Being near the end of my graduate studies, I’ve starting looking at the jobs that other people have a little more critically. Whereas I used to think in terms of “oh, that’s interesting,” I now find myself wondering “am I qualified to do that?” More often than not, the answer is “no,” and my prospects have had me feeling quite depressed as of late. I’ll have spent five full years in graduate school by the time I get my Ph.D., but aside from the letters after my name, what have I really gotten out of it aside from debt?
Let’s take inventory of the qualifications I have developed.
Computational Research Qualifications
|general molecular simulation||intermediate||I’ve spent the better part of a decade doing MD simulations. I know quite a bit about them, but that means I know enough to realize how much I don’t know.|
|electronegativity equalization||intermediate/high||I understand how EEM works, which is to say I realize how much nonsense it is as a semi-empirical theory. I spent a year developing a new EEM-based model and hated every minute of it.|
|potential development||intermediate/high||I can tune and develop potentials, but this work is extremely tedious and decidedly un-fun|
|algorithms||intermediate||I know the basic integrators but don’t fully understand any of the more technical methods (e.g., Nosé-Hoover, Parrinello-Rahman, SHAKE/RATTLE, Ewald, etc). I can write a fully functional MD code using basic algorithms (e.g, velocity rescaling, Verlet, and the Berendsen barostat) but have difficulty implementing extended-system-based algorithms.|
|commercial MD simulation packages||low||I’ve never used any off-the-shelf simulation packages other than LAMMPS and GULP. Even then, I have not used either very extensively. My group has always used its own code.|
|bio/pharma molecular sim||low||I know next to nothing about protein folding, docking, bio-centric models (CHARMM, etc), bonded interactions, SHAKE, etc.|
|quantum simulation||low||I know virtually nothing about quantum calculations. I don’t have any understanding of basis sets, dispersion forces, DFT, Møller-Plesset, path integral, Car-Parrinello, etc.|
|continuum simulation||low||I know nothing about phase-field methods, finite element/finite difference, etc.|
Other Research Qualifications
|data analysis||high||I have a strong grasp of many computational tools useful in efficiently analyzing large data sets and correlating data, and I am quite good at leveraging those tools to extract meaningful data and complex relationships. Some of the tools that I regularly use are Perl, Python, Maple, Mathematica, sh, and awk.|
|technical writing||intermediate/high||I have a strong grasp of the English language and can put together sensible manuscripts handily. Of my three first-author papers published to date, none have ever come back from peer review requiring any major revisions. Roughly 80-90% of the written text in these manuscripts was in my words.|
|technical presentation||intermediate||I’m not a bad speaker and can assemble presentations that follow a logical path. I design presentations for specific audiences that aren’t overbearingly technical but at the same time not superficial. I’ve won a poster award and spoken at several international conferences.|
|laboratory work||none/low||I’m not very good with my hands, which is why I’ve stayed out of experimental labs. I know lab safety but am afraid of dangerous machinery (machine shops, furnaces) and chemicals (highly caustic, toxic, etc) due to lack of experience.|
|ceramics||intermediate/high||I know about ceramics, crystal structures, point defects, grain boundaries, processing, microstructure, etc. I don’t know much about specific technical ceramics|
|glasses||intermediate/high||I know a lot about silica. As you introduce additives and exotic processing, my level of knowledge drops. I know about its atomic structure, general properties, and mechanical behavior. I know less about specific modern silicates (mesoporous, etc)|
|physics (general)||intermediate/high||I have a pretty strong understanding of general physics and why things happen. I’ve also got an aptitude for solving analytical problems. I could teach undergraduate-level physics pretty adeptly.|
|physics (mechanics)||low/intermediate||I know enough to know that I don’t know very much. I do not have a strong background in Lagrangian/Hamiltonian formalisms (which is to say nobody has ever taught me of their existence). I am self-teaching this stuff though.|
|physics (quantum)||low||I know the basics, but I haven’t solved a differential equation in half a decade. I have no real experience working in modern physics outside of a classroom.|
|physics (thermo/stat mech)||intermediate||I’ve taken thermodynamics three or four times and have a fair grasp of it. My limited knowledge of mathematics prevents me from fully grasping more complicated formalisms (e.g., n-dimensional space)|
|physics (chemical)||intermediate||I’m familiar with many chemico-physical processes, reaction pathways, energetics, etc.|
|architecture||intermediate/high||I have a reasonably good understanding of what makes computers fast. I understand memory and cache layouts, pipelining, SIMD/vectorization, bandwidth, data locality, out-of-order execution, registers, and how to program efficiently with these features in mind. I do not know x86 assembly.|
