Friday, November 12, 2010
Your Reward
Listening to Clifford Brown and Louis Armstrong while reading TIME magazine's issue on the human brain you feel the tingling sensations of contentedness. You happen to be reading about Louis Armstrong when a song from a Youtube jazz playlist sounds "When the Saints Go Marching In" performed by Louis Armstrong and others. The music, apparel, and black and white screen indicate it originates from when TVs used to be black and white. The coincidence revitalizes your motivation to be creative. The charisma of Louis is powerful. You are focusing on positivity. Your memory will improve. You have been physically and mentally active. You have the potential to be more active. You feel America is similar. Your euphoric feeling leaves as the music stops, but returns and persists in a mellower key when music begins. You are thankful music is so affectionate. You are patient. Your to-do list is large and involves numerous future appointments. You will fulfill all of the most important obligations. You will meet and get to know people who will help you succeed in the love and course of your life. You will give graciously. You will always find friends. The weight on your shoulders will lift and you will be the better for it. You have found the right path. You are free to go and free to stay. You are welcome.
Sunday, November 7, 2010
Increasing Resolution
My sights have cleared up as I finish off the first semester of graduate school. It felt as though a thick dark haze had been developing on my vision of the future, past, and present during the last month, but I am glad to be seeing clearer now that elderly wisdom rears its head. A visitation from a family member and a friend would seem to be all that it takes to feel good about life. Although, good is a relative term when there are many more battles to be fought. The battles can be broken down into a few categories: Learning, Healing, and Helping. Right now, a battle is raging over the surface of my throat, nose, and chest, the bacterias versus the antibodies, this falls into the healing category. There is another battle over my style of helping, it would seem academia is quite stubborn and applies a pressure of early chemical waste activities. Although, people in higher education generally agree that wasting chemicals is bad, most people do it anyway in an attempt to keep busy I suppose. Where is the progress I ask? The third battle lies in learning. This is by far the toughest, longest lasting, and most strenuous of battles. While my health will likely soon return, my addictions will cease, and my helping attitude will become lighter and more wasteful, the battle of learning will not stop.
Current topics of learning include: Photosynthesis, Water splitting, Carbon Dioxide Splitting, Heterogeneous (porous surface) Catalysis, Electron Transfer, Polynuclear Organometallic complexes, and Ultrafast (Femtosecond) Laser Spectroscopy. These topics are mostly outside of programmed classes although there is some overlap in the course on Organometallics taught by T.Don Tilley, who is also my recently contracted thesis advisor. Furthermore, there will be overlap in the course in Physical Organic Chemistry when Professor Bob Bergman covers Photochemistry, Electrochemistry, and Catalysis. The ultimate goal would be to generate hydrogen gas directly using only sun light, water and metal catalysts at room temperature and pressure.
Luckily, there is a computational project outlined in the Physical Organic course that will involve using supercomputers to calculate molecular ground state energies, excited state energies, and preferred structural geometry information specific to my groups molecular interests. These calculations involve various quantum mechanical and molecular dynamics theoretical electron orbital models that do a reasonable job of giving reliable data that is close to empirically determined data. Becoming adept with these tools could potentially save companies and universities millions of hours of work in the lab and billions of dollars in chemicals. Thus, while I am glad they are enforcing us to learn these programs I am also sad that the project will be completed and finished so soon. The computational faculty are very friendly though, and are willing to serve far beyond the course requirements.
I have bought a plane ride home to Portland, OR during December break. I look forward to taking a break and assimilating/integrating the intensity of the last 3 months while visiting my group support members, my family and friends. Meanwhile, I am preparing for Turkey dinner, and recollection of family recipes for a superepic holiday dinner.
