Bio physics

Internal energy:
In thermodynamics, the internal energy is the total energy contained by a thermodynamic system. It is the energy needed to create the system, but excludes the energy to displace the system's surroundings, any energy associated with a move as a whole, or due to external force fields. Internal energy has two major components, kinetic energy and potential energy. The kinetic energy is due to the motion of the system's particles (translations, rotations, vibrations), and the potential energy is associated with the static constituents of matter. The internal energy of a system can be changed by heating the system or by doing work on it; the first law of thermodynamics states that the increase in internal energy is equal to the total heat added and work done. Related energy quantities which are particularly useful in chemical thermodynamics are enthalpy, Helmholtz free energy, and Gibbs free energy.

Enthalpy:
Four quantities called "thermodynamic potentials" are useful in the chemical thermodynamics of reactions and non-cyclic processes. They are internal energy, the enthalpy, the Helmholtz free energy and the Gibbs free energy. Enthalpy is defined by H = U + PV where P and V are the pressure and volume, and U is internal energy. Enthalpy is then a precisely measurable state variable, since it is defined in terms of three other precisely definable state variables. It is somewhat parallel to the first law of thermodynamics for a constant pressure system Q = U + PV since in this case Q=H. It is a useful quantity for tracking chemical reactions. If as a result of an exothermic reaction some energy is released to a system, it has to show up in some measurable form in terms of the state variables. An increase in the enthalpy H = U + PV might be associated with an increase in internal energy which could nature tends toward maximum entropy for any isolated system, then you do have some insight into the ideas of the second law of thermodynamics.

Free energy/ gibbs free energy:

1. A thermodynamic quantity that is the difference between the internal energy of a system and the product of its absolute temperature and entropy. 2. A thermodynamic quantity that is the difference between the enthalpy and the product of the absolute temperature and entropy of a system also called Gibbs free energy.

free-energy change (G):

The amount of free energy released (negative G) or absorbed (positive G) in a reaction at constant temperature and pressure.

ENTROPY:
One of the ideas involved in the concept of entropy is that nature tends from order to disorder in isolated systems. So we say that entropy is a measure of disorder, and that can be measured by calorimeter, or with work done by the system, or a combination of the two.

ION TRANSPORT ACROSS MEMBERANE:

The relatively static membrane potential of resting cells is called the resting membrane potential (or resting voltage), as opposed to the specific dynamic electrochemical phenomena called action potential and graded membrane potential. Apart from the latter two, which occur in excitable cells (neurons, muscles, and some secretory cells in glands), membrane voltage in the majority of non-excitable cells can also undergo changes in response to environmental or intracellular stimuli. In principle, there is no difference between resting membrane potential and dynamic voltage changes like action potential from biophysical point of view: all these phenomena are caused by specific changes in membrane permeability for potassium, sodium, calcium, and chloride, which in turn result from concerted changes in functional activity of various ion channels, ion transporters, and exchangers. Conventionally, resting membrane potential can be defined as a relatively stable, ground value of transmembrane voltage in animal and plant cells. Any voltage is a difference in electric potential between two points - for example, the separation of positive and negative electric charges on opposite sides of a resistive barrier. The typical resting membrane potential of a cell arises from the separation of potassium ions from intracellular, relatively immobile anions across the membrane of the cell. Because the membrane permeability for potassium is much higher than that for other ions (disregarding voltage-gated channels at this stage), and because of the strong chemical gradient for potassium, potassium ions flow from the cytosol into the extracellular space carrying out positive charge, until their movement is balanced by build-up of negative charge on the inner surface of the membrane. Again, because of the high relative permeability for potassium, the resulting membrane potential is almost always close to the potassium reversal potential. But in order for this process to occur, a concentration gradient of potassium ions must first be set up. This work is done by the ion pumps/transporters and/or exchangers and generally is powered by ATP. In the case of the resting membrane potential across an animal cell's plasma membrane, potassium (and sodium) gradients are established by the Na+/K+ATPase (sodium-potassium pump) which transports 2 potassium ions inside and 3 sodium ions outside at the cost of 1 ATP molecule. In most neurons the resting potential has a value of approximately -70 mV. The resting potential is mostly determined by the

concentrations of the ions in the fluids on both sides of the cell membrane and the ion transport proteins that are in the cell membrane. In a healthy animal cell Na+ permeability is about 5% of the K permeability or even less, whereas the respective reversal potentials are +60 mV for sodium (ENa)and -80 mV for potassium (EK). Thus the membrane potential will not be right at EK, but rather depolarized from EK by an amount of approximately 5% of the 140 mV difference between EK and ENa. Thus, the cell's resting potential will be about 73 mV.

