Mar
10
2014
0

OpenGL, Nvidia, and Linux

Just solved a nasty headache with an Nvidia board. Cuda, openGL and various programs didn’t work together. All the drivers were current and correct.

The motherboard had an onboard Intel chip. Check the bios and make sure the correct graphics card in the correct mode is enabled. (there were two settings that used the Nvidia card only one was correc!)

Written by Rob in: Uncategorized |
Feb
27
2014
0

Another prepublication draft

https://www.createspace.com/Preview/1143412

Not quite the latest version, but very nearly.

Written by Rob in: Uncategorized |
Feb
09
2014
0

Lessons for self-publishing.

I’ve learned a few things about self-publishing the hard way – so I’ll pass them on and hopefully save someone else a headache

  1. Use a search engine to check your title.  My book “new southern vampire” has nothing to do with the “southern vampire” series (only found out about it recently – which is not an excuse for a similar title). They are quite different, but it looks like a cheap attempt at a knock off. Wonder if it’s hard to change titles?
  2. Check to see what are similar books for choosing the book classification.
  3. Page numbers.  This may seem silly but page numbers aren’t generated by the create space book printing engine.  Either you put them there or there aren’t any.  While you’re at it, adjust their template to make the book look more professional. At a minimum play with the paragraph splitting controls to avoid big blank spaces. You should also probably use the text alignment settings to fill paragraphs so that there isn’t a ragged edge.
  4. Proof read. Proof read, Proof read.

Anyway hope this is helpful.

 

Jan
29
2013
0

Never let a Statistician Drive

Coming back from a trip to Oak Ridge Tennessee to see the neutron facilities. (which are decidedly impressive).

Then Tennessee highway patrol had signs up that said 23% of all traffic fatalities involved speeding.   Therefore 77% did not.  So you’re three times safer speeding than not.

Similarly 27% involved drunk driving. Again you’re almost 3 times safer driving drunk than sober.

Combining them, assuming independence, gets (1-0.23)*(1-0.27) = 0.56 or 56%.  So you are even slightly better off speeding and/or driving drunk than being sober and following the speed limit.

(please don’t drive drunk and fast).

Written by Rob in: Uncategorized |
Jul
20
2012
0

Freezing Computational Water

One of the harder things to do in computational chemistry is to model phase changes. Theoretically it is almost impossible as one needs very large scale (infinite) calculations to account for putative large-scale fluctuations. None the less it is a fun problem.

I took 1000 waters, using molecular dynamics constant volume and temperature in the AMMP program, and the tuna potential set (”tuna” refers to the name of the program used to adjust parameters to fit independent data, the potential is similar to the SPC water potential and reproduces radial distributions etc quite well). The goal is to look at pair correlation times as a function of temperature. The pair correlation time (how long two different molecules are close together) should be very long for ice and rather shorter for water.

As a start, though, I looked at the energy of the system. There were no surprises with the total energy which increased more or less linearly with temperature. However, the standard deviations were different, Since Cv, the constant volume heat capacity, is related to the standard deviation of the energy (Cv = c (sigma/T)^2 ) I rescaled the data by the absolute temperature squared and plotted that.

There is a dip around 250-275K! which is just the right place.
Estimated Cv

More detailed, with more time and more temperature values, simulations around the putative phase change are shown below.
Cv calcualted on a longer run and with more temperatures

Cv calcualted on a longer run and with more temperatures

So it looks like it might work.

Written by Rob in: Uncategorized |
Oct
28
2009
0

Some Professional Stuff

I generally don’t discuss my scientific work in detail on this blog because

  1. The proper place for it is the reviewed literature
  2. I don’t want to scoop myself or my collaborators

That said, it is worth giving a link so you can see what we do here.

Pubmed makes this easy. Hitting this link should show most of my more than 200 publications on areas ranging from bioinformatics to molecular design and HIV. My apologies to the occasional other Harrison, RW (actually several – I have a common name) that it grabs.

Written by Rob in: Uncategorized |
Aug
28
2009
0

Bittersweet Smell

It’s raining hard in Atlanta, and finally cold enough to get out the raingear.  It smells of pine/arborvitae smoke from this summer in Canada.  I miss it.

