I'm in a statistical mechanics class this semester, and we have a final project to do. The final project consists of running at least two different stat. mech. simulation types to study some observable properties of a particular chemical species. My group decided to simulate benzene across different pressures and temperature to study phase-change phenomena, amongst other variables.[1] [2]
We're going to run a Monte-Carlo caluclation in a yet-to-be-determined staistical ensemble and molecular dynamics simulation in a microconanical ensemble. [3] If time permits, I want to do a potential of mean force calculation. Aside from phase change phenomena, I want to also study the heat capacity, chemical potential, free energy, viral coefficiant, pair radial distribution function, time-correlation function, and the diffusion constant. [4]
All simluations will hopefully be ran on the supercomputers at LSU. If not, I'll dedicate my desktop's computing powers to the project. [5]
Now, someone give me more time to do this project, because it's due around the same time as my other projects :\
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[1] This group is different than the group for the analytic project.
[2] Benzene is "big enough" to seem complicated, but "simple enough" in the calculations due to some approximations.
[3] My group can't come to a consensus of Gibbs ensemble versus canonical. I have a previously developed binary for the Gibbs model, so I want to use it (I used it to study orthoterphenyl with benzene impurities in a range of temperatures including the temperature of glass-formation). They want the canonical because it's easier for them to understand it >.<
[4] From previous research, I have or have found code that calculates each from the Gibbs model and/or from the output of PLINY_MD. Another reason I want to use Gibbs ensemble >.<
[5] That would suck because I hate how my Windows compiler compiles FORTRAN code. And I hate DOS commands. Period.
Wednesday, April 16, 2008
I'm looking for bad things
Concurrent to the senior synthesis project, the senior analytical project I am involved in is pretty interesting. My group are looking for PAHs and heavy metals in local soil samples. Unfortunately, there isn't enough time available to do a significantly large statistical sampling of different location-types as found in most of the environmental literature, such as comparison between residential and urban areas or high-traffic versus low-traffic locales. But there is enough to compare soil from LSU with soil from two spots on the Mississippi River: one near ExxonMobil and the other near the bridge. For each location we gathered three representative samples.
The bulk of the project is sample preparation (as always is in analytical settings). The PAHs are being extracted from our soil samples using dichloromethane as the solvent. The extraction is being expediated (and made safer) by using a microwave oven instead of other traditional methods. Heavy metal extraction is a simple acid digestion in concentrated nitric acid. Instead of using the "old school" hot plate method of acid digestion, again we're using a microwave oven to expediate extraction (and it simultaneously makes the procedure safer). [1]
We're using GC-MS to quantitate the PAHs, and we're using flame-AAS or flame-AES to quantitate the heavy metals. [2]
Let's see how "clean" these soil samples are? I'll post results in ~two weeks (because that's when it's due).
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[1] An interesting note, we want to study lead and copper particularly. However, our group got into a bit of an argument over whether we would have extracted enough of either within our detection limits. I argued we wouldn't based on a few articles I read from the literature which used hydrofluoric acid to extract lead and copper. We'll see, though.[a]
[a] Funny story, a labmate argued that HF wasn't a dangerous acid because it wasn't a "strong" acid. I think the only thing saving him from serious scorn from me would be the fact that he's a pre-med >.<
[2] I'm arguing we run both the absorption and emission experiments. It's not hard to change experiments on the user interface, and I haven't had the time to peruse the literature or any standard procedures to see which would be better for which metal. It's easier to throw away useless data than realizing you're missing useful data.
The bulk of the project is sample preparation (as always is in analytical settings). The PAHs are being extracted from our soil samples using dichloromethane as the solvent. The extraction is being expediated (and made safer) by using a microwave oven instead of other traditional methods. Heavy metal extraction is a simple acid digestion in concentrated nitric acid. Instead of using the "old school" hot plate method of acid digestion, again we're using a microwave oven to expediate extraction (and it simultaneously makes the procedure safer). [1]
We're using GC-MS to quantitate the PAHs, and we're using flame-AAS or flame-AES to quantitate the heavy metals. [2]
Let's see how "clean" these soil samples are? I'll post results in ~two weeks (because that's when it's due).
----------
[1] An interesting note, we want to study lead and copper particularly. However, our group got into a bit of an argument over whether we would have extracted enough of either within our detection limits. I argued we wouldn't based on a few articles I read from the literature which used hydrofluoric acid to extract lead and copper. We'll see, though.[a]
[a] Funny story, a labmate argued that HF wasn't a dangerous acid because it wasn't a "strong" acid. I think the only thing saving him from serious scorn from me would be the fact that he's a pre-med >.<
[2] I'm arguing we run both the absorption and emission experiments. It's not hard to change experiments on the user interface, and I haven't had the time to peruse the literature or any standard procedures to see which would be better for which metal. It's easier to throw away useless data than realizing you're missing useful data.