Membrane potential equilibrium:

For most animal cells potassium ions (K+) are the most important for the resting potential.[1] Due to the active transport of potassium ions, the concentration of potassium is higher inside cells than outside. Most cells have potassium-selective ion channel proteins that remain open all the time. There will be net movement of positively-charged potassium ions through these potassium channels with a resulting accumulation of excess negative charge inside of the cell. The outward movement of positively-charged potassium ions is due to random molecular motion (diffusion) and continues until enough excess negative charge accumulates inside the cell to form a membrane potential which can balance the difference in concentration of potassium between inside and outside the cell. "Balance" means that the electrical force (potential) that results from the build-up of ionic charge, and which impedes outward diffusion, increases until it is equal in magnitude but opposite in direction to the tendency for outward diffusive movement of potassium. This balance point is an equilibrium potential as the net transmembrane flux (or current) of K+ is zero. The equilibrium potential for a given ion depends only upon the concentrations on either side of the membrane and the temperature. 1-1= - RTV1C2/M2

Chemi osmosis:
Chemiosmosis is the movement of ions across a selectively permeable membrane, down their electrochemical gradient. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane during cellular respiration. Hydrogen ions (protons) will diffuse from an area of high proton concentration to an area of lower proton concentration. Theory : The theory suggests essentially that most ATP synthesis in respiring cells come from the electrochemical gradient across the inner membranes of mitochondria by using the energy of NADH and FADH2 formed from the breaking down of energy rich molecules such as glucose. Molecules such as glucose are metabolized to produce acetyl CoA as an energy-rich intermediate. The oxidation of acetyl CoA in the mitochondrial matrix is coupled to the reduction of a carrier molecule such as NAD and FAD. The carriers pass electrons to the electron transport chain (ETC) in the inner mitochondrial membrane, which in turn

pass them to other proteins in the ETC. The energy available in the electrons is used to pump protons from the matrix across the inner mitochondrial membrane, storing energy in the form of a transmembrane electrochemical gradient. The protons move back across the inner membrane through the enzyme ATP synthase. The flow of protons back into the matrix of the mitochondrion via ATP synthase provides enough energy for ADP to combine with inorganic phosphate to form ATP. The electrons and protons at the last pump in the ETC are taken up by oxygen to form water.

Cellular respiration (substrate level phosphorylation):

Chemiosmotic phosphorylation is the third pathway that produces ATP from inorganic phosphate and an ADP molecule. This process is part of oxidative phosphorylation. The complete breakdown of glucose in the presence of oxygen is called cellular respiration. The last steps of this process occur in mitochondria. The reduced molecules NADH and FADH2 are generated by the Krebs cycle, glycolysis, and pyruvate processing. These molecules pass electrons to an electron transport chain, which uses the energy released to create a proton gradient across the inner mitochondrial membrane. ATP synthase then uses the energy stored in this gradient to make ATP. This process is called oxidative phosphorylation because oxygen is the final electron acceptor and the energy released by reducing oxygen to water is used to phosphorylate ADP and generate ATP.

Biophysics of neural spike:

Following are the theories governing the production of electric current:

ficks law of diffusion:

Fick's law relates the diffusive flux to the concentration, by postulating that the flux goes from regions of high concentration to regions of low concentration, with a magnitude that is proportional to the concentration gradient. This shows that, J= -D(dc/dx) Where, J represents the energy, D represents diffusion coefficient and (dc/dx) shows the concentration gradient.

