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Saturday, August 06, 2011

NSF grant time

It looks as though the molecular dynamics simulations are nearing an end. Think I better get a move on with the scripting business. Unfortunately, no one really writes books with code for the newer languages, so I'm stuck reading Computer Simulations of Liquids by Allen. It's a very helpful tool, but the pseudo-code they give is for FORTRAN and can be a bit unclear. This is especially the case when dealing with for loops and indexing entries in an array based on the values in the loop. You have to learn bits and pieces of nearly every programming language that's made its way to being used in computational science. Books today on languages like Python pretty much suck... I don't care how to plot y = xsin(x), or create an array with all of the y-values when x ranges from 0 to 50. No one does the job the guys of old did when they literally wrote a book that you could code your own fully functional molecular dynamics program from.

My previous coding experience was with MATLAB and so I use GNU Octave now for anything I need plots for. My main programming language is Python... I tried C for a bit and while the indexing issues became non-existent with C (it's very intuitive), debugging is an absolute pain. My first C script I spent 20 minutes debugging the compilation... it created my executable, whew I said relieved. I executed the program and ERROR. So, now I had to debug the executable with the most ambiguous errors I've ever seen. I'll take Python and its quirky indexing any day over C's debugging. We're on a tight time budget here, especially with this NSF grant we're trying to push a paper out for, and I'd rather have myself writing programs in a language that puts a comma on the line below where you have an error, estimating the EXACT spot you have the error.

So right now I'm translating a bunch of old C codes to Python for my use in analyzing our trajectories. The simulations are of 214 waters and an ion, Cl Br F Na and Li. We're using the AMOEBA polarizable forcefield in this work, which allows us to calculate the induced dipoles on every atom in the simulation. Unfortunately this calculation cannot be split into chunks, so it cannot be run in parallel... so it's MUCH slower. When I worked with proteins, I was able to simulate ~1 nanosecond per week in serial (3-4000 atoms + thousands of waters), but I'm able to get only 500 picoseconds in a week with AMOEBA on 643 atoms. After obtaining the trajectories we start running some analysis, first we center and reimage the trajectories. So we take the ion and translate it back to the center, then translate all other atoms by the same amount. Reimaging refers to the fact that the simulations we run are in periodic conditions, which means we have a cube with sides of length, L, that our system evolves in. This cube ispropagatedin every direction (+x, -x, +y, -y, +z, -z) and when a molecule leaves the cube, it simply re-enters the adjacent cube:

| | <--- cube wall
| c| <--- molecule leaving the cube
| |

| | <--- cube wall
|c | <--- location molecule enters the adjacent cube
| |

| || |
|c ||c | ---> now every image of the cube sees the
| || | molecule in this new location

However, sometimes the water doesn't get moved back correctly and a few waters diffuse away a little bit, so we just reimage them back inside the box where they SHOULD be located. You merely translate the diffused waters' X, Y, and Z coordinates by the length of the box, L. It's a very important step, especially if the ion moved its way over to the edge of the box and was coordinating them.

After reimaging we start doing some math... I have a script that calculates a radial distribution function and smooths it, obtains info on the water geometry and plots things like bond angle of the water as a function of the oxygen to ion distance, and we script the setup of 100's of Gaussian09 input files. Gaussian09 is a quantum chemical package. From the radial distribution function, you can calculate the first hydration shell coordination number (integrate the first maxima), but we also use a simple hydrogen bonding scheme as well--if the water has an H closer than ~3 - 3.3 Angstroms (depends on the ion) and the O-closer H-ion bond angle is > 130 degrees, we count it as coordinated. This allows us to input only the waters the ion is coordinating into Gaussian and treat the remaining waters as point charges (no electrons, no basis sets). We run Gaussian to compute the electron density at the MP2 level of theory with the aug-cc-pVDZ basis set. Gaussian spits out a cube file, which contains the electron density at various points on a fine grid. We actually do multiple runs on the same system (full cluster, water only, ion only) to get 3 cube files. After that we use another program that performs Bader analysis on the cube files. This allows us to compute the distribution of charge across all the molecules in the system and being to visualize a concept known as charge transfer. When an ion like Cl is hydrated by a single water, we've calculated that ~20% of the ion's excess charge is transferred to the water.

You can then visualize the crap out of this concept with electron density difference maps which actually show this excess charge having been spread over the coordinated water.

