Finally....

Finally, our group got the desired process....., which mean good and bad -.-;

Good: - to have stuffs to work on
- to get closer to the graduation
- to get closer to be ready for publishing papers

Bad: - no time to do something else
- to have headaches
- to be busy

Well...hope this project goes well....wish me luck!!

Basic terms related to biosensors

1. molecule
an aggregate of two or more atoms in a define arrangement held together by covalent chemical bonds. Chemical substances are not infinitely divisible inot smaller fractions of the same substance: a molecule is generally considered the smallest particle of a pure substance that still retains its composition and chemical properties.

2. particle (입자)
this can refer to (1) molecule (2) atom (3) electron (4) photon (5) proton..

3. ionization
the physical process of conerting an atom or molecule into an ion by changing the difference between the number of protons and electrons
(Atoms ususlly have zero net charge, since the electrons and protons balance. If they don't, the object is called an "ion".)

4. analyte (검출 대상물질)
substance or chemical constituent that is undergoing analysis
(It is substance being measured in analytical procedure)

5. reagent (시약)
any substance used in a chemical reaction
(It is usually implies a chemical that is added in order to bring about the chemical change)

6. assay (분석 시험하다, 시금하다)
a procedure where the concentration of a component part of a mixture of determined

7. covalent bond
an intramolecular form of chemical bonding chracterize by the sharing of one of more pairs of electrons between two components, producting a mutual attraction that holds the resultant molecule together

8. enzyme (효소)
one of bioreceptors
an enzyme is capable of recognizging a specific target molecule . Typically used in biosensors as a bioreceptors. Examples of other bioreceptors are antibodies, nuclesis acid, and receptors.

9. catalyze (촉매 작용을 하다, 촉진시키다)
소량 첨가로 속도가 느린 어떤 특정한 화학반응 속도를 증가 시키는 물질
반응전후에 촉매 그 자체는 변하지 않으며, 반응의 평행에도 영향을 주지 않는다.
catalyzer (촉매)
catalysis (촉매작용) - the acceleration of a chemical reaction by means of a substance, called a catalysis, that is itself not consumed by the overall reaction

10. anabolism (동화작용, 물질 합성대사)
the metabolic process that builds larger molecules from smaller ones. Anabolic processes tend toward "building up" organs and tissues. These processes produce growth and differentiation of cells and increase in body size, a process that involves sysnthesis of complex molecules.
(small molecules --> building blocks of our body (e.g., protein))
- 생물체가 간단한 물질에서 화학적으로 복잡한 물질을 합성하는 과정
(반대말)catabolism

11. catabolism (이화작용)
- 생물체가 화학적으로 복잡한 물질을 간단한 물질로 분해하는 과정
(food --> small molecule)

12. metabolism (물질대사)= anabolism + catabolism
- 생체내에서 진행되는 물질의 분해와 합성과 관련한 화학변화의 총칭
- 물질 교대, 신진대사 또는 단순히 대사라고도 한다

13. luminescence (발광)
- cold light emission
- a process by which light is produced other than by heating
- 종류
1) photo-luminescence (fluorescence, phosphorescence)
2) electro-luminescence
3) chemical-luminescence
4) radio-luminescence
5) thermal-luminescence
(Note) photo-luminescence: chemical substarate absorbs and then re-emits a photon of light

14. spectroscopy
- 분광학
- 스펙트럼을 추구하는 분야

15. fluorometry = fluorescence spectrocopy
a type of electromagnetic spectroscopy used for analyzing fluorescent spectra
(반대말: absorption spectrscopy)

16. fluorescence
- a luminescence that is mostly found as an optical phenomenon in cold boides, in which the molecular absorption of a photon triggers the emission of another photon with a longer wavelength. The energy difference between the absobed and emitted photons ends up as molecular vibrations or heat. Usually the absorbed photon is in the ultraviolet range, and the emitted light is in the visible range, but this depends on the absorbance curve and stroke shift of the particular fluorophore.
- 형광 (높은 에너지 상태의 물질이 낮은 에너지 상태로 되돌아 갈때 전자전이(transition)에 의해 방출되는 빛 또는 그와 같은 발광현상

17. fluorophore (analogy to a chromophore)
- a compound of a molecule which causes a molecule to be fluorescent
It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but eually specific) wavelength. The amount and wavelegth of the emitted energy depend on both fluorophore and the chemical environment of the fluorophore.