|programming||intermediate/high||I have a good sense of proper programming, program structure, and good practices. I have years of experience in C, Fortran 77, Perl, and bash/sh. I have some experience with Python, awk, C++, and Fortran 90.|
|SMP parallel programming||low/intermediate||I am reasonably comfortable with OpenMP. I have basic familiarity with pthreads. I have never applied either of these to a real project.|
|distributed parallel programming||low/intermediate||I am familiar with MPI, but I have not used it very extensively. I am familiar with the concepts and considerations of distributed computing. I have no experience in fault tolerance or large scaling.|
|GPGPU programming||low||I am familiar with the basics of CUDA. I can write basic kernels, but have no experience using CUDA for research.|
|Linux administration||intermediate||I run a few general-purpose Linux servers. I am comfortable compiling from source (e.g., Apache, PHP), implementing basic security measures (firewalls, quotas, IDS), managing user accounts, working with LVM, etc. I do not have much experience with SAN, clustered systems, advanced networking, automatic deployment, PXE, virtualization, packaging, etc.|
|UNIX administration||intermediate||I’ve run a lot of Solaris servers and am comfortable with Solaris 10′s way of doing things. I am experienced with Sun hardware, ZFS, and general administration. I am unfamiliar with the details of SMF and dtrace. I have intermediate familiarity with HP-UX 11i, IRIX 6.5, and AIX 5.|
|cluster administration||low/intermediate||I use clusters and can configure a basic one, but I lack experience in diskless nodes, infiniband, low-level tuning|
|hardware||intermediate/high||I have a lot of experience debugging hardware ranging from workstations to enterprise devices. I have advised purchasing decisions on cluster hardware, assembled clusters, performed upgrades and troubleshooting, and inventory management.|
Granted, the fact that I listed some things as having low qualifications still means I’m probably more qualified than the average Joe off the street who doesn’t even know such things exist. Furthermore, the fact that I’ve listed it means that I know it’s a shortfall and am willing to bone up on that skill if given the time and opportunity.
With that being said, where do my qualifications leave me? I’m more equipped to do molecular simulation than most other researchers since I have intimate knowledge of simulation code, algorithms, and theory, but I also know that there’s a lot of the detail I don’t understand. Do most graduate students know this sort of stuff by the time they finish? My postdoc coworker wrote a Nosé-Hoover + Parrinello-Rahman thermostat-barostat integrator routine for our group’s simulation code back when he was a graduate student. I’m almost done with my degree and I really have no idea how to do this. Granted, his undergraduate degree was in physics while mine was in “ceramic engineering.”
This sort of thing makes me feel like my education is holding me back. I know very few simulations people who are in materials science. The vast majority of molecular modelers are
- in physics and understand the things I wish I understood (e.g., the statistical mechanical implications of various modifications to the Lagrangian)
- in chemistry and also understand things I wish I understood (e.g., potentials of mean force, free energy of reactions, quantum chemical aspects)
- in biology, and understand ??? (I suspect the bio people are using black-box code and don’t really understand or care about the nitty gritty)
I went to graduate school so I wouldn’t have to get silicosis in some batch house or rebuild furnaces for a living, but I’m just not seeing where to go from here. I could slide into a vanilla post doc position and spend the next 2-6 years of my life bouncing around between short-term appointments, pumping out papers about obscure scientific problems about which nobody cares, and floating around technical conferences I hate attending. That’s a miserable existence, but it seems like it’s the one for which I am most qualified.
Contrary to my thoughts going into this business, professional science isn’t all that great. There are a few superstar scientists who make clear and evident breakthroughs, and that’s really exciting. But the majority of scientific progress is in painfully slow, small baby steps. Publications address some tiny facet of some tiny problems that only a tiny group of other scientists care about, and even then, they rarely stand on their own. Nobody will believe it unless there are enough of these tiny findings that don’t contradict each other that pile up.
And when that happens?
There’s still only a dozen people on the planet who care.
There’s no real rewarding fulfillment that comes with publishing these obscure results. Even to the layperson, it’s not like curing cancer. Nobody really benefits from most of the science that gets published today. As I often tell people, being a janitor would be more fulfilling to me. At least in that case, I’d be able to go home at night knowing that I made the toilets cleaner than they were when I started the day.