molecules

Exploring levels of protein structure with molecular models and snake venom

sporte — Thu, 17 Dec 2015 23:47:52 +0000

Exploring levels of protein structure with molecular models and snake venom

Imagine a simple hike in a grassy part of South America. You hear a rattle and feel a quick stab of pain as fangs sink into your leg. Toxins in the snake venom travel through your blood vessels and penetrate your skin. If the snake is a South American rattlesnake, Crotalus terrific duressis, one of those toxins will be a phospholipase. Phospholipases attack cell and mitochondrial membranes destroying nerve and muscle function. Without quick treatment, a snakebite victim may be die or suffer permanent damage (1, 2).

The phospholipase from the South American rattlesnake is called crotoxin. Scientists are interested in studying crotoxin because snake bites are a serious health hazard and better treatments would help save lives and minimize nerve and muscle damage.

Today, we're going to explore crotoxin for a different reason. We're going to use crotoxin to investigate the four levels of protein structure. Crotoxin is a good protein for this activity because it contains both types of secondary structure, metals, disulfide bonds, and multiple protein chains. Some proteins don't work as well for this purpose because they are monomeric, or they only contain one type of secondary structure.

We'll use Molecule World for this activity, but other 3D modeling programs could also be used. Some people also use plastic tubes and magnets but if you have access to iPads, it makes sense to use actual structure models.

The structure we're going to use is 3R0L. If you touch the link on an iPad, the structure will be downloaded from the NCBI and you can open it in Molecule World.

Primary structure

The primary structure of a protein is the sequence of amino acids, joined in a chain, from the amino end to the carboxyl end. Crotoxin has four protein chains, each with a different sequence.

To view the amino acid sequences:

Open the sequence viewer.
Touch the atom icon and choose residues to see how the sequences in four chains are different.
If you open the color key, you can see the colors and abbreviations for each amino acid.

When residue coloring is used, each amino acid appears with a different color. We can see that these four amino acid sequences are all different.

Secondary structure

The two kinds of secondary structure elements are alpha helices and beta sheets. These distinctive shapes are held together by interactions between atoms in the amino acid backbone.

To view both types of secondary structure:

Touch the atom icon and choose Secondary view.
Use the color key to identify both types in the structure.

Both types of secondary structure are shown in this image of the crotoxin B subunit.

A. Explore an alpha helix

To see how an alpha helix is held together:

Find chain 3R0L-D in the sequence viewer.
Touch the first set of green letters (LLQFNKMIKFE). One alpha helix will appear brighter.
Open the Show/Hide menu and choose Hide unselected. The rest of the structure will dissappear.

Touch the atom icon and pick the element coloring style.
Open the Show/Hide menu and choose Complete backbone.
Use the color key to identify the different atoms.
Open the Show/Hide menu again and choose All atoms in residue. Now you can see where the side chains are positioned.

From left to right, this alpha helix shows the amino acid backbone, the backbone plus the oxygens, and the backbone plus the side chains.

In an alpha helix, hydrogen bonds (invisible in this structure) form between the oxygens (red) and nitrogens (blue) in the backbone and hold the structure in a helical shape.

Touch the atom icon and Choose Reset View before going on to the beta sheets.

B. Explore beta sheets

To see how beta sheets are held together:

Touch the atom icon and choose Secondary view.
Scroll through the sequence viewer to find where the beta sheet begins.
Touch all the letters in the beta sheet.
Open the Show/Hide menu and choose Hide unselected.
Touch the atom icon and pick element coloring style. The beta sheet looks like a loop.
Open the Show/Hide menu and choose Complete backbone. This time, you can see the interactions between oxygens and nitrogens in different loops of the chain.
Open the Show/Hide menu again and choose All atoms in residue to see where the side chains are located.

From left to right, this beta sheet shows the amino acid backbone only, the backbone with oxygens, and the backbone plus the side chains.

Tertiary structure

The tertiary structure of a protein consists of a single amino acid chain plus any metals or prosthetic groups like heme or NAD.

Touch the atom icon and Choose Reset View before going on.

To see an example of tertiary structure:

Touch the names 3R0L-D and 3R0L-other. The "other" row is a list of chemicals in the structure.
Open the Show/Hide menu and choose Hide unselected. The objects that remain are a tertiary structure.
Touch the atom icon and choose Secondary view. You can see this chain contains both types of secondary structure.

Explore bonds to metals

Touch the atom icon and Choose Reset View before going on.

Touch the name 3R0L-D.
Open the Show-Hide menu and choose Hide unselected.
Touch the name 3R0L-D again to deselect it.
Touch the Mn (manganese).
Open the Selection menu and choose Select nearby.
Open the Show/Hide menu and choose All atoms in residue.
Touch the atom icon and choose the Ball and Stick drawing style and element coloring style. Now, you can see there are bonds holding the manganese atom in place. Similar bonds hold the sodium atoms in place as well.

Oxygens on amino acid side chains form bonds to manganese and hold it in place.

Explore disulfide bonds

Touch the atom icon and Choose Reset View before going on.

Touch the atom icon and choose Secondary View.
Open the Selection menu and type C.
Open the Show/Hide menu and choose All atoms in residue.
Touch the atom icon and select the Ball and stick drawing style and element coloring style.
Touch the names of chains A, B, and C twice to select and deselect them. Now, the cysteines will only be selected in chain D.
Touch 3R0L-D to select chain D.
Open the Show/Hide menu and choose Hide unselected. The disulfide bonds between chains can be seen.

Yellow disulfide bonds hold alpha helices together in crotoxin.

Quaternary structure

The quaternary structure of a protein consists of the interactions between multiple chains.

Touch the atom icon and Choose Reset View before going on.

To view the quaternary structure of this enzyme:

Touch the atom icon and the Spacefill drawing style and molecule coloring style.
Open the Show/Hide menu and choose all atoms in residue. You can see all four chains.

One last fun thing we can do with this this protein is to identify the active site. In crotoxin, the active site is the place where this enzyme chops up phospholipids.

Exploring the active site

To explore the active site:

Touch the atom icon and Choose Reset View before going on.
Touch the name of chain 3R0L-D to select it.
Open the Show/Hide menu and choose Hide unselected to hide chains A, B, and C. These chains are involved in binding to the cell membrane but they don't contribute to the phospholipase activity.
Touch the atom icon and choose the hydrophobicity coloring style and the spacefill drawing style.
Open the Show/Hide menu and choose Hide unselected.
Open the Show/Hide menu again and choose All atoms in residue.
Touch ACT in the 3R0L-other chain to highlight acetate. Acetate is a product of phospholipase activity.
Hide the sequence viewer and turn the structure around to view the acetate inside the enzyme at the active site.

Crotoxin colored by hydrophobicity with acetate bound in the active site.

References

Harris JB, Scott-Davey T. Secreted phospholipases A2 of snake venoms: effects on the peripheral neuromuscular system with comments on the role of phospholipases A2 in disorders of the CNS and their uses in industry. Toxins (Basel). 2013 Dec 17;5(12):2533-71. doi: 10.3390/toxins5122533.
Faure G, Xu H, Saul FA. Crystal structure of crotoxin reveals key residues involved in the stability and toxicity of this potent heterodimeric β-neurotoxin. J Mol Biol. 2011 Sep 16;412(2):176-91. doi: 10.1016/j.jmb.2011.07.027.

sporte Thu, 12/17/2015 - 18:47

Tags

Chemistry & Biochemistry

classroom activities

molecular modeling

molecular structures

Something scary for Halloween - polio virus

sporte — Wed, 28 Oct 2015 16:15:39 +0000

Something scary for Halloween - polio virus

When my parents were young, summer made cities a scary place for young families. My mother tells me children were often sent away from their homes to relatives in the country, if possible, and swimming pools were definitely off limits. The disease they feared, poliomyelitis, and the havoc it wrecked were the stuff of nightmares. Children could wake up with a headache and end up a few hours later, in an iron lung, struggling to breathe.

Poliovirus colored by molecule in Molecule World.

Today, on Jonas Salk's birthday, I read in the NPR blog Goats and Soda, that we're almost free of this scourge. The two scientists who developed vaccines against polio, Jonas Salk and Alfred Sabin, gave mankind the tools, and several others put them to good use. Be sure to check out Jason Beaubien's article and the amazing graphics showing poliovirus cases dropping across the world.

Since we have the luxury of distance, vaccines, and molecular modeling apps, we can explore the scary poliovirus from the safety of a phone or iPad. The way that I like to explore molecule models is to view a structure with different coloring styles and drawing styles and see if I can find patterns.

To explore poliovirus, I opened Molecule World** and downloaded structure 1XYR (Bubeck, et. al) from the Molecular Modeling Database (MMDB) at the NCBI. The 1XYR model is from a form the virus takes when it's about to enter a cell. It was obtained through cryo-electron microscopy.

In the first image, each protein in the poliovirus capsid is shown in a different color. The resolution isn't great, because electron microscopy can only do so much, so the structure model is built from the alpha carbon backbones of these 420 proteins.

In the image below, I changed the drawing style to tubes and applied secondary structure coloring to make the next image. Beta sheets are shown in orange and they make some interesting patterns on the surface of the capsid.