18. phorsphorescence (인광)
- Unlike fluorescence, a phosphorescent material does not immediately discharge the radiation it absorbs
- 상당히 오랜시간 발광

19. phosphor (인광체)
a substance that exhibits the phenomenon of phosphorescence (sustained glowing without further stimulus)

20. Difference between phosphorescence and fluorescence
- The major difference in the two processes is the decay time of the emitted light fluorescence in fast (of the order of milliseconds) the phosphorescence is slow (of the order of seconds to minutes or even hours). Fluoresence and phosphorescence describe two different ways that an electron can behave in a molecule. They start the same way: a molecule absorbs light, and an electron gets excited to a higher energy level. If the electron drops straight back down to where it started from without undergoing any spin changes (this excited state is called "singlet state"), then you have fluorescence. The electron emits energy in the form of a photon (light) on its way back down. In constrast, when an electron gets excited and its spin does flip (this is called "triple" state), it takes much longer for it to release the energy and come back down to the ground electronic state. This is phosphorescence. Things that phosphorescence "glow" for much longer because the excited electrons take so much longer to come back down to their inintial energies.

21. incandescence (백열광, 고온발광)

22. bioluminescence (생물발광)
- the production and emission of light by a living organism as the result of a chemical reaction during which chemical energy is converted into light
- It is generated by an enzyme-catalyzed chemoluminescence reaction, wherein the pigment luciferin is oxidized by the enzyme luciferase

23. luciferin
- 개똥벌레(firefly) 체내의 발광물질
- a generic name for "light-emitting pigments" found in organisms capable of bioluminescence, like fireflies, deep-sea fish, and microbes (미생물)

24. luciferase (발광효소)
- a generic name for enzymes commonly used in nature for bioluminescence

25. gene expression
- the process by which a gene's DNA sequence is converted into the structures and functions of a cell
- the cellular process by which genetic information flows from gene to messenger RNA (mRNA) to protein

26. Microarray (=biochip, DNA chip, gene chip)
- an ordered array of microscopic elements on a planar substrate tha tallows the specific binding of genes or gene products
- a small analytical device that allows genomic exploration with speed and precision unprecedented in the history of biology. Glass chip contating tens of thousands genes are used to examine fluorescent sampels prepared by labdeling messenger RNA (mRNA) from cells, tissues, and other biological sources. Molecules in the fluorescent sample react with cognate sequences on the chip, causing each spot to glow with an intensity proportional to the activity of the expressed gene. The enormous capacity of these miniature devices allows the analysis of the entire human genome in a single experiment.

27. transcription
- first step in gene expression in which messenger RNA is synthesized from a DNA template

28. Hybridization
- the chemical process by whcih two complementary DNA or RNA strands zipper up to form a double-stranded molecule

29. positive control
- a microaray element or substrate that provides a readable signal, irrespective of the results obtained from the experimental component of the assay
- a reactant that cuases a known effect when applied to a cluster of test organisms

30. negative control (=scientific control)
- a microarray elements or substrate that provides little or no readable signal, irrespective of the results obtained from the experimental component of the assay

31. life cycle
- Experimental cycle of microarray analysis that contains the five components of biological question, sample reparation, biochemical reaction, detection, and data analysis and modeling

32. chlorophyll (엽록소)

33. microbe (미생물, 세균)

(Overview about bio-technology)
http://kr.blog.yahoo.com/nongbau7/947970

(Fundamentals of molecular biology)
http://biochemistry.yonsei.ac.kr/biochem_molecular/

Miscellanous things to remember

1. Sorry for my laziness....
I have faced A/B/C type of unit while studying enigneering. However, sorry for myself, I have not given thought what is equivalent for conventional division form.
Here is ...the answer.
A/B/C = (A/B)/C...keep diving previous terms.

ex) 100 photons/label/sec = 100 (photons/label)/sec = 100 photons/(label x sec)

2. Relationship between independet and uncorelated
Assume that random variables X and Y,
We all know that...

X and Y are "independent" --> joint probability mass function (PMF) for discrete RVs or joint probability density function (PDF) for continous RVs can be represented as each marginal PMF/PDF.

X and Y are "uncorrelated" --> Covariance X and Y: Cov[X,Y] = 0

Since X and Y are independent, then their covariance is zero. However, the reverse action is not neccessaril true. Thus, "independent" is a subset of "uncorrelated".

In engineering, particularily for noise power calculation, if two noise sources are uncorrelated or independent processes, each noise power can be added!!!

(note) Orthogonal RVs
X and Y are orthogonal --> zero correlation = E[XY] = 0!!
Thus, if X and Y are independent and one of (or both) process is zero-mean, then two processes are orthogonal!!!

...the end!

Miscellaneous thoughts on Electricity and Magnetism

This thought and summary are based on the good reference note from UC Berkeley Physics depeartment - descriptive physics.



Electricity usually means the movement of electrons. (It can also be the movement of protons). And, electric force is much much larger - I mean really greater - than gravity.

The electric charge is named for the property of the electron that gives its force! and the charge of proton is q=1.6X10^-19 [Col] and the charge of electron is -q.

