Sunday, February 24, 2013

Photonic crystals

Photonic crystals guide certain wavelengths of electromagnetic radiation that have twice the wavelength as the size of repetitive parts with 2 different refractive indexes in crystal. For example ~650 nm red light can be captured and transmitted in crystals with ~320 nm repeating regions and ~400 nm blue light can be created with ~200 nm structures. These can also be used for larger wavelengths like radio waves or microwaves. Earlier photonic crystals transmitted microwaves as they have wavelength of ~1 mm to 1 meter making it easy to manually stack suitably thick layers. These crystals are basically waveguides like the metallic tunnels that guide microwaves to intended direction and they too transmit mainly certain wavelength that is twice the diameter of tunnel. Photonic crystals are made from 2 different nonconductors or from 1 metal and 1 nonconductor.   

Rainbow colored animals (including birds and insects) usually have structures (made of keratin in vertebrates or chitin in insects/mushrooms) with similar sizes but if light goes through so small openings they tend to diffract in almost every direction and interference combines them into colors that depend at which angle something is viewed.
 
If gold particles were added to photonic crystal they could increase its absorption of infrared and visible light by 62% and light to electricity conversion increased by 41%. 

 Above illustration shows photonic crystal usable as laser light source. Light is created in region surrounded by white dotted line. By skipping air holes in that region they create "quantum well" (QW above) which can capture photon energy and require certain energy to leave the "well". 

Skipping holes in photonic crystals can create waveguides like seen in a and c part. Dark spots show magnetic fields. Apparently having lattice constant (size of repetitive crystal parts)/wavelength=0,26 caused behavior seen in picture a but having that ratio at 0,24 caused Y shaped spreading seen in image c.
Other defects that can capture energy from photons can vary from having larger hole or no hole in area intended to capture photon energy.
Photonic crystal waveguides can slow light and by slowing it becomes more intense (shown with height on illustration) due to more compact size but same energy content.
This also seems to turn initial infrared laser pulse into visible green light (above) while it is in this compact slowed form. That light compacting is often seen as important part of optical computers as by slowing light it can amplify lights interaction with atoms and electrons. 
Cross section of photonic crystal fiber. Hollow holes have diameter of 4 micrometers. Minimum energy loss seems to be at least 10% (0,37 dB) per kilometer. Manufacturing could start with piece more than cm wide, then after heating it gets stretched, narrowing main piece along with the holes drilled in it. Resulting fiber could be over kilometer long and still preserve parallel holes. Light can travel at least in those air channels.

Photonic crystals in quantum cascade (QC) type lasers can be used for infrared lasers but as limitation it creates light that tries to travel within material parallel to surface and also researchers had to cool it to 10 K. Emitted light left this main photon cascade due to diffraction in holes. Material around holes is chosen so that contrast between refractive indexes would be as large as possible to help with reflecting. Holes could be added with narrow electron or ion beams. As last part titanium and gold were added on this structure so plasmons in them could carry light energy out of hole due to photons already pushing electrons perpendicular to surface with electrons in layer of metal transporting this energy to surface.

Infrared frequencies between 1-10 THz have practical use in detecting chemicals as molecules have resonance frequencies in that region. Authors used quantum cascade type laser shown in previous illustration with 5 K working temperature. This detectors could use change in frequency or change in refractive indexes to figure out substance (both change frequency). Gaseous molecules could reach inside of these air channels and get stimulated by light but different substances in these holes affect which frequencies they resonate. Due to low temperature they form solid layer within opening that affects contrast between refractive indexes and in turn causes lower emitted frequency. Afterwards they emit some wavelength specific to them and that can be measured by seeing how it travels through prism. Because this frequency has wavelength of 30-300 micrometers it is relatively easy to produce structures with that scale compared to 22 nm scale in some computer parts. In best case it seems to be able to detect single molecule.

Tuesday, February 19, 2013

Plasmons


Plasmons are oscillating electrons that are common in plasma (including fire) which can vibrate at the frequency of visible light (~400-700 trillion hertz) although large scale alternating currents in copper wires are at most few hundred thousand hertz. Plasmons can capture photons forming polariton (generic name to photon together with material that absorbed it).
Plasmon frequency also determines if material reflects photons or transmits them. If plasmon has higher frequency than photon then material reflects photon but if photon has higher frequency than plasmon then photon gets transmitted through material. In case of metal high frequency x-rays and gamma rays get transmitted through metals with increased frequency increasing transmittance distance but visible light and every EM radiation with slower frequency gets reflected. Plasmons in metals and semiconductors have plasmon frequency in UV light range. Certain narrow wavelengths in copper and gold transmit some visible colors as different electrons around atoms have bit different frequencies. It seems to happen because if plasmon has faster frequency than photon then it can respond to photons electric field but if it is slower than photon then it can't disrupt it well. Also in simplified terms plasmon energy is its frequency times Planck constant which is same formula as energy for photon energy. Predictably whichever particle has higher energy is going to somehow dominate over lower energy particle.  
Surface plasmons exist mainly on surfaces of metals that are exposed to dielectric (nonconducting) environment like air or vacuum. They weaken exponentially with increased distance from this surface area. Electron and photons can both create plasmons which fade fast by being absorbed through material or by getting emitted as photons.