Poliovirus colored by secondary structure in Molecule World

I also found, when using a neutral color and spinning the capsized around that there appeared to be some kind of ring or pore in the structure. In the image below, I used a spacefill drawing style, colored by charge, and put the ring in the center. The amino acids around the "opening" are grey, showing they're uncharged. The images below that show beta sheets in the region around the ring and in residue coloring, the residue color key shows there are leucines, asparagine, and glycine.

Poliovirus colored by charge

Poliovirus drawn as spacefill, colored by secondary structure

I'm not sure what this pore or ring structure means for the virus, but for me, it means I'll have to read the paper and find out.

** I used the iPad version of Molecule World. I think Cn3D might work, too, but I had some problems. 1XYR can also be viewed with the Molecule World for iPhone, but the screen will be black when the structure is downloaded. Change the viewing mode to spacefill and you'll see the structure appear.

Reference:

Bubeck D, Filman DJ, Cheng N, Steven AC, Hogle JM, Belnap DM. The Structure of the Poliovirus 135S Cell Entry Intermediate at 10-Angstrom Resolution Reveals the Location of an Externalized Polypeptide That Binds to Membranes . Journal of Virology. 2005;79(12):7745-7755. doi:10.1128/JVI.79.12.7745-7755.2005.

Madej T, Lanczycki CJ, Zhang D, et al. MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Research. 2014;42(Database issue):D297-D303. doi:10.1093/nar/gkt1208.

sporte Wed, 10/28/2015 - 12:15

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The World Health Organization says TB now rivals AIDS as the leading cause of death from infectious diseases.

Yes, that's correct, but as Laurie Garrett points out that many of the people who have TB, have it because of AIDS. https://twitter.com/Laurie_Garrett/status/659380176657235968

Making the most of Molecule of the Month with Molecule World

sporte — Tue, 08 Sep 2015 20:52:00 +0000

Making the most of Molecule of the Month with Molecule World

We've been fans of the Molecule of the Month series by David Goodsell, for many years. Not only is Dr. Goodsell a talented artist but he writes very clear descriptions of the ways molecules like proteins, RNA, and DNA work together and function inside a cell.

To learn about proteins and their activities, I like to go directly to the Molecule of the Month page, where I can find a list of articles organized by molecule type and name. Many of these articles can also be downloaded in a PDF format.

A really nice of his articles is that he includes PDB IDs for all the structures he discusses. The PDB IDs make it easy to download and interact with the structures in Molecule World.

Structures from the articles can be viewed on-line in Jmol, but we prefer a more interactive method where we can download the structures, view the sequences, and use the sequences to show / hide or modify parts of the structure in Molecule World.

For example, say we want to know more about the genetic engineering tools Cascade and CRISPR. These are pretty exciting because they allow scientists to engineer genomes with greater precision than ever before. To learn more, we select the link to Cascade and CRISPR from the article list.

The articles is great for understanding some of the back story. To find the structures, we can search the web page with the term "PDB". Every time the words "PDB entries" or "PDB entry" appear, they'll be followed by a PDB ID. We can use those PDB IDs to get the structures from the NCBI or PDB databases.

At the PDB site, those IDs are linked to database records where we can download the pdb files, but it's not always so easy to figure out which of the ten files is the one you should download.

A simpler method, is to type the ID in Molecule World and touch the search button. When the file name appears, touch the name of the file and the molecule file will be downloaded and opened.

For Cascade and CRISPR, the PDB IDs and structures in the article are listed below. If you're using Molecule World on the iPhone or iPad, I set the links up so that touching the links will download the file and make it easy to open these in the app.

All the images below were made in Molecule World.

Two views of the cascade surveillance complex, a large complex of proteins and RNA 4TVX, 4U7U,

Cas1 and Cas2, proteins that chop up and store viral DNA 4P6I,

Cas3, a nuclease that attacks viral DNA: 4QQW,

Cas9, a CRISPR system from another type of bacteria (Streptococcus pyogenes), with CRISPR RNA bound to target DNA 4UN3

And more complexes with both the CRISPR RNA and viral target DNA: 4OO8,

And our favorite,4QYZ.

My favorite way to view some of these is to open the sequence viewer, find and select the nucleic sequences, and color by residue to distinguish between the RNA and DNA. We made the RNA residues a little brighter since they're more chemically active. It also helps to draw the models in different ways to see how the RNA is positioned inside the protein complex.

To learn more about CRISPR and the Cascade proteins, iBiology has a great video interview with Jennifer Doudna, the woman who discovered this system.

sporte Tue, 09/08/2015 - 16:52

Tags

biotechnology

classroom activities

Genetics & Molecular Biology

Guest Post: Astrochemistry and how the Universe comes together

esiegel — Thu, 01 Aug 2013 09:41:27 +0000

Guest Post: Astrochemistry and how the Universe comes together

“We are not simply in the universe, we are part of it. We are born from it.” -Neil deGrasse Tyson

The story of the Universe is the story of us all; we all share the same cosmic history, coming from a hot, dense state some 13.8 billion years ago known as the Big Bang and emerging after billions of years of cosmic evolution to the Universe we know and love today.

Image credit: ESA and the Planck collaboration.

It's a beautiful story -- and one I've told before -- but it might seem, at least from our perspective, that something is missing from the astrophysicist's version of events. Yes, we can start with a hot, dense, expanding Universe full of matter, antimatter and radiation, create some asymmetry between matter and antimatter, and then have the Universe expand and cool. Below a certain temperature, the antimatter will annihilate away with the vast majority of the matter, leaving only the tiny, asymmetric amount of matter (less than 1-part-in-a-billion) bathed in a sea of radiation.

Image credit: me, background by Christoph Schaefer.

But this radiation is constantly dropping in temperature as the Universe expands, having its wavelength stretched by the expansion of space. At some point, the Universe becomes cool enough that two types of matter particles you know -- protons and neutrons -- can fuse together without being immediately blasted apart by this sea of radiation.

Images taken from LBL, stitched together by me.

These nuclear fusion reactions give it all they've got, but by time this can happen, it's very difficult to get densities (or energies) high enough to form very heavy elements. During the first few minutes after the Big Bang, we can create a substantial amount of helium in the Universe, and tiny, trace amounts of Lithium and Beryllium, but that's it. The story of Big Bang Nucleosynthesis is amazing, but it doesn't tell us where we come from.

Image credit: Ned Wright's cosmology tutorial; data from Burles, Nollett & Turner (1999).

By number, it gives us a Universe which is 92% hydrogen, 8% helium, and less than 0.0000001% everything else combined. In fact, if we want the elements we consider essential to life -- Carbon, Nitrogen, Oxygen, Phosphorous, etc. -- we have to look well past the early stages of the Universe, and fast-forward to the formation of stars!

Image credit: NASA/JPL-Caltech/L. Allen and the IRAC GTO Team.

The more massive your star is, the heavier the element it's capable of fusing together. Also, the more massive your star is, the faster it burns through its fuel! A star like our Sun will fuse helium into carbon, nitrogen, and oxygen, while a substantially more massive star like Sirius (the brightest in our sky) will fuse those elements further into silicon, sulphur, and all the way up to iron, nickel and cobalt. When these stars run out of fuel, they'll return a fraction of these heavy elements back into the cosmos when they expel a large fraction of their mass into a planetary nebula.

Image credit: Vicent Peris, José Luis Lamadrid, Jack Harvey, Steve Mazlin, Ana Guijarro.

But the elements heavier than that -- as well as the vast majority of all elements heavier than helium -- come from the catastrophic deaths of the most massive stars: the one that die in core-collapse supernovae! Whenever a star more than about 8-to-10 times the mass of the Sun is formed, it burns through all of its nuclear fuel in just a couple of million years, maximum, and its core collapses down to a neutron star or black hole, destroying the rest of the star. Large amounts of the first 28 elements of the periodic table are recycled back into the Universe, where they can form the next generation of planets and stars.

Image credit: ESO / Very Large Telescope / FORS instrument & team.

But a huge number of free neutrons are also created, and through two creatively named processes -- the rapid r-process in the supernova itself and the slow s-process in the later stages of these stars' lives -- the heavier nuclei are created, including everything up-to-and-including Plutonium, and probably even beyond!

Image credit: wikipedia user 28bytes, under CC-BY-SA-3.0.

Yes, these elements will continue on in the next generation of stars, planets, and whatever else happens to come to exist in the Universe, making up as much as 1% of the Universe by mass (although much less than that by number). But there's a long way to go from atomic nuclei to the world we know today. And that connection goes far beyond my expertise. Luckily, I've got a very smart friend whose expertise lies in chemistry (and who has guest blogged for us before), and he's agree to take us through some of the basics of astrochemistry, or how these elements bind together to form molecules in the Universe. [My comments in square brackets.] Take it away, Richard Helmich!

Thanks Ethan for the excellent lead in and introduction. From the many generations of stars, the Universe has generated plenty of elements, and humans have even taken their time to organize them into the periodic table. These are very same elements found in you and me, and out in space these atoms don’t simply float around and do nothing. They react with each other to form all kinds of familiar and exotic molecules. Let’s take a look at what chemicals we’ve found outside of Earth so far…

Image credit: Wikimedia Commons users Cepheus and DePiep.