This work is looked forward to by a number of extremely important people in the business and we think we have a finding that will get some people really riled up. So we're actually doing the study AGAIN! to verify our results weren't just a fluke.

After that, I'll be moved back to my old project of calculating thermodynamic quantities of ion hydration from a quantum chemical prospective using symmetry adapted perturbation theory.
5:41 pm - 0 comments - 0 Kudos
Sunday, July 03, 2011

The science, SHE LIVES!!!!!!

Fuck. GAMESS. Use the same damn basis sets as everyone else.

--> Back story:
Lab asked me to learn GAMESS so we can mess with it, which will get you blacklisted (for serious) from our current quantum program Gaussian. GAMESS and Gaussian MP2 energies for a single water-chloride dimer don't match... I find it's the basis sets that differ. GAMESS compensates with simply more primitive functions. Can't just "plug-in" Gaussian numbers because Gaussian = Jerks... so *insert initial statement*

We need GAMESS for further work using a fancy program that hacks... well, GAMESS... to perform some symmetry-adapted perturbation theory calcs. You might imagine the program is called SAPT... and you'd be right.
10:11 am - 0 comments - 0 Kudos
Thursday, November 12, 2009

Molecular Dynamics: First Molecules

Neato. You're a computational chemist and a total nerd. What do you do all day with your life? That's right. You stare at little balls and sticks [or ribbons] as they dance merrily across a giant black backdrop. And from this... you cure disease. Awesome? With a fucking cherry on top.

Current molecule in the simulation process:
2J9I -- some eye protein

Why one? Why not?

But seriously. The protein has ~66,000 atoms in it. And almost 200,000 water atoms to solvate it. It is a hard drive's worst nightmare.

Want to watch some previously made squiggles?

http://www.youtube.com/watch?v=N8bbZhYs2iM


12:55 am - 1 comments - 2 Kudos
Tuesday, October 27, 2009

God himself hath willed this blog.

I am heading to dinner.



And of course... AMBER10 MD actually works now. Now if only I could find a PDB file of HIV-1 protease sans drug inhibitor.
10:35 pm - 1 comments - 0 Kudos
Sunday, July 26, 2009

Contact Solution Mishaps... and Mayhem Festival

Anybody out there who uses those fancy contact solutions that are used by placing the solution into a container, then placing a little pill or the lid in with a platinum coated bottom piece knows where this 'mishap' lies. The solution itself contains hydrogen peroxide, a mere 3%, but still...

Yesterday, I got up early to head out to the Mayhem Festival to catch some Behemoth and Cannibal Corpse. Would've liked to have seen Slayer, but they were on late and the fans there were beyond the realm of simply being 'drunk' and getting terribly annoying. Not to mention, the sun had been beating down on both the fiance and myself, so we were burnt--we had gotten Trivium brand sun lotion upon entrance, which... amused me--and we had been cut off from meeting Behemoth twice.


Since I will inevitably continue that story lets wrap up the contacts bit... it was early in the AM and I grabbed a solution bottle, squirted the contacts to watch excess hydrogen peroxide off, if there was any, and added it to my eye.

Mistake= that solution bottle was the 3% hydrogen peroxide bottle and yes, it hurts. It felt like someone had stuck an ice cube on my eye, coupled with copious amounts of pain. I wouldn't recommend.

Alright, so we went to the Revolver Magazine tent to meet Behemoth, we were one of the first people there and excited to meet them (we being myself and the aforementioned fiance). That's when the Revolver people decided to tell us that they were only doing photos with fans, and we left the camera at home. Disappointed I devised a way to chill near the back of the tent and wait creepily until they left, we could then say a quick 'hello' and be on our way and they on theirs. I then noticed some thirty or forty minutes later they were signing things (which they weren't doing before) and so we jumped back in line, grabbing a Revolver magazine, finding a page within for them to sign. We didn't care what they signed, just wanted to meet them, share a few words, and go our separate ways. Upon getting in line and chatting with our neighboring fans, we noticed the same Revolver Magazine guy come out and start counting the number of people in the line.

Something smells like disappointment.

He then walks back up front, recounts to the number 10, and cuts off the line. Guess who were lucky number 11 and 12? FML.

Twice denied.

