical Steps to Succeed and Critical Errors to Avoid" by Michael Alley, 2013;

• "Ted Talks: The Official TED Guide to Public Speaking" by Chris Anderson, 2016. This book is great because it stimulates one to think about their presentation on a high level (and it contains a pretty good chapter with technical tips). That is a level where you reflect on the broader meaning and significance of what you are working to present.

• "Promote of perish" an editorial by Steve Cranford, Matter, 2022;

Databases

• AIST Spectral Database for Organic Compounds;

• Molecular Parameters of Carbon Compounds (and much more at Wired Chemist);

Applets

• Energy Unit Conversion (Halas Nanophotonics Group at RiceU);

• Chemistry Reference Resolver (by Alex Zhurakovskyi);

• ChemCalc (molecular formula/mass calculation for mass-spectroscopy); 

Website-building

Personal webpage is a replacement for a paper business card. I encourage every early career researcher (the earlier, the better) to maintain a website. Make it into a single destination for anyone interested in your research and profile (for example, it could be someone looking for a postdoc or a faculty candidate, or a member of interviewing/recruiting committee). The website will also serve as a funnel once you place a link to it across various academic/professional social media (Google Scholar, ORCID, LinkedIn, etc.). For the content, consider an updated CV/resume, list of publications, description of completed/ongoing projects, teaching, outreach activities, science communication blog, recorded presentations, samples of the code, etc.

• Build-your-own website for scientists (11 May 2020, NatureIndex.com);

• Use your lab website to make a compelling first impression (4 May 2020, Nature);

• 27 Examples of Google Sites Websites;

• Inspiring examples of other scientists' websites: Vida Jamali, Stuart Cantrill, Devleena Samanta, Sylvain Deville, Kuno Group;

• Google Domains;

Open access

• "Open Access" by Peter Suber;

• SherpaRomeo, an online resource aggregating publishers' open access policies;

• How Can I Share it? a helpful resource to check by DOI what sharing options are available for a paper;

Crystallography and structure

• "Crystallography: A Very Short Introduction" by Mike Glazer. An informative and entertaining combination of historical account and a crash course.

• "Resources for Crystallographic Education" from the International Union of Crystallography;

• "Lattice versus structure, dimensionality versus periodicity: a crystallographic Babel?" by Massimo Nespolo, J. Appl. Cryst. 2019, 52, 451-456 (Open Access). An article on the correct use of crystallographic terminology in scientific writing, e.g., lattice vs. structure.

• "What Defines a Perovskite?" by Joachim Breternitz and Susan Schorr, Adv. Energy Mater. 2018, 8, 1802366 (Open Access);

• "What Defines a Halide Perovskite?" by Quinten Akkerman and Liberato Manna, ACS Energy Lett. 2020, 5, 604–610 (Open Access);

• "The Scherrer equation versus the 'Debye-Scherrer equation'" by Uwe Holzwarth and Neil Gibson, Nature Nanotech. 2011, 6, 534;

Physics (classical, quantum)

Various interesting and useful resources about the physics of the world around us:

• Music Acoustics, Physics at The University of New South Wales, Australia;

• "Introduction to Quantum Computing for Business" by Koen Groenland (online, Open Access);

• "A free introduction to quantum computing and quantum mechanics" by Andy Matuschak and Michael Nielsen;

Online seminar series

A non-exhaustive list of regular chemistry/nano-related webinars to sustain independent learning:

• https://researchseminars.org/ - constantly updating database of online events across all disciplines;

• News in Nanocrystals (https://nincseminar.wixsite.com/news-in-nanocrystals);

• JAWS (Just Another (Chemistry) Webinar Series, https://jawschem.wixsite.com/home);

• VISTA (Virtual International Seminar on Theoretical Advancements, https://quantum-dynamics-hub.github.io/VISTA/);

• MIT Nano Explorations (https://mitnano.mit.edu/nano-explorations);

• MIT.Nano (https://mitnano.mit.edu/mitnano-seminar-series);

• ACS Physical Chemistry Seminar Series (https://acsphys.wordpress.com/);

• Initiative for Theoretical Sciences (https://itsatcuny.org/, bunch of events on excitons, self-assembly, etc.);

• Coherent Multidimensional Spectroscopy (https://www.cmdsonline.org/);

• Global Inorganic Discussion Weekdays (https://www.cheminst.ca/cic-virtual/seminar-series/gidw/);

• Extreme Mechanics Letters (EML) Seminars, https://twitter.com/EmlWebinar & YouTube playlist;

• Atomic Scale Quantum Materials Colloquium (https://asqm-colloquium.aalto.fi/);

Motivation and resilience

A partial list of resources that I turn to for inspiration and grit.

• "Patience and time are my warriors, my champions," thought Kutuzov. (War and Peace by Leo Tolstoy; Volume 4 in its entirety, or Chapters 16 and 17 for the value of patience and time);

• "Failing to prepare is preparing to fail." - Ed Bradley discusses putting together a "60 Minutes" segment;  

• "Accept all things, deliver excellence now, and never quit, you can win it in the late innings." - Robert Forster recalls getting a part of Max Cherry in Quentin Tarantino's "Jackie Brown";

• "Getting Things Done: The Art of Stress-free Productivity" a book by David Allen (TED talk);

• "Grit: Why Passion and Resilience are The Secrets to Success" a book by Angela Duckworth (TED talk);

• "Leave NO Doubt: A Credo for Chasing Your Dreams" a book by a hockey coach Mike Babcock with Rick Larsen;

• "The only way is through" (as heard from a very resilient friend);

• "There is no spoon" - a clip from The Matrix that helps to fight deadlines;

• "Since our problems have been our creations, they also can be overcome" - from a song by George Harrison "This is Love";