Hang on a minute… what are astrochemists looking for, exactly? Similar to how atoms absorb and emit light characteristic to a particular element in planetary nebulae like the Ring Nebula, whole molecules can absorb energy and emit light of particular frequencies characteristic to that molecule.

Image credit: NASA, ESA, C.R. O'Dell (Vanderbilt), and D. Thompson (Large Binocular Telescope).

The wavelength of light that a molecule absorbs or emits depends on what the atoms in the molecule are doing before and after the light is absorbed or emitted. The atoms in the molecule can vibrate in relation to each other in various ways, or the whole molecule can start or stop spinning as a whole.

Symmetrical stretching	Asymmetrical stretching	Scissoring

Rocking	Wagging	Twisting

The study of the energy atoms and molecules absorb and emit is an entire field of science called spectroscopy. Scientists have been able to discover the identities (and sometimes even the concentrations) of molecules that form throughout the universe by using spectroscopy to examine the infrared and millimeter wavelength light emitted by molecules in outer space. The amount of light given off at these wavelengths is typically very small, but fortunately scientists have been able to build very powerful telescopes such as the Herschel Space Observatory, Spitzer Space Telescope and -- here on Earth -- the Atacama Large Millimeter/Sub-millimeter Array (ALMA) to investigate astrochemistry in the nearer parts of the universe.

Image credit: ALMA (ESO/NAOJ/NRAO) (main); Herschel Space Observatory / ESA (inset).

So what have scientists found out in the vast expanses of space so far?

LOTS!

Here are just a few that have been identified, that are also common on Earth. (And there's a more complete list here.)

A few molecules found in outer space.

2 atoms

Carbon Monoxide

NaCl

Sodium Chloride

Nitrogen Monoxide

Carbon Monosulfide

3 atoms

H₂O

Water

HCN

Hydrogen Cyanide

H₂S

Hydrogen Sulfide

FeCN⁺

Iron (II) Cyanide

4 atoms

C₂H₂
Acetylene

NH₃

Ammonia

H₂CO

Formaldehyde

H₂O₂

Hydrogen Peroxide

Others

CH₃OH

Methanol

SiH₄

Silane

CH₃CHO
Acetaldehyde

C₆₀

Buckminsterfullerene

So let’s follow what happens to the elements created as a star dies and then are recycled again into a new star…our first stop is IRC +10216.

Image credit: Izan Leao (Universidade Federal do Rio Grande do Norte, Brazil).

This star was once between 3 and 5 times the mass of our sun, Sol. This star is in the late stages of becoming a white dwarf, and is in the process of blowing off its outer most layers into interstellar space. An astute scientist studying this star noticed it had a plethora of chemicals and was even able to map the location of some of them.^[1]

Image credit: from Dayal and Bieging, 1993; an older study of this star.

This map is awesome! Some scientists are figuring out various ways to do this for very small objects located on Earth, while others have mapped the molecular makeup of a star hundreds of light years away. [This star, in particular, is some 400 light-years distant from Earth.] This map has given scientists insight into the evolution of this star during its dying moments.

This is a molecular map of the vicinity surrounding IRC+10216 showing the locations of some molecules observed. From reference 1.

The NaCl (the same as the salt you have in your kitchen, minus the added iodine) is only observed near the core where temperatures are hot enough to keep it in the gas phase. Farther away there is likely to still be NaCl, but it has cooled and condensed into dust and is no longer obserable. Magnesium isocyanide, MgNC, is another metal salt like NaCl. This molecule is peculiar because on Earth the magnesium atom would be bound to the carbon (MgCN), but the reaction in outer space is kinetically driven (molecules and atoms bumping into each other) not thermodynamically determined so typically the abundance of each isomer is approximately equal.^[2] Other molecules were also observed such as HC₅N and C₄H. These are acetylenic molecules (similar to acetylene used in welding torches) with alternating single and triple bonds between the carbons atoms.

Later, after the star has proceeded further along its path towards becoming a white dwarf, the amount of UV light it emits increases, forming a planetary nebula when the gases become ionized. The UV light given off by the newly formed white dwarf typically causes much of the previously formed gaseous molecules to decompose, but recently scientists have observed that some molecules are still able to hold together.

Image credit: WFI, MPG/ESO 2.2-m Telescope, La Silla Obs., ESO (L). Concentration of CO (top right) and emission lines for the acetylene radical (bottom right) where the CO signal is strongest; via reference 1.

Moving from the death of stars to the birth of the next generation of stars, other scientists have observed the chemicals present in molecular clouds as they condense and form new stars. Scientists have observed water, carbon dioxide, silicates (similar to the grains of sand found on any beach), and even polyaromatic hydocarbons (also found in crude oil).^[3]

Image credit: ESO, HAWK-1 Instrument Team (top); spectra indicating various chemical compounds via reference 3 (bottom).

This group of scientists observed the molecular fingerprints of many newly forming stars before stumbling on protostar IRS46 in Ophiuchus. The protostar showed a very interesting mix of acetylene (C₂H₂), hydrogen cyanide (HCN), and carbon dioxide (CO₂) gases.

Images credit: via reference 3, below.

None of the other protostars observed had these gases, possibly because IRS46 is oriented with it’s planet forming plane directly along Earth’s line of sight. Observing these gases around protostars is very exciting, because they are some of the most basic building blocks of protein and DNA! [Other protostars, such as HH46 IRS, offer some spectacular absorption features of some common molecules as well in their outflows.]

Image credit: Noriega-Crespo et al. 2004, ApJS, 154, 352.

So there you have it, a taste of astrochemistry! Our universe is full of fantastic stars that are fusing heavier elements from the hydrogen and helium created during the Big Bang and recycling them into supernovae and planetary nebulae, more stars, planets, and even you and me. When you look up into the night sky now, I hope you’ll keep in mind that while there’s a lot of hydrogen floating around out there, there’s also much, much more.

BONUS: “BUT WAIT! How do these reactions happen when the universe is generally so COLD?!”

Good Question! Some scientists recently suggested quantum tunneling might be the answer.^[4] If you get a smirky ‘cool’ smile anytime quantum tunneling is mentioned, don’t worry, I do too. Let me take a second to explain more clearly what quantum tunneling is, exactly. Quantum tunneling is a process where a very small portion of many particles are able to tunnel through an insurmountable energy barrier instead of traveling up and over the energy barrier. So what does quantum tunneling have to do with chemistry in interstellar space? Well, every chemical reaction has some energy barrier between the reactants and products. This energy barrier is called the activation energy of the reaction. Sometimes the thermal energy at room temperature is enough of a kick for a reaction (acid-base reactions), while other reactions require a much harder push (a spark to ignite the gas in your car’s engine).

Image credit: Richard Helmich.

Back to astrochemistry, among the more common molecules found in the universe are methanol (CH₃OH) and hydroxyl radicals (·OH). These chemicals react to create a methoxy radical (CH₃O·) and water. All of these have been observed in outer space, but the activation energy required for this reaction was thought to effectively prevent it from happening at the temperatures found in outer space, ~ 20 K. No one had actually attempted to measure how well these chemical reacted with each other at temperatures approximating those in space. Until now!

Image credit: Arrhenius plot of the reaction rate constant, k1, verses temperature for CH3OH + -OH ↔ CH3O+ + H2O. Via reference 4.

This graph shows the reaction rate constant for methanol reacting with hydroxyl radicals. Data on the left are historical and show the thermodynamic reaction path. As the temperature decreases, the rate of the reaction also decreases, but those two points on the upper right (2σ-shown) show that at even lower temperatures, the rate increases. One of the ways for a chemical reaction to form products faster than the thermodynamic path (and the most likely culprit for this reaction) is for quantum tunneling to occur. The solid line is the combined thermodynamic and quantum tunneling best fit computer model.

The Universe is an amazing place to live, and nature always finds a way to do what it wants. Even if that means a little cheating via quantum tunneling. ☺

References:

Ziurys, Lucy M. The chemistry in circumstellar envelopes of evolved stars: Following the origin of the elements to the origin of life Proceedings of the National Academy of Sciences2006, 103, 12274-12279.
Klemperer, William Interstellar Chemistry Proceedings of the National Academy of Sciences of the United States of America 2006, 103, 12232-12234.
Dishoeck, Ewine F. Chemistry in low-mass protostellar and protoplanetary regions Proceedings of the National Academy of Sciences 2006, 103, 12249-12256.
Shannon, Robin J.; Blitz, Mark A.; Goddard, Andrew; Heard, Dwayne E. Accelerated chemistry in the reaction between the hydroxyl radical and methanol at interstellar temperatures facilitated by tunnelling Nat Chem, advance online publication.

esiegel Thu, 08/01/2013 - 05:41

Tags

Thanks so much for the guest post. That was awesome.

Thank you Richard and Ethan

I hope this isn't too off topic... In the period just before the formation of the first suns [380M years after BB] could there have been all the elements present, but in absolutely minute quantities for those above Be-8? I'm thinking that there must have been instances of fortuitous collisions between atoms where the energies were sufficient to form minuscule amounts of the elements B, C, N, O etc without processing through stars

Just a thought...