Tuesday, April 15, 2008
Previous Outburst
The previous outburst was generated by a frustrating aspect of my senior synthesis project. The full schematic is shown below:
The product (1) seems simple enough of a reaction to me. But, the cursed side product (dicyclohexylurea, DCU, a white solid) is driven strongly by Le Chatelier's principle. So, to slow it down, it's a good idea to stick it in a refrigerator once dicyclohexylcarbodiimide (DCC) had been added (if the reaction vessel wasn't iced, expect everything to crash out VERY quickly) [1].
So I thought I did everything well according to procedure. Prepare a round bottom flask with ~250mL THF, and dissolve the ether-acetic acid and hydroxysuccinimide in the vessel. Dissolve the DCC in ~50mL THF [2]. Ice both for ~30 minutes. Pour. Cap. Stick in refridgerator. Have beer.
So you would expect some DCU. But I didn't expect 13.8g, especially when I used ~14g of the DCC. Granted, I haven't done the calculations to determine how much of my DCC was lost to DCU, but ~13.8g seems like a bit much.
And I haven't even gotten all of it out of my reaction vessel. DCU is stubborn and wants to stay in my reaction vessel and not come out of solution. Plus, I think the pumps to the roto-vap lack sucking power and create a poor vacuum to remove the THF from the r.b.f.
At the end of the day I need a 140ppm solution of the pyrole-ether-acetate product. Hope for the best? If not, expect more inane bitching about synthesis. [3]
----------------------
[1] DCC is disgusting to use. It's a very chunky solid that requires chiseling to obtain. Secondly, it's very, very soluble in organic solvents and oils, particularly those found on your skin. So, it's readily absorbed through your skin. And, it's a sensitizer, so I feel bad for anyone who continuously uses DCC, like protein chemists. (Oh, and I know there's worse chemicals, but I'm not working with those at the moment)
[2] Oh, did I mention DCC has a high vapor pressure as a solid? Scared now? Muhahaha!
[3] Why oh why did i not change my concentration to chemical physics? The silly notion of being a well-rounded chemist has given me headaches, lol!
The product (1) seems simple enough of a reaction to me. But, the cursed side product (dicyclohexylurea, DCU, a white solid) is driven strongly by Le Chatelier's principle. So, to slow it down, it's a good idea to stick it in a refrigerator once dicyclohexylcarbodiimide (DCC) had been added (if the reaction vessel wasn't iced, expect everything to crash out VERY quickly) [1].So I thought I did everything well according to procedure. Prepare a round bottom flask with ~250mL THF, and dissolve the ether-acetic acid and hydroxysuccinimide in the vessel. Dissolve the DCC in ~50mL THF [2]. Ice both for ~30 minutes. Pour. Cap. Stick in refridgerator. Have beer.
So you would expect some DCU. But I didn't expect 13.8g, especially when I used ~14g of the DCC. Granted, I haven't done the calculations to determine how much of my DCC was lost to DCU, but ~13.8g seems like a bit much.
And I haven't even gotten all of it out of my reaction vessel. DCU is stubborn and wants to stay in my reaction vessel and not come out of solution. Plus, I think the pumps to the roto-vap lack sucking power and create a poor vacuum to remove the THF from the r.b.f.
At the end of the day I need a 140ppm solution of the pyrole-ether-acetate product. Hope for the best? If not, expect more inane bitching about synthesis. [3]
----------------------
[1] DCC is disgusting to use. It's a very chunky solid that requires chiseling to obtain. Secondly, it's very, very soluble in organic solvents and oils, particularly those found on your skin. So, it's readily absorbed through your skin. And, it's a sensitizer, so I feel bad for anyone who continuously uses DCC, like protein chemists. (Oh, and I know there's worse chemicals, but I'm not working with those at the moment)
[2] Oh, did I mention DCC has a high vapor pressure as a solid? Scared now? Muhahaha!
[3] Why oh why did i not change my concentration to chemical physics? The silly notion of being a well-rounded chemist has given me headaches, lol!
Wednesday, April 9, 2008
Expelled Lulz
Remember that intelligent design movie called Expelled that has been circling around the blogosphere causing all sorts of hoots and laughter? Want to know something very funny? FOX News didn't like it. Serious lulz!
(Look for the subtitle "Ben Stein: Win His Career")
(Look for the subtitle "Ben Stein: Win His Career")
Rush Limbaugh: Dishing teh stoopid
I had the unfortunate opportunity to hear Rush Limbaugh's show yesterday. Even worse, I read the transcript. See anything stricking:
By the way, it is this vast particle collider at the CERN research centre that
they say could replace the Internet, with speeds so fast that you'll be able to
download a high definition movie, a two-hour high definition movie in three
seconds. They're going to use a particle accelerator and collider for it.