Surface plasmon polaritons are infrared or visible light waves trapped on surface of metal where they have smaller wavelength than in form of photons. Surface plasmons move parallel to surface but with much more compact wave sizes.
Plasmons can be limited to area with size of about 0,007-0,02 cubic wavelengths.

Surface plasmon resonance (SPR) refers to plasmon oscillation in response to light. SPR is often considered in certain detectors like in above one. It need consistent laser (same distance and angle), metal for plasmon waves and prism to make different wavelengths pass prism in bit different directions so certain part of detector gets light only from certain wavelength making it easier for detector to see which wavelength did or didn't reflect back. Reflectivity depends on bumps on surface in addition to electric fields.
To create resonance light should reflect from given metal and it needs to be polarized parallel to surface so electrons would be pushed parallel to surface. If polarization is perpendicular to surface then plasmons can't build up resonance energy.

SPR can be used in molecular biology to test presence of certain antigens like organic toxins or any molecule that binds with antibodies. If antibody binds with antigen it can increase resonance unit (RU) signal with 1000 RU causing ~0,1 degree difference in angle of reflection and further binding with antibody receptor can increase it further. 



Above images (source 1, 2) illustrate plasmonic laser from 2009 that creates light in 5 nm insulating solid transparent gap between nanowire and silver. As one use this could allow use of visible light in much smaller scales than their wavelength.
Even blue light has wavelength that is at least 16 times larger than processors with present time 22 nm architecture but since 2009 it seems light can be compacted to within 5 nm gaps.
Above nanolaser was created by 2012. These gold using "bowtie" laser are about as large as a virus with size of ~150 nm. Laser light is produced within 30 nm region and plasmon electrons can have almost any frequency without needing to have wavelength that photons have with same frequency.  

Thursday, February 7, 2013

Insulin, IGF and cancer risks


Insulin, IGF (insulin-like growth factor) and other growth factors have tendency to stimulate cell division while somewhat blocking programmed cell death that could remove cancerous cells. This in turn makes high insulin activity more likely to stimulate growth of cancers almost through entire body. This is probably main reason why fattening diets get associated with cancers (usually with intestinal or rectal cancers but many other cancers seem also connected).
Also blocking their receptors is not likely to become good method for curing cancer as too much blockade can kill fast due to type of diabetic coma. If insulin receptors were blocked brain couldn't absorb glucose and that's almost like losing blood flow to brain. Within minute people could pass out into coma and if it persist for 5+ minutes in can lead to permanent brain damage. Probably much easier to just eat less to avoid cancers.

Type 2 diabetes that causes high insulin levels is associated with increased colorectal cancer rate. Also those who keep injecting insulin risk with increased chance of colorectal cancers. Same risks could come from physical inactivity, fat around abdominal organs and obesity as they cause type 2 diabetes type high insulin levels.
Authors didn't find relation between non-diabetic obesity and cancer rates when they did  26 year long study on non-diabetic 86 740 women and 46 146 men. In this case they didn't notice extra colorectal cancer rates and other cancers were not mentioned. Their calorie intakes were considered (they were questioned every 2-4 years) but it seemed unrelated to cancers. Insulin is released with the intake of carbohydrates, fats and proteins. 
Difference in diabetic and just fatty diets could be that food increases insulin release temporarily but diabetes keeps free insulin levels constantly high.

Comparison of glargine and insulin effects on cancer. High dose (over 40 U) of glargine caused almost 3 times more cancers than low dose of glargine (20-40 U). More specifically 5,26 vs 1,86 cancer cases per 100 patient years. With high and low insulin doses these 3,1 vs 1,7 cancer cases per 100 patient years. Due to ~13% of glargine users getting high dose and ~46% using high dose of insulin, both drugs tend to have in general similar chances of causing cancer (~2,4 vs 2,6 cases per 100 patient years).  
High insulin activity can increase risk of breast, prostate, colon and thyroid cancers.  