Michael,

According to my calculations, Beryllium-9 is a pretty hard limit. The Coulomb barrier becomes very large and the Universe is pretty cold by time Helium forms, so while it's conceivable that you might get lucky and wind up with a few atoms of Boron, I don't see how Carbon-and-higher will be formed. That is to say, there are only around 10^80 atoms in the observable Universe, and the odds of forming Carbon (or higher) during Big Bang Nucleosynthesis is somewhere in the vicinity of less than 10^-80, probabilistically.

The universe would have more atoms in it before inflation took them away, Ethan.

Though that would have to be a hell of a lot more to get *Carbon* forming, since the energies aren't appropriate until you add a million degrees of heat in the atmosphere of a large sun to make up the difference.

But it could give a chance of an over-production of Helium making Carbon possible.

Hyper-stars would be an easier option and may be the only (if extremely rare) type of star that could form that early in the universe.

A prof at my university has some pet theories about that, never took it far enough to put limits on the options made possible, though.

Maths beyond ten fingers is hard... :-)

Very interesting post. I find it mind-blowing that detailed knowledge of the chemical constituents of such remote astrophysical bodies can be gleaned from astronomical instruments. To find evidence of the molecules that make up building blocks of proteins and DNA, already formed around nascent stars -- that's stupendous stuff. Part of me feels that people should be shouting this stuff in the streets -- but my family would dismiss that as the geek within me talking. Keep up the good work on this excellent blog.

Really awesome post !!! a taste of real chemistry behind dark science.

A very fascinating book giving the history (and physics) of these discoveries is one by Marcus Chown entitled "The Magic Furnace (The search for the origin of Atoms)"

"a taste of real chemistry behind dark science."

If you want a real "taste" of chemistry, how about this: The center of the milky way tastes like raspberries and smells of rum! Think I'm lying? Look it up!

I've seen reports recently on how neutron star collisions, as a hypothetical source of short-duration gamma ray bursts, may be responsible for quite a bit of the synthesis of "neutron rich" heavy elements (e.g. gold). How significant this is compared to say "standard(?)" nucleosynthesis via supernovae?

http://arstechnica.com/science/2013/07/making-heavy-elements-by-collidi…

love your site .

An Atom in the Universe

esiegel — Wed, 06 Mar 2013 17:55:13 +0000

An Atom in the Universe

"The atoms come into my brain, dance a dance, and then go out - there are always new atoms, but always doing the same dance, remembering what the dance was yesterday." -Richard Feynman

Here you are, a human being, a grand Universe of atoms that have organized themselves into simple monomers, assembled together into giant macromolecules, which in turn comprise the organelles that make up your cells. And here you are, a collection of around 75 trillion specialized cells, organized in such a way as to make up you.

Image credit: J. Roche at Ohio University.

But at your core, you are still just atoms. A mind-bogglingly large number of atoms -- some 10²⁸ of them -- but atoms nonetheless.

Image credit: Ed Uthman.

Those two things -- you and an atom -- may seem so different in scale and size that it's hard to wrap your head around. Here's a fun way to think about atoms: if you broke down a human being into all the atoms that make you up, there are about as many atoms that make up you (~10²⁸) as there are "a-human's-worth-of-atoms" to make up the entire Solar System!

Image credit: Superb Wallpapers, via http://www.desktoplemming.com/.

All the matter in the Solar System, all summed together, contains about 10⁵⁷ atoms, or 10²⁹ human-beings-worth of atoms. So an atom, compared to you, is as tiny as you are in comparison to the entire Solar System, combined.

But that's just for perspective. The 10²⁸ atoms that are existing-as-you-right-now each have their own story stretching back to the very birth of the Universe. Each one has its own story, and so today I bring you the story of just one atom in the Universe.

Image credit: Lawrence Berkeley National Lab / UC Berkeley / US Dept. of Energy.

There was a time in the distant past -- some 13.7 billion years ago -- when there were no atoms. Yes, the energy was all there, but it was far too hot and too dense to have even a single atom. Imagine all the matter in the entire Universe, some 10⁹¹ particles, in a volume of space about equal to that of a single, giant star.

The whole Universe, compressed into a volume of space that one large star takes up.

Yes, back then it was too hot to have any atoms at all. But the Universe didn't stay that way for long: it may have been incredibly hot and dense, but it was expanding and cooling incredibly rapidly back then. After less than a second, the quarks and gluons had condensed into stable protons and neutrons, the building blocks of all atomic nuclei.

Image credit: Gauss Centre for Supercomputing (GCS) / Sabine Höfler-Thierfeldt.

The atom we're thinking of started out as a neutron. Protons tried to fuse with it to create deuterium, but the Universe was too hot for that to happen, and each time it formed deuterium, it was blasted apart less than a nanosecond later.

After about three minutes, a few of the neutrons had decayed into protons, but this one remained, and finally the Universe had cooled enough so that nuclear fusion could proceed. The neutron quickly formed deuterium, then Helium-3, and finally found another deuteron to become a Helium-4 nucleus. Only about 8% of the atoms in the Universe became Helium-4 like this one; the other 92% were just plain old protons, also known as Hydrogen nuclei.

Image credit: Pearson Education, Inc., 2011.

It took another 380,000 years for the Universe to cool enough for this to become a neutral atom, and for two electrons to join this nucleus. The Universe -- despite its rapid expansion and cooling -- remains 100% ionized until the temperature drops to just a few thousands of degrees, which simply takes that much time.

Image credit: James N. Imamura of University of Oregon.

Over the next hundred-million years or so, this atom found itself caught up in the gravitational pull of the Universe, which began to form stars and galaxies. But the vast majority of atoms -- more than 95% -- weren't a part of the first generation of stars, and neither was this one in particular.

Instead, when the first stars formed, they kicked the electrons out of the atoms that surrounded them, creating ions once again.

Image credit: NASA/JPL-Caltech.

It was only by luck that this atom we're following wound up in a dense molecular cloud, shielded from this radiation. After more than a billion years in this collection of neutral atoms, it finally found itself pulled in by gravitational attraction to what would become a giant star.

Image credit: NASA, ESA, and F. Paresce, R. O'Connell, and the WFC3 Committee.

This atom lost its electrons and fell to the core of the star, where it lay dormant for millions of years, as hydrogen nuclei fused into other helium nuclei just like this one. When the core ran out of hydrogen fuel, helium fusion began, and our atom fused with two others to become a carbon nucleus!

Image credit: Nicolle Rager Fuller / NSF.

While other atoms even closer to the center of the star fused further, carbon was as far as this particular atom went. When the core of the star collapsed and the star went supernova, our atom was blown out into the interstellar medium, where it resided for billions of years.

Image credit: X-ray: NASA/CXC/Caltech/S.Kulkarni et al.; Optical: NASA/STScI/UIUC/Y.H.Chu & R.Williams et al.; IR: NASA/JPL-Caltech/R.Gehrz et al.

While billions of other stars went through the life-and-death cycle, this carbon atom remained in interstellar space, eventually picking up six electrons to become neutral. It found its way into a gravitational collection of neutral gas, and cooled, eventually getting sucked in to another gravitational perturbation, as star-formation happened all over again.

Image credit: Tony Hallas of http://www.astrophoto.com/.

This time, the atom didn't find its way into the central star of its system, but rather into the dusty disk that surrounded it. Over time, the disk separated into planetoids and planetesimals, and this atom found itself aboard one of those.

Image credit: NASA.

It first joined together with four hydrogen atoms, becoming methane, and went through millions of different chemical reactions over time.

Image credit: 2009, Zappa, via http://macroworlds.com/.

After life took hold on Earth, it became a part of a bacterium's DNA, then a part of a plant's cell wall, and eventually became part of a complex organism that would find itself consumed by you.

Image credit: Anna of http://mtkilimonjaro.blogspot.com/.

The atom is currently in a red blood cell of yours, where it will remain for a total of about 120 days, until the cell is destroyed and replaced by a different one.

Image credit: Mohamed Zakzouk, ~zakzak008 of deviantART.

Although the cell -- and all cells in your body -- will be destroyed and replaced, you will remain the same person you are, and the atom will simply take on a different function, whether in your body or out of it. The atoms in your body are temporary, and can all be replaced -- unnoticed by you -- by another of the same type.

Image credit: Youngester of http://technicalstudies.youngester.com/

And each of the 10²⁸ atoms in your body has a story as spectacular and unique as this one! As Feynman famously said,

"I / a Universe of atoms / an atom in the Universe."

The story of the Universe is inside every atom in your body, each and every one. And after 13.7 billion years, 10,000,000,000,000,000,000,000,000,000 of them have come together, and that's you. The Universe is inside of you, as surely as you're inside the Universe.

Image credit: ESO / the VIsible MultiObject Spectrograph (VIMOS) at the VLT.

