Special Issue Preface pubs.acs.org/JPCB
Tribute to J. Andrew McCammon Andy also published the Ermak−McCammon algorithm in 1978. This algorithm is still widely used today for simulating the Brownian motions of biological molecules. Particularly noteworthy is its earlier applications to studying efficient enzymes that operate at diffusion-controlled rates. His research group developed the popular University of Houston Brownian Dynamics simulation program (UHBD) for these applications. Over the years, UHBD has evolved to become even more versatile, allowing it to explore the electrostatics of biomolecules and to calculate the pKa’s of amino acids inside proteins. This program, as well as other software packages developed in his laboratory, has been distributed freely to academic researchers around the world. Andy has maintained a deep interest in understanding the elements of molecular recognition at the atomic level, and he subsequently developed a rigorous computational method for determining free energies of binding between a ligand and a protein. This technique, called free energy perturbation or alchemical transformation, is still considered the gold standard for rigorously determining molecular recognition events. Applications of this method are routinely used in computeraided drug design and other studies of complex biophysical phenomena, and are undergoing a renaissance as methodological and computational innovations are now enabling broad application of this technique. Over the course of his remarkable career, Andy has tirelessly mentored over 70 graduate students, over 120 postdoctoral fellows, and dozens of undergraduate students and sabbatical visitors. Over 50 of his former students hold tenure or tenuretrack faculty positions at leading universities and research institutes, with many others making significant contributions to the pharmaceutical and other industries. As an example of Andy’s mentoring, during a group meeting in the late 1980s, he handed out a document titled “Practical Hints for Success in Science.” The list included the following: • Become an Expert in Something: Master at least one widely applicable technique, and preferably two different techniques. • Pick Interesting Research Topics: Your research problems should be ones you are really dying to know the answers to. They should also be something that any other scientist would be interested in. • Work on Something You Can Do: Your main project at any given time should be one that is well-defined and that is solvable within 6 months. • Work Hard: Work not less than 60 h per week and not more than 80 h per week. Plan to do this through graduate school, postdoctoral study, and at least your first ten years in a permanent position.
Photograph taken by Paul Fetters
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he Joseph E. Mayer Chair of Theoretical Chemistry and a Distinguished Professor of Pharmacology at the University of California, San Diego, a Howard Hughes Medical Investigator, a member of the National Academy of Sciences, elected fellow of the American Association for the Advancement of Science, the Biophysical Society, and the American Academy of Arts and Sciences are only some of Professor J. Andrew McCammon’s recognitions during his career as a scientist. This festschrift celebrates some of his scientific and career achievements, which includes over 700 publications. In the late 1970s, Andy pioneered the application of molecular dynamics to study protein dynamics. This work was presented in a series of seminal articles, two of which were published in Nature in 1977 (“Dynamics of Folded Proteins”, “Internal Motions of Antibody Molecules”) and the third in Nature in 1979 (“Protein Structural Fluctuations during a Period of 100 ps”). The number of papers published in the area of (bio)molecular dynamics has exploded exponentially over the past four decades since these landmark accomplishments. Modern applications of molecular dynamics include numerous studies of protein−ligand recognition, the refinement of biomolecular structures, understanding of the selective passage of ions through biological channels, assistance in drug design, uncovering of the folding mechanisms of proteins, and the decoding of the inner workings of biomolecular motors. © 2016 American Chemical Society
Special Issue: J. Andrew McCammon Festschrift Published: August 25, 2016 8055
DOI: 10.1021/acs.jpcb.6b07015 J. Phys. Chem. B 2016, 120, 8055−8056
Special Issue Preface
The Journal of Physical Chemistry B • Read: One half of your time (30−40 h per week) should be spent reading. Half of your reading should be immediately related to your current research; the other half should be potentially related to your current or future research. You should always be reading one textbook or monograph, and you should look at each issue of key journals and serials. Know how to read journals to extract the most useful information in the least time. • Write: One half of your time (30−40 h per week) should be spent conducting research. Plan your research from the outset using an outline of the article you hope to write. You need to write at least two really good papers per year, starting in the latter part of your graduate work. Learn to write well. Use an outline, and be complete and concise. In planning the introduction to a paper, imagine that you are presenting the material in a lecture. For style questions, consult Strunk & White. • Speak: Take advantage of opportunities to give lectures about your research. Preparing a talk helps you to review what you are doing, why you are doing it, and what you still need to do. In lecturing, look at the audience, not at the board or screen. Pretend you are talking to someone in the back row, which will help you speak loudly enough. Use more colorful pictures and fewer messy equations on your slides. • Manage Your Time: Set daily, weekly, and long-term goals. Review your goals and progress frequently. If you are consistently falling short of your goals, try keeping track of how you actually spend your time for a few days. Use this inventory to help plan adjustments. Know when to be meticulous and when you can be sloppy. If you are banging your head against an obstacle in your research, step back, rethink the problem, and try to go around the obstacle instead of through it. • Hoard Ideas: Whenever you have an idea for a possible research project, write it down immediately and save it in your Ideas Notebook. Review your ideas occasionally. Move the best ones to the front of your notebook and keep developing them. • Consult Other Experts: When you run into a technical problem that is peripheral to your main research goal, consult someone who is an expert in that area instead of spending weeks trying to find and absorb all the relevant literature. • Be Intensely Interested in Your Work: If you are not consumed by interest in your research project, pick another project. If you are not consumed by interest in some project, pick another career. • Work on Two Different Projects at the Same Time • Be Ambitious and Reasonably Aggressive • Be Persistent Andy received a bachelor degree from Pomona College. He started his graduate work with Professor John Deutsch of MIT before working with Martin Karplus (Nobel laureate 2013) at Harvard University. Ready to start at Harvard, Andy sketched a plan on what he would do (the original note was unearthed by Peter Langhoff from an old book in Andy’s library in early 2016):
Although many of his students, especially the younger ones, do not know whether he had done all these things during his graduate career at Harvard University, few would doubt that he studied theoretical chemistry very hard and biochemistry very hard during his time as a graduate student. As an Advisor, Andy has also worked very hard and has challenged his students and postdocs to work very hard. Most of us will also not be surprised to see item “0.5” in this sketch, “be responsible”. Andy has been a model of responsibility and good citizenship, showing trustworthiness, respect, fairness, and caring to all who work with him. Indeed, Andy’s rare combination of unmatched character with exceptional scientif ic achievement cements his standing among the very best scientists of his generation. Thank you, Andy, for serving as such a bright and shining inspiration to us all.
Rommie E. Amaro Jeffry D. Madura Chung F. Wong
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DOI: 10.1021/acs.jpcb.6b07015 J. Phys. Chem. B 2016, 120, 8055−8056