At least IGF can increase risks of melanoma which causes around 75% of skin cancer deaths. IGF can also bind with insulin receptors along with IGF receptors and like insulin IGF seems to stimulate cell growth, division and inhibit programmed cell death. IGF-1 receptor seems to make cells divide while IGF-2 seems to avoid cancers as mutated IGF-2 receptors could be found in cancers.
High IGF-1 levels could increase cancer rates in prostate, bones, genitalia, bladder, central nervous system, lungs, colon and breasts. IGF BP-3 receptors seem to protect against cancers and lower IGF-1 concentration.
People with growth hormone deficiency (Laron syndrome) seems to protect against cancers but growth is often stunted to childlike height (also those with Laron syndrome where younger during comparison). Caloric restriction in mice reduced IGF in bloodstream by 25% and had some slowing effect of bladder cancer.
IGF-II levels seem higher both in cancers and normal tissues among black women compared to whites. Also breast cancers among black women tend to be faster growing and more likely to kill.    

Some breast cancers depend on estrogen receptors and can be slowed with estrogen blockers but those breast cancer cells that don't need estrogen seem to depend on IGF receptors and could possibly be slowed with IGF blockers.

IGF is commonly also released due to effects of growth hormone. IGF and insulin receptors seem similar to each other in structure and the small proteins that form insulin or IGF receptors can randomly combine together and these hybrid receptor bind with IGF and insulin. Insulin receptor mediates glucose entry to cell and both receptors stimulate cell division. Ingesting IGF can increase risk of liver,colon, esophageal, gastric and pancreatic cancer.   
IGF and insulin receptors with many phosphate groups seem to be present in "all" breast cancer case.
IGF receptor blocking drugs are tested for possible chemotherapy use but as they block cell growth they are suspected to also retard growth of children including IGF dependent growth of their brains and heart muscles. Also some cancer cell types may not have IGF receptors. Tumor suppressing IGF receptor types could be solved in water in drank to reach gastrointestinal tumors. 

Tuesday, February 5, 2013

Bose-Einstein condensate


Bose-Einstein condensate (BEC) is a state of matter that forms with certain elements near absolute zero with identical enough atoms. Temperatures usually have to be so low that movements of elements slow below 1 mm per second compared to usual 0,5 km/s at room temperature. BEC requires thorough vacuum as BEC's produced usually have around 1000 atoms and if they move so slowly then 1 room temperature air molecule can increase their average speed a lot.  Special thing about BEC is that it can slow light down to speeds people can run like 25 km/h and it seems to have 0 viscosity. Bose sent this idea about existence of BEC to Einstein around 1924 and temperature needed to create it was reached in 1995 with few thousand rubidium atoms cooled to 170 nanokelvins. Using this calculator it looks like rubidium would have to move move 0,57 mm/s (20 meters per hour). In 1938 helium-4 that got cooled to 2,17 K (about 100 m/s) showed also partial BEC attributes like lack of viscosity and slowed light but less than 10% of gas was considered BEC.
During cooling atoms go to minimal energy they are known to have so far and this allows them to go together more densely in one place. Experiments with lithium seemed to show that they also form dense BEC due to their attractive forces (unlike rubidium atoms that repel each other) but after some maximum number of lithium atoms is reached their attraction can cause sudden collapse somewhat similar to star imploding shortly before supernova explosion. In case of rubidium strong magnetic fields can cause sudden attractive forces that imploded atoms enough to hide them temporarily and then they got energy to fly away from each other.
One way to slow light is to make material transparent to very narrow wavelength while it blocks other wavelengths.  

In 2009 a 0,1 mm cloud of sodium in form of BEC seemed to store light for 1,5 seconds.

From 1999 article. BEC state seems to turn entire gas cloud into single atom or somewhat liquid "laser" with waves similar to radio waves shared by atoms spreading through it. Vacuum has to be at least hundreds of trillions times thinner than atmospheric pressure.

2001 article. Sodium BEC seems mostly nontransparent but lasers can affect transparency. Photons are fast due to their zero or near-zero mass but BEC and atoms have mass. If that electromagnetic fluctuation common to light photon gets absorbed with atoms it forms "polariton" that carries electromagnetic activity but is much slower due to extra mass and in case of BEC entire gas cloud can turn into polariton with further increased mass and slowed light speed (additional BEC mass seems to help in this slowing until cloud is too large to stay BEC). Lasers had to be adjusted (weakened) to increase transparency of BEC and proportion of polaritons that were atoms while reducing proportion of photon type polaritons. After atomic polaritons formed they released their light after turning up the laser. Kinda like low light charges them with light and extra energy makes it release again but such light storage happens at low temperatures.