You, a Universe of atoms, an atom in this Universe.

esiegel Wed, 03/06/2013 - 12:55

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Giving thanks for our place in the Universe

esiegel — Wed, 21 Nov 2012 15:51:09 +0000

Giving thanks for our place in the Universe

“We live in an atmosphere of shame. We are ashamed of everything that is real about us; ashamed of ourselves, of our relatives, of our incomes, of our accents, of our opinions, of our experience, just as we are ashamed of our naked skins.” -George Bernard Shaw

All that is real about ourselves is nothing to be ashamed about; quite to the contrary, it's something to be eminently thankful for. This very existence is all we have, and while it's minuscule compared to the entire Universe, it required the entire Universe to bring us to the point where it's possible for us to exist.

What do I mean by that?

I mean that everything we've ever known about our existence owes its origins to something far grander than our experiences here on Earth would have us believe. Yes, it's true that our experiences on Earth, stemming from the very first proto-cell ever to reproduce itself billions of years ago, whose legacy is encoded in the nucleic acids of every creature in existence today, provide us with a remarkable and rich natural history that managed to lead to us. Without the events of the past four billion years on Earth, each one of us, to say nothing of the trillions of generations of living creatures that we're descended from, would never have existed.

Image credit & copyright: Leonard Eisenberg, 2008, of http://evogeneao.com/.

(The turkey that many of us will be eating tomorrow is perhaps our 160,000,000th cousin, some 50,000,000 times removed.)

But those same atoms that now make us up -- that millions of years ago made up our ancestors -- have been around on our planet since its birth, some 4.5 billion years ago.

Image credit: ESA / Rosetta Spacecraft.

And where did those atoms come from?

Practically all of the atoms we find on Earth: Nitrogen, Oxygen, Carbon, Iron, Silicon, Sulphur, Nickel, Magnesium and Calcium -- over 99% of the atoms on our planet -- were once inside of a star that went through its entire life cycle, burned up all of its nuclear fuel, and died in a spectacular supernova explosion.

Image credit: NASA / JPL-Caltech / S. Stolovy (SSC/Caltech).

That burned-up fuel from prior generations of stars that lived and died created practically all the heavy elements -- every single atom heavier than element #4, Beryllium -- that exists in the Universe today. Only after multiple generations of stars, living and dying, their fused atoms recycled into star-forming regions rich in unburned hydrogen and helium, could a star system like ours, complete with rocky planets and the ingredients for life, be formed.

Image credit: GIMP user and astronomer Griatch; http://tinyurl.com/GriatchAstro.

In order for those stars to exist, burn, recycle their elements, and eventually form successive generations containing planets, heavy elements, and life, it required a Universe full of massive galaxies, loaded with the light elements capable of forming stars in the first place.

Image credit: NASA, ESA, M. Postman (STScI), and the CLASH Team.

The galaxies themselves, great cosmic spirals, ellipticals, and irregular behemonths, collections of billions or even trillions of suns' worth of matter, are the gifts of a matter-filled Universe operating under the laws of gravity. Given the history of the Universe, some small fluctuations away from a perfectly uniform density, and general relativity, gravitation ensures that you'll get a Universe filled with hundreds of billions of galaxies, each containing, on average, hundreds of billions of stars.

It took the first 9 billion years of stars forming and galaxies merging and growing to set the stage to form our Solar System and the planet that we all call home. And it took the entire Universe, complete with our expanding spacetime and the laws of physics that govern everything that exists, to do it.

Image credit: NASA, ESA, Hubble Heritage Team (STScI / AURA); J. Blakeslee.

And what's amazing is that -- if you're willing to start with expanding spacetime and the laws of physics -- a Universe that looks a whole lot like ours, complete with clusters, galaxies, stars, planets, heavy elements, and, most probably, life, is inevitable. And it's inevitable all over the Universe.

Image credit: NASA, ESA, and the Hubble Heritage (STScI/AURA)-ESA/Hubble Collaboration.

So don't be ashamed of what you are; be thankful for all that you are!

Tomorrow (Thursday) marks American Thanksgiving, an annual harvest festival and feast where we celebrate a variety of things, particularly the good things that have come to us in life. While I myself have a great number of personal things to be thankful for, including six wonderful years with my partner, Jamie, and nearly five years of sharing this Universe with you here at Starts With A Bang, the story of where we come from is universal to us all, and it's something we can all be thankful for together.

Image credit: HD Desktop Wallpapers, of Snake River in Grand Teton National Park.

Happy Thanksgiving to each and every one of you out there -- whether you celebrate it or not -- and may your lives be filled with a wonderful bounty of things to be thankful for, today and all the days of the year!

esiegel Wed, 11/21/2012 - 10:51

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Happy Thanksgiving to you and yours, and thanks for the wonderful blog!!

Your thanksgiving blog is indeed magnificent! To me "God" and "Universe" are equivalent terms and so let me wholeheartedly join you in this Thanksgiving.

Better than any pray I'll be forced into listening to today. Thankyou. I love the Shaw quote.

Thanks, and thanks for your ongoing creativity on this blog, and very best wishes!

Family, friends, good rational people, enthusiastic teachers like Ethan. There are a lot of candles in the dark to thank for lighting our journey through this fascinating place.

How do you get matter from an exploding star to reconverge into things such as planets, complete with angular velocity/rotation?

Collisions.

Some lose energy and leave, some gain and fall in.

Thank you for the inspiring reminder. May I never be distracted from our wonderfully infinite and eternal Being-in Love....

Thank you and happy thanksgiving! Today I am thankful for my existence, my family, friends, good health, and this blog!

Uh that should have been the other way round.

For those who feel like the universe is trying to kill them.It probably is.You can't get out of the universe either.And time is never going to end. I don't envy them and its because I am in a better position.For this I am greatful.

Shame has been used by the elite to control. That doesn't mean, however, that humans should abandon the very real and useful tool of shame. There ARE very real reasons one should be ashamed: such as lying, cheating, stealing, etc. Unfortunately, articles such as this simply re-inforce the new age notion that we should abandon all shame: which leads to a free for all of "anything goes."

The analogy is our relationship to anger. Our culture has given us the notion that anger=violence, which it does not. However, that brainwashing has successfully stripped us of our sense of justice and taking action based on the outrages of inequality.

DISCERNMENT is key in understanding the nuances of all of the natural emotions of humans. I'd like to see a bit more going on here in this article.

I am most thankful for the work that you and all scientists do, and particularly for this blog in which you make it accessible and understandable for lay people like myself.

"Unfortunately, articles such as this simply re-inforce the new age notion that we should abandon all shame"

OK, I'm confused.

Where does it say that? Or should you feel ashamed for posting to the wrong thread?

May all praise and glory be given to our heavenly father, Jehovah. He created all things in existence, through his son Jesus Christ and for his son.

A cascade of ecological events with unforeseen consequences is occurring around us. There are multiple causes. But human overpopulation of Earth is the prime factor.

Not really.

USA have a per-person footprint 6x the average.

I.e. maybe 8x the mode.

If the USA went to the average (and everyone above the average did so too), we'd have the ecological footprint for many things of a planetary population around a billion.

Are you maintaining that the planet cannot handle a billion people?

Thaks for this blog!! great story.. and great evo chart.. I took my son to the American Natural History Museum for Thanksgiving!

Well, I've been wanting to say "thanks" to Ethan for his new comment policy. It's helped to keep discussions on the point of the post and science and civil. So thanks Ethan.

It's so nice to see people communicate civilly. fundamentally, I believe in and like people. All kinds of people. People and relationships (e.g. through their activities in arts, science, play and ideas, etc. family, friendship, nature) are the real riches, the only richness to be desired and values.

So thanks Ethan for your excellent and welcoming blog. Yes this blog is a very welcome place to listen, learn, participate with seriousness, or humor, to join in wonderful astrophysics (i.e. human) discussion.

As to giving thanks for my place in the universe, who exactly am I thanking? Ahh yes, each you. Yes you friend, family, adversary, whether near or far, whether physical, virtual and/or psuedononimous (is that a word, well it is now).

Yes it is you, each personally, to whom I give thanks.
My toast to each of you, "To you, all the best.".

Hey Chris Bush,

To those of us who don't believe your creation myths, I suppose eternal torment in Hell awaits us.

Your Jehovah is not worth believing in.

What Goes Around Is Really Round: "Improved measurement of the shape of the electron"

drorzel — Fri, 27 May 2011 08:02:28 +0000

What Goes Around Is Really Round: "Improved measurement of the shape of the electron"

The big physics story of the week is undoubtedly the new limit on the electric dipole moment (EDM) of the electron from Ed Hinds's group at Imperial College in the UK. As this is something I wrote a long article on for Physics World, I'm pretty psyched to see this getting lots of media attention, and not just from physics outlets.

My extremely hectic end-of-term schedule and general laziness almost make me want to just point to my earlier article and have done with it. But really, it's a big story, and one I've been following for a while, so how can I pass up the chance for a ResearchBlogging post on this?