We then watched Cannibal Corpse after waiting in line for a cup of $4.00 water for forty minutes and opted to stay back in the back. We were both drained from the sun and being pummeled by crowd surfers during Behemoth, standing a mere 5 ft. from the stage (including fenced area), and standing back proved wise as the crowd of drunken idiots started chucking their beers and full water bottles into the air, and shoes... and goth jackets.
Also, we had the displeasure of standing next to two hideous Asian goths as they dry-humped to 'Fucked With a Knife.'

Good show they put on, as always. No 'I Cum Blood' but oh well, Slayer and Manson had their own shows to put on in the amphitheater. We left after Cannibal, sick of the Slayer fans ruining all the other shows (most of them were deliriously, dehydratedly drunk and middle-aged) and the Manson fans being so androgynous.

Lesson learned, if you wish to see death metal or blackened death metal, or black metal, go when they do their own mini-tours and not when they jump onto these bigger tours, especially older thrash metal bands (I do like Slayer, I just hate the fans). You encounter far fewer assholes this way who ruin your show experience by insulting the band you came to see, throwing their beers and full water bottles into the crowd, and stumbling around harassing your fiance.

Also, it amuses me how people suddenly become absolute chain-smokers when going to concerts. Well, actually the amusement passes as soon as I start choking on it.

Last point, Seth, of Behemoth, apparently loves kids. He was the most interactive of the group with the kids and enjoyed the photo portion of the meeting with fans. He won a little more respect in my book, but who knows, he may really, really like kids... if you know what I mean.
6:57 pm - 0 comments - 0 Kudos
Tuesday, March 31, 2009

#93

Current mood: accomplished

So, somehow I got voted to be the 93rd best UGer... I personally don't know how, but it's pretty sweet to be so recognized...

On an internet forum...

About guitars...

(suicide)...

(Burns in hell)...
11:28 pm - 0 comments - 0 Kudos
Saturday, September 27, 2008

OWNED FINALE

[QUOTE=cocodrilo83]10. The scientific method can only test existing data—it cannot draw conclusions about origins. Micro-evolution, changes within a species on a small scale, is observable. But evidence for macro-evolution, changes transcending species, is conspicuous by its absence. To prove the possibility of anything, science must be able to reproduce exact original conditions. Even when it proves something is possible, it doesn't mean it therefore happened. Since no man was there to record or even witness the beginning, conclusions must be made only on the basis of interpreting presently available information. If I put on rose-colored glasses, I will always see red. I accept the Bible's teaching on creation, and see the evidence as being consistently supportive of that belief. When dealing with origins, everyone who believes anything does so by faith, whether faith in God, the Bible, himself, modern science, or the dependability of his own subjective interpretations of existing data. I would rather put my faith in God's revealed Word.[/QUOTE]

Our evidence for macroevolution relies by looking at the past and seeing that ‘Hey! That wasn’t here before, what is this?’ To observe speciation today, above the microevolution scale is hard because it takes a great deal of time to do. But, allopatric speciation of the Grand Canyon’s squirrel species is my favorite to use because it shows how a simple separation of populations of squirrels can yield different evolutionary paths.

http://www.talkorigins.org/faqs/macroevolution.htm l

http://www.talkorigins.org/faqs/comdesc/

Here, this is about how effective your Bible is at ‘science.’ I did it myself and posted the sources within the video.

http://www.youtube.com/watch?v=yyUNmYNtavM

8:35 am - 1 comments - 0 Kudos
Saturday, September 27, 2008

OWNED Part 7

[QUOTE=cocodrilo83]8. Uses continue to be found for supposedly "leftover" body structures. Evolutionists point to useless and vestigial (leftover) body structures as evidence of evolution. However, it's impossible to prove that an organ is useless, because there's always the possibility that a use may be discovered in the future. That's been the case for over 100 supposedly useless organs which are now known to be essential. Scientists continue to discover uses for such organs. It's worth noting that even if an organ were no longer needed (e.g., eyes of blind creatures in caves), it would prove devolution not evolution. The evolutionary hypothesis needs to find examples of developing organs—those that are increasing in complexity. [/QUOTE]

Vestigial does not mean ‘useless’ it means that there is a trace of an organ or structure that is now lost or vanished. Snakes have remnants of leg bones, the blind fish have remnants of eye structures, extra toe bones in horses, molars in vampire bats, etc. It is true a lot of vestigial organs are left because evolution isn’t perfect, it isn’t instant, and by way of leaving these sort of traces, is sometimes not even absolute. Vestigial organs are more harmful to creation than they would ever be for evolution—after all, if they were specially created, what purpose would the ones that do not better the chances of survival of the organism serve? You have to still provide energy to the area of the body, even if it doesn’t help you any, so wouldn’t it be more beneficial to just have it fully removed by the creator? Since evolution isn’t always absolute, isn’t perfect, and isn’t instant, it explains why we find these organs or structures.