Written by Rob in: Uncategorized |
Jan
04
2009
0

More Lake Weiss Trilobites

I had a chance to find more trilobite fossils this weekend, and unlike before they were not just impressions, but the whole critter.
a trilobite
The picture below shows a very small fossil that was already loose from wave action.
a trilobite
Looking at the local rocks and their layering suggests an explanation for the spotty distribution of fossils. When the mudstone was laid down in the Cambrian the area was a wide tidal mud flat. Much like the area around Tybee Island
Tybee beach(but not as sandy and NO trees) or the mudflats near the Severn river or the Gower pennisula.
Severn Mudflats
Mud flats are not really flat, but tend to have little pockets where biological detritus collects.
a horseshoe crab These pockets become hotspots for fossil collection when covered with silt by tidal floods. There are occasional quasi-stable areas and these can also support a colony of animals that is subject to being covered in a local flood event and we have found a few dense patches of Crinoid stems – including one with a trilobite in it that I don’t have a picture of (yet). Shallow water above mud flats is a great location for small crustaceans and various small mollusc’s which is just what we find in the fossil evidence. Some of them were just unlucky (or lucky – it depends on your viewpoint) to get caught in a small pool at low tide and have their remains preserved for us.

One of the stronger pieces of evidence that this was an estuarine environment comes from about 100-1000 layers above the fossil rich layer(if each major layer in the mudstone reflects a season – then maybe only about 1000 years later) the river shifted and deposited a layer of gravel on top of the mudstone. There is a continuous shift in the color of the sediment from a dark gray – where the fossils are found to a lighter gray or tan and we don’t see visual evidence of a discontinuity event. It looks just like a gravel bank deposited on the side of a river. In some ways it is a pity that it is so old -because it would be a great place to look for land animal fossils – just that there aren’t any from the Cambrian.

Written by Rob in: outdoors,science,Uncategorized,Wildlife |
Dec
20
2008
0

Let’s hope he “walks the talk”

From a recent speech by our president-elect:

Whether it’s the science to slow global warming; the technology to protect our troops and confront bioterror and weapons of mass destruction; the research to find life-saving cures; or the innovations to remake our industries and create twenty-first century jobs – today, more than ever before, science holds the key to our survival as a planet and our security and prosperity as a nation.  It’s time we once again put science at the top of our agenda and worked to restore America’s place as the world leader in science and technology.

Right now, in labs, classrooms and companies across America, our leading minds are hard at work chasing the next big idea, on the cusp of breakthroughs that could revolutionize our lives.  But history tells us that they can’t do it alone.  From landing on the moon, to sequencing the human genome, to inventing the Internet, America has been the first to cross that new frontier because we had leaders who paved the way: leaders like President Kennedy, who inspired us to push the boundaries of the known world and achieve the impossible; leaders who not only invested in our scientists, but who respected the integrity of the scientific process.

Because the truth is that promoting science isn’t just about providing resources – it’s about protecting free and open inquiry.  It’s about ensuring that facts and evidence are never twisted or obscured by politics or ideology.  It’s about listening to what our scientists have to say, even when it’s inconvenient – especially when it’s inconvenient. Because the highest purpose of science is the search for knowledge, truth and a greater understanding of the world around us.

I heard part of this speech this morning, and the parts I’ve emphasized are why we scientists do it. It is very rare that I am moved by what any politician says, but these statements so clearly express the ideals of science that is is hard not to be moved. This is the ethos that I try to instill in my students.  It is a succinct and clear statement of the hypothesis that underlies the entire scientific revolution – from the 1600′s to the 2000′s – namely that by understanding the world we can make life better for those who inhabit it.

Written by Rob in: Uncategorized |
Dec
17
2008
0

more on casp

Part of the reason for my recent hiatus at writing entries is a combination of attending meetings and finishing up with semester business.  Anyway, I have some interesting results from casp-8.

  1. We did pretty well on the targets where there was one good template and we found it.  (by some measures we were #1 and #2 on a couple of targets).  This is good because high-quality molecular mechanics is a major research focus for my group.  Our potential probably slightly enlarges protein models and one of the “tricks of casp” is to compress your model.
  2. Our server was not designed to handle many simultaneous hits and one of the neat features of profile-profile methods is the number of homologs that they can fish out.  Usually if it finds one, it finds 20.  The problem is which combination of these 20 is the best model.
  3. It is critical to keep the profiles up to date.  Psi-blast has its problems and one of them is non-stationarity.  If you run on different databases then you get radically different profiles – and with updates over time the profiles sort of “rot”.   (Its other problems include some rather poor software engineering and a context dependence).  It doesn’t run in my hands with the non-redundant database (nr) but does work much better with the refseq_protein database.  This caused a number of problems where we missed the best profiles.  ARRGH!
  4. It is probably a good idea to move from a single geometric measure (gdt and related variations) to explaining the data.  For NMR this means can your model reproduce the NOE’s and backbone restraints used to produce the “structure”.  For crystallography, it is probably good to ask what is the height of the cross-rotation function.  I’m debating building a server for this.  There are more than one group that does very well by having trained their method to generate models with poor geometry (useless models) that generate good scores on the geometric measures.  Forcing evaluation against data would fix this issue as well as be statistically and mathematically the best measure.  – you can argue about measures but you can’t argue against data.
Written by Rob in: Uncategorized |

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