OK, you said this is about a dipole moment, but the headlines all talk about measuring the shape of an electron. What do these have to do with one another? A "dipole moment" is just a bit of mathematical apparatus used to describe a non-spherical distribution of charge. It turns out to be mathematically convenient to talk about "polar moments" of various fields in electricity and magnetism. The simplest sort of field is a "monopole," made by a point charge, which pushes other like charges directly outward from itself. Slightly more complicated than that is a "dipole" pattern, which is like what you get when you sprinkle iron filings over a magnet-- the field pushes out at one end, and pulls in at the other, and has some sideways component in between. You can make an electric dipole by putting a negative point charge close to but not exactly on top of a positive point charge.

So, an electron is made up of a little positive thing stuck to a bigger negative thing? There doesn't need to be actual positive charge present-- you can just take some of the negative charge from one pole of a spherical ball of charge and move it to the other pole. That creates a little bit of a dipole moment, too, without needing any of the opposite charge.

OK, so an electron is supposed to be like a ball of charge with a bump on one side and a divot on the other? Well, it could effectively look like that, but this measurement shows that it doesn't. Which in some ways isn't surprising, because it shouldn't be anything but round, according to the simplest models of physics.

Wait, what? These guys set out to measure something that shouldn't exist, and they're getting in all the papers for not finding it? Isn't that kind of a racket? Yes and no. The simplest models of physics tell us that the electron shouldn't have an EDM, because it would violate time-reversal symmetry.

What does making an electron lumpy have to do with time? The thing is, the electron isn't just a point charge. It also has a magnetic dipole moment, which is associated with a property called "spin," because it looks like what you would get if the electron were a spinning ball of charge (it's not literally a spinning ball, but it behaves as if it were). The magnetic dipole moment points along the axis of the spin, and the electric dipole moment, if it exists, must also point along the spin axis, in either the same direction or exactly the opposite direction.

Now, the laws of physics should be symmetric in time-- that is, if you made a movie of a simple particle's behavior, and ran it backwards, there shouldn't be any way to tell which direction the video was playing. An electron EDM violates this, though, as seen in this picture lifted from my Physics World article:

In the figure, the blue arrow represents the direction of the spin of the electron, the purplish ball of charge. If you take a little bit of charge from one pole and move it to the other, as in the second figure, you create an EDM, shown by the red arrow in the middle figure, which points in the same direction as the spin.

When you reverse the flow of time, though, as shown in the picture on the right, the blue spin arrow reverses its direction, because the electron is now "spinning" the other direction. The EDM, however, stays where it is, because reversing the spin direction doesn't affect the position of the extra lump of charge. So, the electron with time going forward has both arrows in the same direction, while with time going backwards, they point in opposite directions. This violates time-reversal symmetry.

So the electron shouldn't have an EDM, and these guys were wasting their time looking for it. Why is this news? The thing is, we know that there should be some processes in the universe that violate time-reversal symmetry. If time-reversal symmetry were never violated, then another symmetry of the universe, "CP" symmetry would never be violated, either. But if CP-symmetry wasn't violated, the Big Bang would've created equal amounts of matter and antimatter, which would've annihiliated leaving nothing but photons. Since nearly everything we see in the visible universe is matter, not antimatter, we know there must be CP-violation, which means there must also be T-violation. Thus, it should be possible for an electron to have an EDM.

So, wait, if there are time-reversal symmetry violations, does that explain the arrow of time? Do I look like Sean Carroll? Go ask him.

OK, OK, don't get touchy. So, now you're telling me that this EDM thing ought to exist, even though it shouldn't, and that's why it's big news that they didn't find it? Well, it can exist. The problem is, the Standard Model of particle physics predicts an absurdly tiny EDM, so small you could never hope to measure it.

We know that the Standard Model can't be the complete story, though, and most theories of particle physics that go beyond the Standard Model predict the existence of exotic particles that would allow a bigger electron EDM. The predictions of those models are much larger, in a range that a really clever experiment can hope to detect.

So, this experiment is looking for an EDM that would only exist if some exotic theory of physics was true? Right. The basic situation is summed up in this plot, again lifted from the Physics World article, which I got from Dave DeMille at Yale before that:

The horizontal axis here represents the size of the EDM predicted by various theories, with smaller EDM's to the right, and each line representing an order of magnitude decrease in size (it's like an astronomy plot, basically-- backwards and logarithmic). The red blob in the upper right is the Standard Model prediction, while the other colored blobs represent the possible ranges of EDM's predicted by a host of more exotic theories. The solid line represents the best experimental limit on the electron EDM, which you can see is already cutting into the theoretical predictions.

And this new paper shifts that line to the right? Exactly. It moves the experimental limit most of the way to the next tick mark.

And they did this by, what, grabbing a bunch of electrons and sticking them in an electric field? Not exactly. If you just stuck a bunch of electrons in an electric field, you would just make a particle accelerator-- they'd go whoosing off toward the positive side of your field, and not stick around to be measured.

To do this sort of measurement, you need electrons that will stick around for a while, but that experience a big electric field at the same time. The way to do that is with polar molecules.

Polar molecules? Molecules from Antarctica? No, molecules that are positive on one end, and negative on the other (very roughly speaking). If you take a really heavy atom (ytterbium, in this case), and bind it into a molecule with a really light atom (fluorine, in this case), you get a situation where the electrons inside the YbF molecule see a really big electric field. And if you apply a moderately large electric field to a sample of these molecules, you can line them all up in a way that produces a measurable shift in the energy levels of those electrons. You can measure that shift using clever techniques from atomic spectroscopy, which are explained in more detail in that Physics World article.

You're really high on that, aren't you? It's some of my best work. Anyway, the point is, you can measure exceedingly tiny shifts in the energy levels of these molecules. And the direction of the shift should depend on the direction of the electric field that you apply to the molecules. For one field direction, they shift up, while for the opposite direction of the field, they shift down.

So, you take a bunch of them, put an electric field on and measure the energy levels, then reverse the field and see what happens? In broad outline, yes. Of course, it's much more complicated than that, because there are all sorts of systematic effects that might make it look like the shift changed due to the changing field, when really it didn't. The bulk of the work for this paper, like any precision measurement paper, was in tracking down and ruling out as many of these systematic errors as possible.

Such as? They looked at things like a possible slight offset in the field, which would prevent them making a complete reversal. And a possible leakage current from the high-voltage electric fields plates slowly discharging through the rest of their vacuum system. And a possible stray magnetic field cause by induced polarization of their magnetic shields due to the transient current when they switched the electric field direction. And lots of other things.

That sounds... Kind of maddening, really. It does take a certain personality type to succeed in that business.

And after all that, they measured nothing? Yes. They measured nothing better than anybody has ever measured nothing before. Their data look deceptively simple:

Those eight points represent a total of 25 million individual measurements of the edm shift, not counting a bunch of additional checks on systematic errors. The error bars are due to the uncertainties in the individual measurements, while the solid line represents the average of all eight. The dashed lines give the uncertainty in the average, which you can see is more than big enough to include zero. Thus, the end result of all the work is that they have not detected any EDM distinguishable from zero.

That's... not as dramatic as it might be. Which is probably a big reason why they phrase the report in terms of an absurdly precise measurement of the "roundness" of the electron charge distribution. They're accentuating the positive.

So, does this answer any outstanding questions in particle physics? Not yet, no. It does make life even tougher for some moderately popular theories, though. It takes another small bite out of that theory graph up above.

But is that it? I mean, they've done their best measurement, so is it hopeless from here? Hardly. They've done a really spectacular job with this measurement, but there are some clear steps forward to the next round. They know what they need to do to reduce some of their biggest sources of systematic uncertainty, and push the limit down even farther.

There are also lots of other groups at work in this area, trying to find an electron EDM in other types of molecules-- thorium monoxide is a fun new contender-- and other systems as well. DAMOP has a whole session on precision measurements coming up in a couple of weeks, with about half of the talks having to do with EDM searches, and there are probably a slew of posters on the subject as well. It's a hot field right now.

Thanks, that was very helpful. Would you like to close this with a cheap shot at particle physicists? Not a real cheap shot, no, but I do think it's worth pointing out that these experiments explore some of the same areas of fundamental physics that you get in experiments at the LHC, with a budget 3-4 orders of magnitude smaller than the cost of the LHC. These are incredibly impressive examples of the art of experimental physics, and all these experiments fit into ordinary-size labs in physics departments all over the world.

I think these are amazing experiments that don't get enough publicity most of the time, so it's good to see them finally getting some press. And I think it would be absolutely awesome if one of the many EDM search experiments managed to scoop the LHC by either ruling out all the popular variants of supersymmetry by pushing the EDM limit down below the range they can predict, or turned up the first positive proof of some beyond-the-Standard-Model theory by finding a non-zero EDM. But then, I'm biased, because this stuff originates in my little corner of physics...

(In addition to the oft-mentioned Physics World article, there's a good ResearchBlogging write-up of this over at A Quantum of Knowledge, which I discovered when I went to ResearchBlogging to get the citation code below.)

Hudson, J., Kara, D., Smallman, I., Sauer, B., Tarbutt, M., & Hinds, E. (2011). Improved measurement of the shape of the electron Nature, 473 (7348), 493-496 DOI: 10.1038/nature10104

drorzel Fri, 05/27/2011 - 04:02

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Thanks for the link back! I've been a big fan of your writing for a long time!