Current topics of learning include: Photosynthesis, Water splitting, Carbon Dioxide Splitting, Heterogeneous (porous surface) Catalysis, Electron Transfer, Polynuclear Organometallic complexes, and Ultrafast (Femtosecond) Laser Spectroscopy. These topics are mostly outside of programmed classes although there is some overlap in the course on Organometallics taught by T.Don Tilley, who is also my recently contracted thesis advisor. Furthermore, there will be overlap in the course in Physical Organic Chemistry when Professor Bob Bergman covers Photochemistry, Electrochemistry, and Catalysis. The ultimate goal would be to generate hydrogen gas directly using only sun light, water and metal catalysts at room temperature and pressure.
Luckily, there is a computational project outlined in the Physical Organic course that will involve using supercomputers to calculate molecular ground state energies, excited state energies, and preferred structural geometry information specific to my groups molecular interests. These calculations involve various quantum mechanical and molecular dynamics theoretical electron orbital models that do a reasonable job of giving reliable data that is close to empirically determined data. Becoming adept with these tools could potentially save companies and universities millions of hours of work in the lab and billions of dollars in chemicals. Thus, while I am glad they are enforcing us to learn these programs I am also sad that the project will be completed and finished so soon. The computational faculty are very friendly though, and are willing to serve far beyond the course requirements.
I have bought a plane ride home to Portland, OR during December break. I look forward to taking a break and assimilating/integrating the intensity of the last 3 months while visiting my group support members, my family and friends. Meanwhile, I am preparing for Turkey dinner, and recollection of family recipes for a superepic holiday dinner.
Sunday, October 24, 2010
Hydrogen for a Hydrogen-based economy?
What is the direction of learning in on-line and in-class institutions? What are the real-world applications of advanced knowledge? Can in-depth study reveal information that can be broadly applicable to everyday technologies?
Recent examples of in-depth study revealing new technology is in photocatalysis. Materials discovered by group heads such as, Nate Lewis at Caltech, Peidong Yang, Mike Crommie, Jefferey Long, Chris Chang, and T. Don Tilley at UC Berkeley, Daniel Nocera at MIT and Heinz Frei at Berkeley Lab are breaking ground in the artificial photosynthesis field. They are all using metal ions stabilized by carbon, oxygen, nitrogen, and/or silicon-based molecules. These molecules are able to absorb an amount of visible light which is directly related to the excitability of the electrons within these atoms. Not unlike freshman chemistry models of electrons being shared between atoms in molecules to make bonds, these metal-organic (organometallic) systems share their electrons with all of the atoms in the molecule (although not equally). The organic terminology refers to the presence of carbon. Therefore, these molecules are energized by light of a longer wavelength and lower energy than is typical for these atoms on their own; save carbon because it is very versatile when in nano-sized formations. The lower energy (longer wavelength and lower frequency) light absorbed is in the visible spectrum which resonates with the dispersed electron wavefunctions that model the molecule's surface in modern quantum mechanics allowing the molecule's electron to absorb light and become more energetic.
The outstanding properties of some metal complexes comes from the difference between the resting energy (ground state) of the valence (outermost) electron and the next highest allowed energy (excited state) of that electron. The allowed and resting state energy levels are dependent on factors directly related to the unique structure of the molecule. For example, the level of symmetry the molecule has largely affects the allowed electron energies. Almost all octahedral arrangements of atoms around a metal ion (in the center of the octahedron) will have characteristic allowed energies (eg* and t2g). Furthermore, an increase in the effective nuclear charge the valence electron feels reduces it's resting energy making it less excitable by lower energy longer wavelength visible light. For example, the molecules that Frei and Nocera are studying absorb visible light and so are brightly colored, thus they have relatively unstable resting state electrons. Moreover, the metal ions being largely affected by their new electronic environment are able to oxidize water H2O molecules into oxygen gas O2, protons H+, and electrons e-. The enhanced reactivity of metal ions bound to other molecules (glutamate, aspartate, lysine, tyrosine, and other amino acids present in our enzymes)) is how plants achieve photosynthesis; plants use Manganese oxide cube shaped clusters that are buried and bound inside enzymes to do a water oxidation process, then the protons and electrons are transferred through and to several other proteins and small molecules to ultimately be used in converting Carbon Dioxide CO2 into sugar CxH2xOx which is their form of sunlight energy storage and our own body's energy source. Interestingly enough, we do the opposite process in our bodies by converting sugars CxH2xOx and oxygen O2 into carbon dioxide CO2 and water H20.