Possible simplified explanation

BEC could work because while atomic nuclei are moving at ~1 mm/s their electrons will have plenty time to respond to each others aligning electrons so voltage differences between atoms would minimize. As they cool and get closer they also get their electrons closer to each other which could make them react to each other faster increasing conductivity with that. If photons reach conductive enough material they give their electromagnetic fluctuations over to that material. In metal this absorbed photon energy could move fast but in very cold gas with electrons bit more further from each other they could respond by slowly giving their electric field to neighboring atoms.

Consider that almost all elements (except helium) used for making BEC had 1 outer electron to manipulate with laser as they were from 1st periodic table group like lithium, sodium, rubidium and cesium. They get minimal energy they would align their only electron in ways that there would be least pushing between them. If laser forces electrons to one side they could all do it at almost same time like single atom trying to align its electron with outer electric field and they lose this energy as electromagnetic radiation when they fall down to their minimal energy state. 

Size of atoms was probably major reason why lithium and rubidium behaved differently. Lithium is relatively smaller and bit more electronegative making it attract electron more due to smaller distance between positive charge of atomic nucleus and atom surface while in rubidium there are many more negative electrons between rubidiums nucleus and surface making it likelier that atoms repel.

Monday, February 4, 2013

Metal ions in proteins and other organic substances


Many proteins in body use metals for many reasons from molecule transport to chemical reactions and fetal development. Due to their electronegativity metals mixed with water get around +1 or +2 charge that makes them some of the most positively charged elements in body.

Above structure describes one chelation agent EDTA that is used to bind with metals including calcium and remove them from body (overuse of chelation agents can kill due to low calcium). Proteins that have metals have often similar regions with 4-6 nitrogen or oxygen atoms creating negatively charged zone for metal ion.


One of the most common structure that body uses is porphyrin structure shown above. It could contain different metals and participate in very different roles. For example in hemoglobin this structure surrounds iron and in chlorophyll it surrounds magnesium. If bound with iron this group gets called heme.

Iron containing proteins can carry oxygen without reacting with them chemically. Cytoglobin may be most common as it is present in most tissues. Hemoglobin is mainly in blood, myoglobin in muscles and neuroglobin in neurons. Having more of those proteins tends to make tissues more resistant to lack of oxygen. They seem to have somewhat fluid way of transporting oxygen by temporarily binding and releasing them often but most likely attraction is towards heme group that doesn't have same charged oxygen already there so they tend to even out oxygen levels through body (free dissolved oxygen can easily go through cell walls unlike globin proteins). 
At least myoglobin seems to be produced more in case of low oxygen levels like during exercise. This seems to also apply on hemoglobin. That's probably reason why living in high altitude or exhausting bodies oxygen stores with activity cause additional hemoglobin and myoglobin so body could store more oxygen. Increase in calcium release seemed to be that maybe main signal substance for muscles that also increases their production. Superficial search (1, 2) of "calcium" and "muscle growth" seemed to show that blocking calcium also block growth and division of muscle cell and that it is involved in growth of muscles starting from fetal development and extra activity of calcium due to extra muscle activity increase growth of muscle cells.

Another substance that uses porphyrin + iron is catalase that converts hydrogen peroxide to water and oxygen with 4 such structures in each catalase molecule turning millions of peroxide molecules to water and oxygen each second making it one of the fastest working protein. It's speed makes sense if considering electric charges. Oxygen is most negatively charged part in this cycle and all elements in porphyrin are relatively positive compared to oxygen. 
Events that cause it to break could go something like this: In HOOH structure H are more positive atoms and middle oxygen atoms stay negatively charged. In center of catalase is iron with probably +2 charge and it's surrounded by somewhat negatively charged nitrogen. This makes oxygens attracted to metal and hydrogen atoms to nitrogen or carbon groups around metal probably accelerating all atoms involved towards each other. If they get close enough metal becomes most likely source of electrons to oxygen and stronger temporary connections form between iron and oxygen. If free electrons of O are used to connect with Fe then oxygen atoms likely loses electrons that used to connect it with other oxygen atom and also while getting electrons from metals, oxygens will not have connecting electrons but will have similar negative charges that further push them apart.  

Some proteins that break up proteins also need metals. For example metalloproteases need at least zinc and if EDTA removes metals then these proteins can't break other proteins by possibly similar to catalase mechanism of offering easy electron source that disrupts the usual flow of electrons that keeps molecules together.

Maybe voltage differences between metals and oxygen or nitrogen is strong enough that when proteins force other molecules against this unusual (for body) voltage difference breaks them up.

Probably largest voltage difference between atoms in reactive proteins/enzymes is the part where metal is held. This could make it most likely place to send out more energetic electrons as this place has elements with largest difference in electronegativity. In chlorophyll it seems like likely place for getting free electrons.