Really nice post. In particular I agree completely with:

"I think these are amazing experiments that don't get enough publicity most of the time, so it's good to see them finally getting some press. And I think it would be absolutely awesome if one of the many EDM search experiments managed to scoop the LHC by either ruling out all the popular variants of supersymmetry by pushing the EDM limit down below the range they can predict"

thanks
Marco

Wow! That was the most compelling writing on physics I've read in as long as I can remember. Very clear and interesting explanation of a tough topic. Much appreciated.

Nice writeup.

How much an improvement is this on the previous best result?

A lot of work put into this post, thanks. Note that even though the electron could in principle have (effectively) and EDM, it is also to be considered a "point charge." To rehash some physics history: Electric field has some energy content, proportional to E^2. If you integrate the simplistic field of an electron to the "classical electron radius" you get the entire mass of the electron. Well, if you simplistically include "all the way down" to a point, you get infinite energy. (Classically, even w/o QM.) This energy must have inertia, which causes trouble if it exceeds electron mass.

The QM solution is roughly, that the e-field polarizes the vacuum of temporary virtual electron-positron pairs. This draws positrons closer to the electron etc. which makes the field near the "singularity" less intense. It's a sort of renormalization. However I still don't see how we could avoid an effective electromagnetic mass larger than m_e with this. There would have to be very much weakening of electron field in the vicinity of the CER value to have integrated field energy not overshoot (which even then wouldn't explain why the electron has the basic, "undressed" mass and charge it needs.) I'd like to see a chart that compares actual electron E field (like from e to e collisions) to the Coulomb value, at various radii from center. What integrated inertia does that produce? Maybe I'm oversimplifying or missing some angles, but it should be a legitimate start to an answer from someone. (Maybe the author could deign to start replying again ;-)

Is one of the theories really called "extended technicolor"? Or is it there just to see if anyone is paying attention?

@6 don't you own a wikipedia?

Amit:

There's also the problem with "The Axis of Evil" in cosmology. Really, I'm not joking - look it up.

electrons r not sphere shaped their like needle shaped like compass needles.ck out the works of Maurice Cotterell.mainstream particle physics is bs...

You should have made a stronger point about measuring nothing better than anyone had before. Anything that pushes the boundaries of experiment is a challenge, and at both extremes (a very crude measurement of something at high energy or a very precise measurement of nothing at low energy) you have to put most of your attention on statistics and the possible uncertainties in your measurement.

Noise or signal? Bump or fluctuation? Same problem.

Do I look like Sean Carroll?

No, he's a cat person.

Inconstant Constants: "Probing fundamental constant evolution with redshifted conjugate-satellite OH lines"

drorzel — Wed, 12 May 2010 12:09:18 +0000

Inconstant Constants: "Probing fundamental constant evolution with redshifted conjugate-satellite OH lines"

Via Jennifer Ouellette on Twitter, I ran across a Discovery News story touting a recent arxiv preprint claiming to see variation in the fine-structure constant. It's a basically OK story, but garbles a few details, so I thought it would be worth giving it the ResearchBlogging treatment, in the now-traditional Q&A format.

What did they do? The paper looks at some spectral lines in radio emission from a moderately distant galaxy with the poetic name "PKS1413+135." These lines are produced by OH molecules in interstellar gas clouds, and the frequencies they see suggest that there may have been changes in some dimensionless constants during the not quite three billion years since the light was emitted.

Dimensionless constants? What are those? Most of the things we tend to think of as fundamental constants-- particle masses, Planck's constant, and that sort of thing-- are numbers with units. The only way to really measure one of these things, though, is by measuring it relative to one or more of the others. As a result, people who think about hard-core particle physics and cosmology and that sort of thing prefer to talk about "dimensionless constants," which are ratios of these things arranged so that all the units cancel. The most famous is the "fine structure constant" α which is the ratio of the electron charge squared to Planck's Constant times the speed of light, helpfully shown in an image lifted from Wikipedia. Other dimensionless constants of interest are the ratio of the proton and electron masses, and the "gyromagnetic ratio" which relates the spin of a fundamental particle to its magnetic moment. These ratios are the things that really matter if you want to look for changes in the fundamental constants.

Changes in the fundamental constants? Aren't they, you know, constant? You'd like to think that, but they don't necessarily have to be. And a lot of the tricks particle theorists pull when they're trying to explain fundamental forces end up giving you fundamental "constants" that change in time. This is something that you can look for experimentally, and that's what the current paper is about.

How do you do that? It's not like you can get a three billion year old proton and weigh it, can you? No, but you can look at the light emitted by really old atoms and molecules. The frequencies at which atoms and molecules emit light depend on the exact values of those dimensionless constants, so if the constants change, then the frequencies change.

How can you tell, though? Doesn't the Doppler shift from the expanding universe shift all the frequencies we see, anyway? The trick is to compare the light emitted by different transitions in the same atoms or molecules. Some states will shift up in frequency with a change in the fine structure constant (for example), while other states will shift down. Doppler shifts due to the motion of the universe or objects in it will always go in the same direction, depending on the velocity of the source. If you look at the relative frequencies of light from these different states, then, you can take out the Doppler shift, and still see if there's been a change in the relative frequencies.

Isn't that really difficult? It is, and while several attempts have been made to do this sort of analysis, it's hard to do well, and the results are not without controversy. This paper reports on a cleaner way of doing this basic measurement, using two different transitions in OH molecules.

How does that work? It's a really clever trick. They use a pair of radio-frequency lines emitted by OH molecules, one at 1720 MHz, the other at 1612 MHz (for reference, the FM radio station I listen to around here has a frequency of 102.7 MHz). These lines shift in different directions in response to changes in the constants. And, better yet, they behave differently in response to light, thanks to a maser effect.

A who what? Under the right conditions, you can get an astrophysical maser, in which gas clouds out in space absorb energy from radio waves at one frequency, and are stimulated to re-emit it at a different frequency, in much the same way that a laser takes energy from a pump, and uses it to produce photons at a different output wavelength. In particular, you can get a situation where OH molecules will absorb radio waves at 1720 MHz, and emit more radio waves at 1612 MHz.

So that's what this graph is? Right. It's actually half of a figure from the paper, but the other half is more or less identical, and just confuses matters. The blue line at the top is the absorption feature they see at 1720 MHz, flipped over so it forms an upward-going peak (so the peak is actually a place where they see less light). The red line is the emission feature at 1612 MHz, where they see increased light. To make this plot, the two lines have been shifted so they line up at the same point. The black curve is the sum of the two, showing that they really have the same shape, which confirms that they're coming from the same gas cloud.

So how does this tell us about changes in the constants? Well, careful analysis of the amount they need to correct each line to get the two to line up suggests that the values of the fundamental constants were different when these molecules were emitting light three billion years ago than they are now. The change isn't very big-- the change in the relevant parameter divided by the current value of that parameter is about -1.18 ± 0.48 × 10^-5, which is right at the edge of being trustworthy, statistically speaking (a bit more than twice the uncertainty). If you attributed all the change to changes in the fine structure comment, the fractional change would be -3.1 ± 1.2 × 10^-6, which is a little smaller than the other big result claiming a change (which looked over a longer time period), and bigger than other measurements that claim to see no change.

Well, that's pretty good. Yeah, it's very good for this sort of thing. It's also a very clean measurement-- the maser effect ensures that the lines they're looking at are from the same cloud of gas, and there's nothing else along the line of sight in the relevant frequency range that would mess up their signal. They even did it with two different radio telescopes, the big one at Arecibo, and the Westerbork Synthesis Radio Telescope in the Netherlands. Granted, this is not my exact field, but it looks like a fairly solid number, though at only 2.6 standard deviations, I wouldn't bet huge money on it yet.

So, they just need to do this a bunch more times, right? That's the catch. They can certainly do more observations of this particular source, for longer periods of time, which might get them an even better result, but the maser effect they're looking at it pretty rare, and there aren't a lot of known sources.

How many is "not a lot?" According to the paper, there's one other, PMNJ0134â0931. Which means they're not really going to be able to fight off claims that there's something anomalous about the source they're looking at, unless somebody finds a whole bunch more of these gas clouds to look at. (The earlier optical measurements used something like 140 different sources, and are still highly controversial.)

So, it's a cute technique and a suggestive result, but nothing that's going to rock particle astrophysics to its core? Pretty much. It's a very clever technique, and a nice analysis, but not conclusive by a long shot. If your Theory of Everything predicts that the fine-structure constant was a few parts per million smaller three billion years ago, it's reason to keep your hopes up (if you think it used to be bigger, you're screwed), but you shouldn't be expecting a call from the Nobel committee any time soon on the basis of this observation.

Nissim Kanekar, Jayaram N. Chengalur, & Tapasi Ghosh (2010). Probing fundamental constant evolution with redshifted
conjugate-satellite OH lines Astrophysical Journal Letters arXiv: 1004.5383v1

drorzel Wed, 05/12/2010 - 08:09

I think you mean g factor rather than gyromagnetic ratio. The gyromagnetic ratio has units of Hz/T (or gamma/2pi does anyway). The g factor is hbar*gamma/mu_b which is unitless and for a free electron g = 2.0023.