NO! The Large Hadron Collider (LHC) outputs large datasets that data-transfer is burdened by current technologies. By utilizing essentially parallel computing technologies (interfacing both hardware and software) you can overcome the data-transfer problem. The 'Grid' is not equivalent to the LHC, though it was developed as an answer to the so-called large data problem.
In other words, he's looking for a "God particle." He's looking for a
particle to prove God. Dr. Higgs, please, just look out the window. You see that
tree? You see the grass? Whatever is outside your window, all of it, it's God
particles. Every aspect of it is God particles.
I liked Leon Lederman's book. It was a fun read. Limbaugh has ruined the book for me. Thank you idiotic commentator on current events for ruining science for me.
But in all seriousness, the Higg's boson, which would essentially explain the reason for the massless photon and heavy W and Z bosons, is an important fundamental particle of the Standard Model. I wouldn't have called it the "God particle" as Lederman playfully called in his book, but that's just a diversion from the more important aspect of its discovery: electroweak symmetry breaking.
But Limbaugh and other media sources have sipped from teh stoopid kool-aid. They lacked reading comprehension to see why Lederman called the Higgs boson the God particle. I'm too frustrated at the moment to expand any further. Teh stoopid hurts my brain too much.
These scientists, they fear God because God has the answers, God's smarter
than they are.
God's a civil engineer. Only a civil engineer would put a recreational area in a waste zone.
But seriously, the above quote is one of those "he didn't just say it, right?" *shrug* I don't fear God. His followers scare me enough as it is.
In fact, one of these guys in Ben Stein's movie, guy named Hawkins who's over at
Oxford I think, Oxford or Cambridge, Ben Stein goes over and interviews him in
this movie, Expelled.
Hawking is a theoretical physicist from Cambridge. Dawkins is an ethologist and evolutionary biologist from Oxford. Only Limbaugh would be capable of combining the names together in a horrific screed.
And the movie is the laughing stock of the blogosphere. Especially when PZ Myers was kicked-out of a screening despite him actually being in the film.
Ugh. The internet has exemplified teh stoopid which existed even before the internet was popular outside of physicists. Shame on the internet for promoting teh stoopid to higher levels. And shame on Limbaugh for being a participant in teh stoopid.
Tuesday, April 8, 2008
Offsetting "teh stoopid"
Human civilization has an impact on the local and global environment. Everytime we cook food or drive to the grocery store, we are creating waste products that are literally dumped into the local ecology to handle.
There are several thingss we can do that lessens or offsets our impact on our environments. The most obvious first step is to do a cost-benefit analysis of our activities and remove those activities which are deemed more wasteful than beneficial, such as showering three times a day or flushing twice after fecal expulsion. The next step is to invest our resources into developing new methods to accomplish the same goals that decrease our impact on the environment, such as researching for alternative fuel sources or cost-efficient, energy-efficient white-light sources.
Obviously there is a need to determine what resources we have for such endeavors. Not everyone has the necessary background to be actively involved in the research. However, we can be passively involved. Such endeavors require money, both for materials and to pay for the labor involved. [1] The best method for the average citizen would be to write your Congressman or Congresswoman and demand more funding for the National Science Foundation, the Department of Energy, and other government institutions that are the prime source of scientific funding.[2] You could also purchase carbon offsets to account for the necessary activities of your daily life that releases carbon emissions by offsetting such release via supporting energy resources that sequester such carbon instead.
Just like the environment, there are necessary evils involved in entertainment. Some of us are drawn to "teh stoopid" because we get some marginal enjoyment from observing "teh stoopid" in action. Our enjoyment has come to where it has become necessary for us sometimes to econimcally support "teh stoopid" on accident just to get our kicks. This is obviously bad for the total intelligence of human society. We need a way to offset our finacnical support of "teh stoopid".
One route is to write our Congress again. However, sometimes "teh stoopid" infects our politicians. It would be better to invest in lobby groups to simultaneously combat "teh stoopid" in politics and in general.
Thus, if you do an activity that somehow gives money to "teh stoopid", then I recommend offsetting your contribution by donating to an organization that opposes "teh stoopid". For example, if you purchase a book on creationism, purchase a book on evolution. If you purchase a conservative's screed (eg. Anne Coulter) purchase a more balanced analysis of the current event topic. If you bought materials from a company that denies global warming, invest more in lobbying groups that are pushing for anti-global warming legislation through Congress. If you watch YouTube or MySpace and click their ads, then listen to NPR or watch PBS and donate money to your local broadcasting station. [3]
"Teh stoopid", however entertaining it is, must not be allowed to gain an economic advantage from those of us who are purely entertained by its existence. Thus, we must donate and offset our contribution to "teh stoopid".