Increasing complexity huh? Try these two:

http://books.google.com/books?id=yMAK06tbIQEC& pg=PA62&lpg=PA62&dq=increasing+complexity+ in+organs&source=web&ots=ar1d4e_jlN&si g=dZ7A1bpipoKFve5VXnAr7m6vGyc&hl=en&sa=X&a mp;oi=book_result&resnum=5&ct=result

http://www.jstor.org/pss/2401015

[QUOTE=cocodrilo83]9. Evolution is said to have begun by spontaneous generation—a concept ridiculed by biology. When I was a sophomore in high school, and a brand new Christian, my biology class spent the first semester discussing how ignorant people used to believe that garbage gave rise to rats, and raw meat produced maggots. This now disproven concept was called "spontaneous generation." Louis Pasteur proved that life only comes from life—this is the law of biogenesis. The next semester we studied evolution, where we learned that the first living cell came from a freak combination of nonliving material (where that nonliving material came from we were not told). "Chemical Evolution" is just another way of saying "spontaneous generation"—life comes from nonlife. Evolution is therefore built on a fallacy science long ago proved to be impossible. Evolutionists admit that the chances of evolutionary progress are extremely low. Yet, they believe that given enough time, the apparently impossible becomes possible. If I flip a coin, I have a 50/50 chance of getting heads. To get five "heads" in a row is unlikely but possible. If I flipped the coin long enough, I would eventually get five in a row. If I flipped it for years nonstop, I might get 50 or even 100 in a row. But this is only because getting heads is an inherent possibility. What are the chances of me flipping a coin, and then seeing it sprout arms and legs, and go sit in a corner and read a magazine? No chance. Given billions of years, the chances would never increase. Great periods of time make the possible likely but never make the impossible possible. No matter how long it's given, non-life will not become alive. [/QUOTE]

For one, abiogenesis is independent of organic evolution (the type we are most familiar with), although, evolution would apply to the chemicals being involved. The odds of abiogenesis on its own, yes, are quite staggering, but there ARE NO DEFINITIVE NUMBERS, NOR is there A DEFINITE PROBABILITY. In fact, it is more likely that chondrites, which are known to be able to house left-handed amino acids (left handed is extremely important as almost every life form is constructed of it) and survive even after impact. The heat provided from the blast would allow for rapid reactions to take place and given time and an impact in the right place could provide for the combination of these amino acids, with the amino acids already on Earth, forming proteins which bend and warp around—which happen easiest while in an aqueous environment which includes open water and inside lipid membranes—the predicted membrane structure of the earliest ‘cells.’ We have been able to create, in labs, stable sugars, carbs, the lipid membrane, a healthy portion of the amino acids, pieces of RNA and DNA, and have been able to form the RNA ribozyme, which is the theoretical self-replicating molecule that abiogenesis hinges a great deal upon. This is a joint effort between water and land and with a simple flood… life. Improbable, sure, possible, yes.
8:35 am - 0 comments - 0 Kudos
Saturday, September 27, 2008

OWNED Part 6

[QUOTE=cocodrilo83]7. The dating methods that evolutionists rely upon to assign millions and billions of years to rocks are very inconsistent and based on unproven (and questionable) assumptions. Dating methods that use radioactive decay to determine age assume that radioactive decay rates have always been constant. Yet, research has shown that decay rates can change according to the chemical environment of the material being tested. In fact, decay rates have been increased in the laboratory by a factor of a billion. All such dating methods also assume a closed system—that no isotopes were gained or lost by the rock since it formed. It's common knowledge that hydrothermal waters, at temperatures of only a few hundred degrees Centigrade, can create an open system where chemicals move easily from one rock system to another. In fact, this process is one of the excuses used by evolutionists to reject dates that don't fit their expectations. What's not commonly known is that the majority of dates are not even consistent for the same rock. Furthermore, 20th century lava flows often register dates in the millions to billions of years. There are many different ways of dating the earth, and many of them point to an earth much too young for evolution to have had a chance. All age-dating methods rely on unprovable assumptions. [/QUOTE]