Honestly I'm not sure why the media has latched onto changes in fundamental constants as something interesting. Is there any credible data out there that this actually happens? More likely I suspect that they love this because the it reeks of "foundational issues" and thus goes nicely with their obsession with particle physics.

Could (or should) inconstancy of our constants be related to the rate of expansion of the universe (especially inflation)?

Thanks

How consistent is this result with the data from Oklo two billion years ago?

Honestly I'm not sure why the media has latched onto changes in fundamental constants as something interesting. Is there any credible data out there that this actually happens?

I don't want to sound like a dick, but did you read the post? To the limited extent that one Discovery News story constitutes "latching on," the justification is that this paper claims that it actually happens, at the 2.6 sigma level. So, yes, there's some credible evidence.

Could (or should) inconstancy of our constants be related to the rate of expansion of the universe (especially inflation)?

I will say "yes," based not on any actual knowledge, but on the observation that there seem to be theories relating the expansion of the universe to everything. I suspect you could probably find somebody crediting inflation for trends in pop music.

I don't know the current state of play for these sorts of theories, though.

How consistent is this result with the data from Oklo two billion years ago?

As I understand it, the Oklo results are consistent with no change, or possibly a change that is significantly smaller than that observed here. The analysis of those results is horrifically complicated, though, and has changed a few times.

Not to be a dick or anything, but quoting from the post: "It's a very clever technique, and a nice analysis, but not conclusive by a long shot."

So yes, thank you, I did read the post.

Many, many years ago there were a couple of theories floating around that variation in physical constants was directly related to the expansion of the universe. The idea was that certain large numbers often turned up. For example, the ratio of the electical force between a proton and electron and the gravitational force is ten to the 42. Similarly, the ratio of the size of a proton and the size of the universe (as known then) was also ten to the 42. The second varies in time, so therefore the first does as well. Jordan did one such theory and Brans and Dicke for another. IIRC neither stood up to any serious study.

and Mulder's apartment was #42!

Amazing Laser Application 2: Laser Cooling!

drorzel — Wed, 10 Feb 2010 08:47:20 +0000

Amazing Laser Application 2: Laser Cooling!

What's the application? Using lasers to reduce the speed of a sample of atoms, thereby reducing their temperature to a tiny fraction of a degree above absolute zero.

What problem(s) is it the solution to? 1) "How can I make this sample of atoms move slowly enough to measure their properties very accurately?" 2) "How can I make this sample of atoms move slowly enough for their quantum wave-like character to become apparent?"

How does it work? I've written about laser cooling before, but the nickel version of the explanation is this: You can think of a beam of light as being made up of photons, little particles of light each carrying a discrete amount of energy. In addition to having energy, those photons also carry a little bit of momentum (despite having zero mass). when an atom absorbs a photon, it picks up that momentum, so a stationary atom absorbing one photon gets a "kick" that starts it moving in the same direction the photon was headed. And atom that is moving either speeds up a little (if it was headed in the same direction as the photon), or slows down a little (if it was headed in the opposite direction).

So, you can use light to exert forces on atoms, and change their motion. Laser cooling is based on using these forces to make atoms move very slowly. The temperature of a gas of atoms is a measure of the kinetic energy due to the motion of the atoms, so slow atoms are cold atoms. Using laser cooling, you can take a gas of atoms from their room-temperature speed of something close to the speed of sound down to a pokey few centimeters per second-- from the speed of a jet airplane, to the speed of a crawling insect.

"Don't lasers usually heat things?" you ask. The key to cooling rather than heating is the Doppler effect. Atoms will only absorb very specific frequencies of light, and if you tune your laser to a frequency slightly below that which the atoms want to absorb, stationary atoms will not absorb any of the photons, and won't start moving. Atoms that happen to be moving toward the laser, though, will see the laser frequency Doppler shifted closer to their resonant frequency. This makes them more likely to absorb photons from the laser, which slows them down, because the alser is headed in the opposite direction from their motion. This gives you a way to selectively slow atoms down, cooling the sample.

Why are lasers essential? For laser cooling to work, you need a very narrow spread of frequencies in your light source, and you need to control the frequency of the light very precisely in order to take advantage of the Doppler cooling mechanism. Typical Doppler shifts are around one millionth of the overall frequency of the light used (MHz, rather than THz). The best way to get this kind of control over light is through using lasers.

Why is it cool? Dude, you can get a gas of atoms within a few one-millionths of a degree of absolute zero! If that doesn't count as "cool," I don't know what does.

At those temperatures, atoms are moving so slowly that you can do exquisitely precise spectroscopic studies of their properties, because the Doppler shifts due to their motion are so small. Laser-cooled atoms are now the basis for the best atomic clocks in the world.

You can also use laser-cooled atoms to look at the quantum-mechanical behavior of atoms as matter waves, for example, in collisions. Using laser cooling as a starting point, you can use other techniques to cool the atoms still further, eventually reaching Bose-Einstein Condensation, where all the atoms in the sample "condense" into a single quantum state, occupying a single wavefunction. This allows you to study a huge range of phenomena in quantum physics, atom optics, and condensed matter physics.

If you don't want to take my word for it, how about the Nobel committee? They've given two Nobel Prizes in physics for related work: 1997 for laser cooling and 2001 for BEC. That's pretty darn cool.

Why isn't it cool enough? Laser cooling only works well for a limited number of atoms and molecules, due to limitations of laser technology. There are other ways to make cold atoms an molecules that are more generally applicable, and some of them can be employed to reach BEC.

(This post is the second of twelve highlighting amazing laser applications, in honor of the 50th anniversary of the first laser. These posts serve as a lead-up to an audience poll asking what the coolest laser application is, so if you like lasers and radio buttons, watch this space over the next week or so.)

drorzel Wed, 02/10/2010 - 03:47

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Make a merry molecule mug!

sporte — Sat, 01 Dec 2007 12:36:08 +0000

Make a merry molecule mug!

The grocery store magazine covers all say that home made gifts are big this year. So I thought, some of you might like to channel your inner Martha Stewart and make gifts with a science theme.

I'm here to help to you make a merry mug with one of our favorite molecules. Yep, we're talking caffeine.

1. First, we'll go to PubChem at the NCBI. It's not an exclusive (or even last) resort but there are lots of fancy molecules hanging around, just waiting to be discovered and put onto drinking containers.

2. Now, we'll look for a molecule. I'm going to use caffeine for this example since I drink it religiously and many of the science instructors, that I know, are seriously addicted. What could be better than a mug shot of your favorite drug?

Type the word "caffeine" into the search box at the top of the page and click "Go".
I found 84 listings. It looks like caffeine is popular with NIH researchers, too.

If caffeine is too tame, you always search with the names of other drugs or small molecules. If you can't think of any drugs that you'd like to see on a coffee cup, Molecule of the Day has lots of ideas.

3.I clicked the link to the first reference to get the PubChem record that you see below.

At this point, I use my mouse to drag the image onto my desktop and now I have a picture like the one at the beginning that I can put on a mug. Since I use a Mac, I also like to crop the image with Preview and remove some of the grey background.

Getting a 3D structure image
If I really want to be fancy, I like to use a different kind of structure drawing. The PubMed record for caffeine (above) shows that there are five structures of proteins that also contain caffeine.

4. If I click a link to the top record, 2A3B, I get a structure from the Molecular Modeling Database that contains caffeine.

5.From there, I can click the structure image to download the structure to my computer. You will also have to download Cn3D (from the same page) to view the structure. Cn3D works on Windows, Macs, and Unix-based computers.

6.Now, you'll want to hide everything else so that caffeine is the only structure you see. First, I have to find the caffeine molecule in the structure and select it by clicking it.

7. Then, I open the Cn3D Show/Hide menu and choose "Show Selected Structures." Now, the only visible structure will be the caffeine.

8. I also like to open the Style menu, select Edit Global Style, and change the background color to white instead of black.

Now, I have a caffeine image that I can use for making a mug.

9.Last, I need to open the Cn3D File menu and choose Export PNG.

The last thing that I need to do is find a printing service and have my image printed on the mug. I often use the "Make your own stuff" service at CafePress, but there are many different places where you can get pictures printed on all kinds of items and shipped to your friends and family.

And, if you have truly crafty people on your gift list, you can always give them a fantastic book called "A Beginner's Guide to Molecular Structures" (yes, I wrote it!). The book shows all kinds of things you can do with structures of molecules.

Happy gifting!

sporte Sat, 12/01/2007 - 07:36

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Arts & Crafts

Chemistry & Biochemistry

I have a screen saver like this...

Does it help keep your computer awake?

A very pretty 3D model! If your readers want something flatter, though, one has to but surf over to ThinkGeek. :) Ceramic and travel mugs included!

I'm not selling mugs, or mouse-mats, or anything else - except my ideas :)

But if you click through my initials then you'll see that just yesterday I wrote on how every blog has its very own "molecular structure".

I have a blank white coffee mug which is great for doodling molecular structures on using whiteboard markers. You can just rub it off afterwards. Hours of fun. So you could probably put a blank, glossy white mug and some whiteboard markers together as a gift for a synthetic organic chemist.