Electric current is a flow of electric charges - charged particle movement.
1[A] = 1 [Col]/1[sec] --> I = Q/t [A]=[Col/sec]
How many electrons much flow for 1 A of current?
--> 1 [Col] = 1/q = 6.25X10^18 [electrons], thus for 1A = 6.25 X 10^18 electrons must flow per second.

Metal: electrons can flow easily through it
Glass: lights can easily pass through it

Electrons can move easily inside a piece of metal, but they can't easily leave the surface of the metal. They are held back by the attraction of the positively-charged nuclei. Free movement of electrons can take place only if the moving electrons are replaced by other electrons. For this reason, electron current usually flows in circle or closed paths.
(ex1) electric code have two wires in it.
(ex2) Coaxial cable - TV tube serves as the electron "return path"
(ex3) When a bird lands on an electric power line, some electrons will immediately flow into the bird. But with nowehere to go, the electrons soon repel other electrons from coming, so the flow will stop. Very few electrons are needed to stop the flow.


Resistance
ex1) tunsten (high resistance) is used in filament in a light bulb so that it first generate heat then later light. Exept illuminating part (made of tungsten) in the bulb, the rest of electricity must flow through low resistance wire, such as copper.
ex2) fuse has high resistance so that when much current flows through it, it blow out. Other wires in a house are made of coppers.


Volt and electron energy
Amps tell you how many electrons are flowing past a point each second.
Volts tell you the energy of the electrons.

The energy unit called the electron volt or eV is defined as "1eV = 1.6 X 10^-19 [J]".
The eV is a typical amount of energy for a single atom or molecule!!!!!!

(Note)
If a piece of metal has a largee number of electrons, each with energy of 1eV, the metal is at one volt!!
--> a voltage of one volt or a potential of one volt
It is okay to refer to the energy of an electron in volts, rather than in eV.
Remember that when a piece of metal is at one volt, it means that every electron in that metal has that energy!!!!

To know the power, you must know the energy per particle AND the number of particles per second. In static electricity, for those daily sparks we feel, the voltage was probably between 40,000 and 100,000V! Yet it doesn't kill us because the current is low, limited by the small number of electrons we picked up. However, a similiar voltage in the back of TV set is very dangerous. That's because the amount of current that can flow to you is much greater.



Electric Power

The power delivered by electrons depends on the energy of the electrons, and the number per second that arrive!
1-volt electron is 1.6 X 10^-19 [J]
1-amp means 6 X 10^18 electrons per second flow.
Thus, 1[V] X 1[A] = 1 [J/sec] = [W]. ==> Power = Volt X Amp

Note that high votlage does not always mean high power. If the amps are tiny, then high voltage can be safe! It is important for you to know tha thigh voltage is not dangerous if there isn't much currnet and if it doesn't last for very long.
- Lighting: high voltage and high current --> dangerous!



House Power

The power company works very hard to keep the voltage at 120V even when you start using more appliances. The voltage doesn't change, only the current!!

In US, V = 120, Power (in W) = 120 X current (in amps).
Thus, a appliance has current of Power/120.

In Europe, the typical house voltage is 240V rather than 120V. This means that for typical power, the voltage is higher and the current is less. Higher voltage makes the electricity more dangerous than in the US, but lower ucrrent means that there is less energy lost in the wires that deliver electricity to the outlet. (or, alternatively, it means that they can use cheaper wires without getting too much heating)

Most long-distance transmission of electricity is done at extremely high voltage, several tens of thousands of volts. High-voltage lines have less current (for the same power delivered) than do low-voltage lines. But heating from resistance depends only on the current, not on the voltage! So, if we use high-voltage lines, then we can reduce the amps, and that reduces the loss of power from resistive heating!!!!

Since high voltage can make electricity dangerous, there are special devicess that raise the voltage V and lower the current I, while keeping the power P unchanged. - transformer!

Capacitor/Inductor voltage and current

We learned that the impedance of a capacitor gets shorted as frequency gets higher. Why a capaictor can be modeled as short at high frequencies?

The answer is simple as we learned in Sophomore in a university. Since voltage cannot change abruptly, if a high frequency input voltage is applied, the voltage across the capacitor cannot follow the frequency change of an input voltage signal applied.

Thus, the voltage across the capacitor eventually won't change (move) much. This voltage can be thought as ~ short!!!! if it is seen by high frequency components - NO voltage change across the capacitor! It can be modeled as a short circuit!

In a same token, static voltage (DC) in ac signal analysis also can be modeled as a short circuit!

Let's recall what we learned about Capacitor/Inductor circuit in basic circuit class.

1) Capacitor circuit

2) Inductor circuit

Similarily, (but duality to a capacitor), the current cannot change instantly. Thus, the current lags the applied voltage!!

The current through the inductor is said to be lagged the applied voltage!

(Summary)

1. Capacitor --> voltage cannot change instantly --> voltage lags current by 90 degree

2. Inductor --> current cannot change instantly --> current lags voltage by 90 degree