Indeed there are problems with some dating, some materials have had their parent:daughter ratios ruined by such processes you mention, or simple leaks, etc. But, scientists have been working on this and they have come up with a solution, much like how you apply a ‘best fit’ curve to plots in a graph, scientists have devised a curve to portray their level of uncertainty in their results which I will explain using C-14 dating. As of today, the results of a reliable source (meaning no leakage, no tampering, dead before 1895, which is regarded as year 0 in the field because since then we have utterly ruined the chance of any future generation getting accurate results off us) the uncertainty is down to +- about 300 years, back to 30,000-40,000 years ago. Why can’t we date things after 1895 with radiocarbon dating? Well, the industrial revolution decreased the amount of C-14 that would be made naturally, the atom bomb testing doubled the amount of C-14 in the atmosphere and today, we simply have to estimate how much C-14 would be present had we not ruined it. Other than that, when we use one of literally dozens of radiometric dating processes, we try to triangulate results in multiple labs, multiple scientists, multiple results samples, etc. to try to see if the numbers are complimentary to one another. There is no objective way to figure out exactly how old something is, but we can conclude by logic, the universe had to be here before everything else, the galaxy had to be formed/forming before our solar system, and the sun had to be forming with an accretion disk around it to form the planets—something Genesis does not agree with, but has been known since 1734 to be true—see solar nebular disk model, or the actual 1734 idea of the nebular hypothesis which is the same thing, but the SNDM is the modern version. We can also use the amount of the heavier elements in our solar system as proof of concept for the age of our solar system and the Earth—some heavy elements that exist today cannot be formed in the core of a star, therefore, by looking at supernova explosions we have concluded that in these explosions is where the heaviest elements were formed. Since we have an even higher abundance of these elements than some other confirmed solar systems do, we can conclude there have been multiple supernova and thus stars before our own. We feel confident that our own star is one of a third generation, with two previous stars having existed before it. Given current life cycles of stars and evidence from stars we are seeing, as far as 13 billion light years away (which I believe is the record right now) we conclude that there was no other factor in the length of time stars burned other than how massive they are—where more massive stars burn up quickly (a few million years) and less massive stars can shine, but very faintly for 15 billion years.

8:35 am - 0 comments - 0 Kudos
Saturday, September 27, 2008

OWNED Part 5

[QUOTE=cocodrilo83]6. Pictures of ape-to-human "missing links" are extremely subjective and based on evolutionists' already-formed assumptions. Often they are simply contrived. The series of pictures or models that show progressive development from a little monkey to modern man are an insult to scientific research. These are often based on fragmentary remains that can be "reconstructed" a hundred different ways. The fact is, many supposed "ape-men" are very clearly apes. Evolutionists now admit that other so-called "ape-men" would be able to have children by modern humans, which makes them the same species as humans. The main species said to bridge this gap, Homo habilis, is thought by many to be a mixture of ape and human fossils. In other words, the "missing link" (in reality there would have to be millions of them) is still missing. The body hair and the blank expressions of sub-humans in these models doesn't come from the bones, but the assumptions of the artist. Virtually nothing can be determined about hair and the look in someone's eyes based on a few old bones. [/QUOTE]

While most ‘links’ have been thrown away such as Lucy, or the Java Man, it appears that the finding of the missing link will act like the Higgs boson to physics. The Higgs boson is the only particle in the Standard Model yet to be observed, that we know of, and yet even without it being known to exist, we know something had to give matter the ability to acquire mass. Similarly, the idea of the common ancestor is backed up by the irrefutable evidence that the human chromosome number 2 is actually comprised of two chromosomes stuck together and that ERV positions in humans and the great apes, chimpanzees, etc.

You can download this article by clicking Full Text PDF which is on the upper right corner of the page and view it:

http://www.hindawi.com/getarticle.aspx?doi=10.1002 /cfg.216

Or you can watch this:

http://www.youtube.com/watch?v=TUxLR9hdorI

8:35 am - 0 comments - 0 Kudos
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