Do it. Nao! I demand it.
-----------------------------------
[1] Graduate students need money to buy ramen, too!).
[2] And if you're rich, please donate to a research institute to create an endowed chair. That simultaneously creates a source of funding for research as well as recruits top-notch researchers to that institution. And, your name will be immortalized; so, that's always cool!
[3] YouTube, however funny internet phenomena is, needs to be offset by the introduction of news and current events. Tron man IS NOT a current event.
There are several thingss we can do that lessens or offsets our impact on our environments. The most obvious first step is to do a cost-benefit analysis of our activities and remove those activities which are deemed more wasteful than beneficial, such as showering three times a day or flushing twice after fecal expulsion. The next step is to invest our resources into developing new methods to accomplish the same goals that decrease our impact on the environment, such as researching for alternative fuel sources or cost-efficient, energy-efficient white-light sources.
Obviously there is a need to determine what resources we have for such endeavors. Not everyone has the necessary background to be actively involved in the research. However, we can be passively involved. Such endeavors require money, both for materials and to pay for the labor involved. [1] The best method for the average citizen would be to write your Congressman or Congresswoman and demand more funding for the National Science Foundation, the Department of Energy, and other government institutions that are the prime source of scientific funding.[2] You could also purchase carbon offsets to account for the necessary activities of your daily life that releases carbon emissions by offsetting such release via supporting energy resources that sequester such carbon instead.
Just like the environment, there are necessary evils involved in entertainment. Some of us are drawn to "teh stoopid" because we get some marginal enjoyment from observing "teh stoopid" in action. Our enjoyment has come to where it has become necessary for us sometimes to econimcally support "teh stoopid" on accident just to get our kicks. This is obviously bad for the total intelligence of human society. We need a way to offset our finacnical support of "teh stoopid".
One route is to write our Congress again. However, sometimes "teh stoopid" infects our politicians. It would be better to invest in lobby groups to simultaneously combat "teh stoopid" in politics and in general.
Thus, if you do an activity that somehow gives money to "teh stoopid", then I recommend offsetting your contribution by donating to an organization that opposes "teh stoopid". For example, if you purchase a book on creationism, purchase a book on evolution. If you purchase a conservative's screed (eg. Anne Coulter) purchase a more balanced analysis of the current event topic. If you bought materials from a company that denies global warming, invest more in lobbying groups that are pushing for anti-global warming legislation through Congress. If you watch YouTube or MySpace and click their ads, then listen to NPR or watch PBS and donate money to your local broadcasting station. [3]
"Teh stoopid", however entertaining it is, must not be allowed to gain an economic advantage from those of us who are purely entertained by its existence. Thus, we must donate and offset our contribution to "teh stoopid".
Do it. Nao! I demand it.
-----------------------------------
[1] Graduate students need money to buy ramen, too!).
[2] And if you're rich, please donate to a research institute to create an endowed chair. That simultaneously creates a source of funding for research as well as recruits top-notch researchers to that institution. And, your name will be immortalized; so, that's always cool!
[3] YouTube, however funny internet phenomena is, needs to be offset by the introduction of news and current events. Tron man IS NOT a current event.
Friday, April 4, 2008
ACS convention
The national ACS meeting starts Sunday in New Orleans, LA. This means I will be boozing it up in New Orleans this weekend. Send me a facebook or a myspace or email my gmail (recspecz) if you'll be in town and want to booze, talk about chemistry/physics, bitch about being an undergraduate/graduate, or booze some more.
I'll be at the undergraduate poster session Monday from 2-4pm. Check out my poster (#944: "Application of a kink-based path integral formulation to molecular systems"). Unfortunately, it isn't an open bar environment so my science may be weakened by my socially-awkward, sober self.
Did I mention there will be booze in New Orleans?
I'll be at the undergraduate poster session Monday from 2-4pm. Check out my poster (#944: "Application of a kink-based path integral formulation to molecular systems"). Unfortunately, it isn't an open bar environment so my science may be weakened by my socially-awkward, sober self.
Did I mention there will be booze in New Orleans?
Wednesday, April 2, 2008
Give her the Shock(er) Absorber
The burning question of why women wear sports bras has finally been answered for those of us who prefer to learn visually. This website will show you the awesome power athletic activity has on boobs.
Do FF+G on extreme activity level. It really looks like to me that the nipples would cut the girl's elbow in two. Maybe it's just me.
Do FF+G on extreme activity level. It really looks like to me that the nipples would cut the girl's elbow in two. Maybe it's just me.
Tuesday, April 1, 2008
This is me right now
Yeah, my hair is in a very confirmationally irregular poisition as well and tends to stay that way all day.
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