A prime example of light absorbing metal complexes that transfer energy through excited electrons is chlorophyll a which is a Magnesium ion surrounded by 4 Nitrogen atoms. The nitrogen atoms along with 20 carbon atoms come to form planar cyclic ring molecule that acts as a light antennae for increasing the surface area and energy range of photons that can be absorbed. This forms what is called a square planar metal complex. This complex absorbs light strongly and broadly in the red region of the visible spectrum thereby appearing bright green to our light sensing retinas. Many plants are green due to chlorophyll a and b which absorb light energy and transfer it to other chromophores that shuttle electrons to an enzyme that oxidizes 2 water molecules H20 into oxygen gas O2 and 4 electrons e- and 4 protons H+. The enzyme which does water oxidation has a Magnanese and oxygen MnO cubic cluster that accepts excited electrons from molecules that previously accepted electron energy (chromophores) from chlorophyll that previously accepted energy from photons (light quanta or bundles of energy). The Manganese oxide clusters then react with water to convert it or split it into oxygen gas O2. The resulting electrons and protons H+ from the reaction are then combined with CO2 to produce sugar and water by other enzymes that contain metal ions at their centers, collectively termed metalloenzymes, they use Iron, Nickel, and Copper, among other metals. It turns out our bodies need many of these metal ions to perform these crucial catalytic reactions. Light or electron energy is transported molecule to molecule by a process called charge transfer. Charge transfer occurs when the donor molecule's excited electron energy closely matches the energy of a potential allowed electron configuration in the acceptor molecule (LUMO = Lowest Occupied Molecular Orbital).
My proposal involves using synthetic molecules that absorb the maximum amount of sunlight and coupling them to metal ions which are active for converting 2 protons H+ and 2 electrons to generate hydrogen gas H2. To do this will require a knowledge of inherent allowed excited and resting states of the valence electrons in the proposed molecules. These energies can be probed using ultraviolet and visible light spectroscopy, x-ray photoelectron spectroscopy, and edge x-ray absorption fine structure spectroscopy. The structure of the complexes also play a crucial role in the rate at which electrons are transported across and between molecules. The structure will be probed using x-ray diffraction, nuclear magnetic resonance spectroscopy, diffuse reflectance and infrared spectroscopy. Finally, the catalytic rate of production of hydrogen gas and lifetime of the catalyst will be monitored using gas chromatography and pre and post-test assays. Nature performs proton reduction elegantly using a very complex system, but nature has a lot of other things to worry about, our goal is simply to isolate and amplify a particular chemical transformations to facilitate our energy independence and promote environmental reform. This technology will allow energy to be directly stored in the form of hydrogen gas using only water and sunlight. The trick will be to create a catalyst which is long-lasting, created from abundant metals, and is active enough to produce industrial amounts of hydrogen. This green process will usurp the current coal and natural gas-based cracking processes that generate hydrogen gas and carbon dioxide CO2 using wasting electricity and fossil fuels.
I find myself pensive lately, I have been told I am a doppleganger of a professor of chemistry that will likely be my thesis advisor.
Recent examples of in-depth study revealing new technology is in photocatalysis. Materials discovered by group heads such as, Nate Lewis at Caltech, Peidong Yang, Mike Crommie, Jefferey Long, Chris Chang, and T. Don Tilley at UC Berkeley, Daniel Nocera at MIT and Heinz Frei at Berkeley Lab are breaking ground in the artificial photosynthesis field. They are all using metal ions stabilized by carbon, oxygen, nitrogen, and/or silicon-based molecules. These molecules are able to absorb an amount of visible light which is directly related to the excitability of the electrons within these atoms. Not unlike freshman chemistry models of electrons being shared between atoms in molecules to make bonds, these metal-organic (organometallic) systems share their electrons with all of the atoms in the molecule (although not equally). The organic terminology refers to the presence of carbon. Therefore, these molecules are energized by light of a longer wavelength and lower energy than is typical for these atoms on their own; save carbon because it is very versatile when in nano-sized formations. The lower energy (longer wavelength and lower frequency) light absorbed is in the visible spectrum which resonates with the dispersed electron wavefunctions that model the molecule's surface in modern quantum mechanics allowing the molecule's electron to absorb light and become more energetic.