Structure of chlorophyll c1. Light photons are polarized in some direction which could also push or pull electrons along this polarization direction. If electrons are already close to moving in some direction then electromagnetic radiation of light can add further push in that direction. Chlorophyll needs water molecules which attract oxygen and its hydrogen atoms may be attracted to negatively charged nitrogen atoms somewhat similar to catalase protein but in case of chlorophyll light is also needed to start chemical reaction. Maybe porphyrin with water creating electron flow could be useful for solar energy.

Chlorophyll molecules are in PSII and PSI and they are not the only ones there (each with around 100 molecules or elements including iron and other charged ions). It seems like 1 chlorophyll molecule can turn 1 photon into 1 electron plus this process break up water into oxygen and free protons which in turn are both used to produce energy by plants and animals. These free hydrogen ions produce ATP by ATP synthases and even there electrostatic interactions seem to help explain ATP synthesis. It usually takes around 3 H+ flowing through ATP synthase to produce 1 ATP from ADP by adding extra phosphate groups.

Phosphate groups usually have negative charges unless they get neutralized with 3 hydrogen atoms. ATP has energy because its 3 phosphate groups in row have strong repelling force pushing away from each other but in ATP synthase they manage to get close enough for connecting. It could possibly happen because ADP gets in, hydrogen ions neutralize one of the phosphate groups so they would not try to repel. Possible that added hydrogen on phosphate is attracted to some still charged phosphate with such strength that it bounces of -OH from one phosphate which could grab some free H+ to become water and connect 3rd phosphate group to ADP turning it to ATP.

Emulsifiers


Emulsifiers are substances that can mix oil and water by being one large molecule that has nonpolar (only carbon and hydrogen like most of fat molecules)  parts for dissolving fats + other non-polar substances and polar parts (basically other elements besides carbon and hydrogen) to dissolve water, metals and charged organic substances.
In food industry these molecules are used to avoid fat and water separating but bodies use similar molecules to keep fats dissolved in water and to avoid waterproof oil droplets from forming in blood vessels.
Animal and plant cells many brownish-yellowish lecithin type molecules and above substance is one such example. It has long areas that bind preferably to fats and somewhat long area in black and red that binds polar substances. Substances of this class are used in food as natural emulsifiers.

Soap is also one type of emulsifier with typical long non-polar area together with charged very small area which demonstrates how little of it has to be charged to help dissolve charged particles like dust.
Sodium stearoyl lactylate is example of emulsifier approved for use in food.


Bile acids illustrated above. One of the roles for bile is to dissolve fat in digestive tract so it wouldn't try to float on top. Emulsifiers in bile are produced from cholesterol with charged parts usually at opposite ends of molecule. One common molecule that is added to cholesterol by body is taurine that is common in energy drinks. Emulsifiers in bile are toxic to body and one study mentioned that starting from 10 micro-moles of some bile acid per liter started to show some minor damage to biliary cells from biliary tract themselves although large scale damage was not seen even with 5 times that concentration. More hydrophobic ones seemed more damaging.     

Emulsifier are also potentially toxic by dissolving cell membranes as their non-polar part tries to be in cell membranes while polar area is more attracted to water outside membrane which combined with thermal motion and bumping together with other molecules can pry cell membranes open.

One the other hand huge number of proteins seem mainly safe although they have some emulsifier role. For example every receptor on surface of cell has non-polar parts that go through membranes and polar parts that stay outside membrane. Probably every protein has enough differently charged amino acids to turn entire protein into emulsifier. If body didn't have emulsifiers its fat could float up to maybe brain which sounds deadly but i don't know any health problem causing that as body has enough emulsifiers to avoid it and even if some mutation caused such oil layering then they wouldn't be likely to survive in fetal development to reach live birth.  

In bloodstream lipoproteins are freely moving partially water soluble proteins that carry around fat molecules. Some of them are connected to longevity. In general lipoproteins carry fats and cholesterol between liver and body tissues (some move them out of liver while other lipoproteins carry fats back to liver). Low density lipoproteins (LDL) carries cholesterol from liver to other tissues and it is sometimes called "bad cholesterol" lipoprotein (although "bad" and "good" is misleading as cholesterol is same but direction of transport between liver-body determines these "good-bad" labels). "Good cholesterol" lipoproteins are also called high density lipoproteins (HDL) as they are smaller than LDL (diameter difference is ~2-5 fold). HDL seem helpful because they carry cholesterol from body to liver and in general people that for some reason have relatively more HDL than other people tend to have less cardiovascular diseases.