The outstanding properties of some metal complexes comes from the difference between the resting energy (ground state) of the valence (outermost) electron and the next highest allowed energy (excited state) of that electron. The allowed and resting state energy levels are dependent on factors directly related to the unique structure of the molecule. For example, the level of symmetry the molecule has largely affects the allowed electron energies. Almost all octahedral arrangements of atoms around a metal ion (in the center of the octahedron) will have characteristic allowed energies (eg* and t2g). Furthermore, an increase in the effective nuclear charge the valence electron feels reduces it's resting energy making it less excitable by lower energy longer wavelength visible light. For example, the molecules that Frei and Nocera are studying absorb visible light and so are brightly colored, thus they have relatively unstable resting state electrons. Moreover, the metal ions being largely affected by their new electronic environment are able to oxidize water H2O molecules into oxygen gas O2, protons H+, and electrons e-. The enhanced reactivity of metal ions bound to other molecules (glutamate, aspartate, lysine, tyrosine, and other amino acids present in our enzymes)) is how plants achieve photosynthesis; plants use Manganese oxide cube shaped clusters that are buried and bound inside enzymes to do a water oxidation process, then the protons and electrons are transferred through and to several other proteins and small molecules to ultimately be used in converting Carbon Dioxide CO2 into sugar CxH2xOx which is their form of sunlight energy storage and our own body's energy source. Interestingly enough, we do the opposite process in our bodies by converting sugars CxH2xOx and oxygen O2 into carbon dioxide CO2 and water H20.
A prime example of light absorbing metal complexes that transfer energy through excited electrons is chlorophyll a which is a Magnesium ion surrounded by 4 Nitrogen atoms. The nitrogen atoms along with 20 carbon atoms come to form planar cyclic ring molecule that acts as a light antennae for increasing the surface area and energy range of photons that can be absorbed. This forms what is called a square planar metal complex. This complex absorbs light strongly and broadly in the red region of the visible spectrum thereby appearing bright green to our light sensing retinas. Many plants are green due to chlorophyll a and b which absorb light energy and transfer it to other chromophores that shuttle electrons to an enzyme that oxidizes 2 water molecules H20 into oxygen gas O2 and 4 electrons e- and 4 protons H+. The enzyme which does water oxidation has a Magnanese and oxygen MnO cubic cluster that accepts excited electrons from molecules that previously accepted electron energy (chromophores) from chlorophyll that previously accepted energy from photons (light quanta or bundles of energy). The Manganese oxide clusters then react with water to convert it or split it into oxygen gas O2. The resulting electrons and protons H+ from the reaction are then combined with CO2 to produce sugar and water by other enzymes that contain metal ions at their centers, collectively termed metalloenzymes, they use Iron, Nickel, and Copper, among other metals. It turns out our bodies need many of these metal ions to perform these crucial catalytic reactions. Light or electron energy is transported molecule to molecule by a process called charge transfer. Charge transfer occurs when the donor molecule's excited electron energy closely matches the energy of a potential allowed electron configuration in the acceptor molecule (LUMO = Lowest Occupied Molecular Orbital).
My proposal involves using synthetic molecules that absorb the maximum amount of sunlight and coupling them to metal ions which are active for converting 2 protons H+ and 2 electrons to generate hydrogen gas H2. To do this will require a knowledge of inherent allowed excited and resting states of the valence electrons in the proposed molecules. These energies can be probed using ultraviolet and visible light spectroscopy, x-ray photoelectron spectroscopy, and edge x-ray absorption fine structure spectroscopy. The structure of the complexes also play a crucial role in the rate at which electrons are transported across and between molecules. The structure will be probed using x-ray diffraction, nuclear magnetic resonance spectroscopy, diffuse reflectance and infrared spectroscopy. Finally, the catalytic rate of production of hydrogen gas and lifetime of the catalyst will be monitored using gas chromatography and pre and post-test assays. Nature performs proton reduction elegantly using a very complex system, but nature has a lot of other things to worry about, our goal is simply to isolate and amplify a particular chemical transformations to facilitate our energy independence and promote environmental reform. This technology will allow energy to be directly stored in the form of hydrogen gas using only water and sunlight. The trick will be to create a catalyst which is long-lasting, created from abundant metals, and is active enough to produce industrial amounts of hydrogen. This green process will usurp the current coal and natural gas-based cracking processes that generate hydrogen gas and carbon dioxide CO2 using wasting electricity and fossil fuels.
I find myself pensive lately, I have been told I am a doppleganger of a professor of chemistry that will likely be my thesis advisor.
Saturday, October 9, 2010
LBNL Runaround
Friday, October 8, 2010
The Runaround
Today was the 33rd annual 3 kilometre race
3000 meters = 1.86411358 miles
around the Lawrence Berkeley National Laboratories. LBNL is located on steep hilly terrain perched loftily above the UC Berkeley campus. The sun shining brightly and the wind had a cool touch. I shuffled around the crowd just before the start of the race to find a position within the top 1/8th of the 780 runners. I wanted to be ahead of the slow people, but not ahead of the fast runners. As the man with the megaphone hollered, "ready, set, go" I started jogging, but quickly realised everyone around me was going too slow so I started weaving between the foot traffic like a crazed teenager with a sports car (which used to be myself). I should have positioned myself at the starting line. While the fastest male runner came in somewhere around 9 minutes and 30 seconds, an astonishingly short amount of time for almost, I came in at 12 minutes 33 seconds which is a pleasant surprise. I heard a graduate student in the Tilley lab had won first place for women with a 12 minute time so I am feeling proud, plus I got a free shirt out of the deal.Friday, October 1, 2010
A Momentary Lapse of Time
Here I sit, in the laboratory, visualising a muscle pumping that I suppose is my brain. There has been some time since posting which I attribute to maintaining my psychological health while making a decision about a research lab. I silence the world news because it really is far from my daily reality, train crashes, bombings, shootings, political visitations. It seems our nations best efforts are not good enough, and in some sense they are making things worse. The exorbitant defense budget, rising healthcare costs, and increasing taxes, it seems like these topics are beyond the reach of everyone. Hopeless is what it seems, but there are more ways ahead than imaginable. This is analogous to life. I choose to study, read, and work long hours while accomplishing nothing. My decisions seem monumental and yet arbitrary. As if anything I decide to do will place me in a situation I would have arrived in anyway. Although, I feel this couldn't be true according to nature, I am rolling dice with unsure remembrance as to how to flick my wrist right to get 7's. I came into graduate school wanting to make paint that is a solar electric and lighting material. I still believe in this idea, but I am spending all my time studying books and information which only etch away very slowly at the packaging that encloses my dreams.
Monday, September 6, 2010
Labor Day Weekend
On Saturday I hit up the San Francisco Museum of Modern Art, and the Yerba-Beuna Gardens Festival, the latter of which had some live musicians playing for free, Rob Reich, Darren Johnston, and Daniel Fabricant. The prior was less inspiring than I expected. Most of the art at the MoMA looked as though it took little work and had little aesthetic beauty. Don't get me wrong I love giant murals of paint and big sculptures, plus the facilities are really nice, pictured below. There were certainly plenty of exceptions, like the detailed photorealism of Chuck Close and the classic style of Henri Matisse but for the most part I was unimpressed. At the free festival the band playing was a trio, an accordion player, a trumpet player, and a stand-up bassist. Their flow was natural and free and they were accompanied by a potent string quartet that tied the risky jazz solos together to form something capricious, elegant, and rewarding. There is something about the accordion that is extraordinarily French sounding.
Yesterday I ran to the Emeryville marina which is a couple square miles of tall masts and antennas protruding from sailboats and yachts. I became one of those topless runners wearing shorts you see and think wow they are hardcore. Today, my legs are achy and my thighs are speckled with crimson dots from the friction of thousands of paces. I will save you from the photo I took as evidence. Either way, I ran 9.2 miles yesterday.
Today I woke up thinking I had to go to a group meeting at 11am. I got out of bed slowly at 8am and proceeded to make tea and breakfast. While bicycling to work on the UCB campus I recalled a question a person asked me about what I had in store for this labor day weekend several days ago. Boom, it hit me, today is labor day. Wow, what a shocker. I know it would be a lot more exciting had I been with someone else who I could share my excitement with. Oh well, such is the life of I for today.
Plucking various chords and melodies on the fret board of an Epiphone Les Paul Junior I am sure to fully pronounce each note to its fullest amplitude, this still remains a mixed challenge in spite having owned and played a guitar for many years now. I hope to play with good musicians someday and have them say that they enjoyed my music. That will be the day. I am thankful to the corner supermarket operating on labor day ran by what looked to be a middle eastern couple judging by the arabic font on the storefront. Their daughter was in control of the cash register and would dictate the prices out loud to customers ears. Her mother stood close by ensuring accurate arithmetic. She seemed surprised when I told her I was going to use the bag I had brought with me into the store, out of which I had just pulled all of my merchandise. She told me I should put the fruit on the top of items in the bag instead of the bottom. I quickly accepted she was right and removed the fruit I had placed first in the bottom of the bag. I thought about my use of temporal logic. Item 1 received, Place Item 1 in Bag. Item 2 received, Place item 2 in Bag, and so on. I sometimes wonder where my brain is at moments like this, was I focused on the daughter-mother interaction? Or maybe I was preoccupied with the fact that I brought my own bag, or even better, the logical thinking section of my brain was on it's day off just like the rest of the nation.
Yesterday I ran to the Emeryville marina which is a couple square miles of tall masts and antennas protruding from sailboats and yachts. I became one of those topless runners wearing shorts you see and think wow they are hardcore. Today, my legs are achy and my thighs are speckled with crimson dots from the friction of thousands of paces. I will save you from the photo I took as evidence. Either way, I ran 9.2 miles yesterday.
Today I woke up thinking I had to go to a group meeting at 11am. I got out of bed slowly at 8am and proceeded to make tea and breakfast. While bicycling to work on the UCB campus I recalled a question a person asked me about what I had in store for this labor day weekend several days ago. Boom, it hit me, today is labor day. Wow, what a shocker. I know it would be a lot more exciting had I been with someone else who I could share my excitement with. Oh well, such is the life of I for today.
Plucking various chords and melodies on the fret board of an Epiphone Les Paul Junior I am sure to fully pronounce each note to its fullest amplitude, this still remains a mixed challenge in spite having owned and played a guitar for many years now. I hope to play with good musicians someday and have them say that they enjoyed my music. That will be the day. I am thankful to the corner supermarket operating on labor day ran by what looked to be a middle eastern couple judging by the arabic font on the storefront. Their daughter was in control of the cash register and would dictate the prices out loud to customers ears. Her mother stood close by ensuring accurate arithmetic. She seemed surprised when I told her I was going to use the bag I had brought with me into the store, out of which I had just pulled all of my merchandise. She told me I should put the fruit on the top of items in the bag instead of the bottom. I quickly accepted she was right and removed the fruit I had placed first in the bottom of the bag. I thought about my use of temporal logic. Item 1 received, Place Item 1 in Bag. Item 2 received, Place item 2 in Bag, and so on. I sometimes wonder where my brain is at moments like this, was I focused on the daughter-mother interaction? Or maybe I was preoccupied with the fact that I brought my own bag, or even better, the logical thinking section of my brain was on it's day off just like the rest of the nation.
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