PARTICLE DRIFT:
The drift velocity is the average velocity that a particle, such as an electron, attains due to an electric field. It can also be referred to as Axial Drift Velocity since particles defined are assumed to be moving along a plane. In general, an electron will 'rattle around' in a conductor at the Fermi velocity randomly. An applied electric field will give this random motion a small net velocity in one direction. It is shown as J= -Z(dv/dx)[c] Where, J is current is mobility (in l/amp.volt.meter.mol) Z is ion valency dv is voltage and dx is distance and c is concentration.

einsteins equation:
This equation was given by Einstein for explaining the diffusion of a charged particle. It is frequently used in electrodiffusion phenomenon and for finding out the membrane potential in biological cells. It is also known as electrical mobility equation. This equation is represented as D = RT/q Where q is the charge, T is absolute temperature, D is diffusion constant, is electrical mobility of the charge and R is Boltzmanns constant.

Spike potential:
Spike potentials are one of the action potentials, which occur in electrical activity of smooth muscle contraction in animals. These are true action potentials. In the human gut they occur automatically when the resting membrane potential of the gastrointestinal smooth muscle becomes more positive than about -40 millivolts (the normal resting membrane potential in the smooth muscle fibers of the gut is between 50 and -60 millivolts). The spike potentials last 10 to 40 times as long in gastrointestinal muscle as the action potentials in large nerve fibers, each gastrointestinal spike lasting as long as 10 to 20 milliseconds.

Human eye vision:

The crystalline lens is a transparent, biconvex structure in the eye that, along with the cornea, helps to refract light to be focused on the retina. The lens is held by radial fibers and circular fibers. Crystallins are water-soluble proteins that compose over 90% of the protein within the lens. The three main crystallin types found in the human eye are -, -, and -crystallins. Crystallins tend to form soluble, high-molecular weight aggregates that pack tightly in lens fibers, thus increasing the index of refraction of the lens while maintaining its transparency. The retina consists of a large number

of photoreceptor cells which contain particular protein molecules called opsins. In humans, two types of opsins are involved in conscious vision: rod opsins and cone opsins. An opsin absorbs a photon and transmits a signal to the cell through a signal transduction pathway, resulting in hyperpolarization of the photoreceptor. Rods and cones differ in function. The rods are more numerous, some 120 million, and are more sensitive than the cones. However, they are not sensitive to color. The 6 to 7 million cones provide the eye's color sensitivity and they are much more concentrated in the central yellow spot known as the macula. In the retina, the photoreceptors synapse directly onto bipolar cells, which in turn synapse onto ganglion cells of the outermost layer, which will then conduct action potentials to the brain. A significant amount of visual processing arises from the patterns of communication between neurons in the retina. About 130 million photoreceptors absorb light, yet roughly 1.2 million axons of ganglion cells transmit information from the retina to the brain. The processing in the retina includes the formation of center-surround receptive fields of bipolar and ganglion cells in the retina, as well as convergence and divergence from photoreceptor to bipolar cell. In addition, other neurons in the retina, transmit information laterally (from a neuron in one layer to an adjacent neuron in the same layer), resulting in more complex receptive fields that can be either indifferent to color and sensitive to motion or sensitive to color and indifferent to motion. The retina adapts to its change in light through the use of the rods. In the dark, the retinal has a bent shape called cisretinal. When light is present, the retinal changes to a straight form called trans-retinal and breaks away from the opsin. This is called bleaching because the purified rhodopsin changes from violet to colorless in the light. In the dark, the rhodopsin absorbs no light therefore releasing glutamate cells which inhibit the bipolar cell. This inhibits the release of neurotransmitters to the ganglion cell. In the light, glutamate secretion ceases which no longer inhibits the bipolar cell from releasing neurotransmitters to the ganglion cell and therefore an image can be detected. Rhodopsin: The protein Rhodopsin contains the protonated retinal-Schiffs base complex which naturally lies in the inter-membrane pocket formed by the seven trans-membrane ahelical receptors. There are many flat discs of rhodopsin within the outer segment of a rod cell which upon light detection undergo a photo-isomeric change from Rhodopsin (11-cis) to all-trans retinal. After the photoisomerisation cascade which occurs via 5 shortlived intermediates (flowchart 1), trans retinal diffuses away and is converted back into 11-cis retinal before re-entry into the cycle. This process occurs via reduction to alltrans retinol followed by oxidation/isomerisation in the dark. Photoexcited Rhodopsin (4th of the 5 intermediates) triggers an enzymatic cascade process resulting in the hydrolysis of GMP. This in turn closes cation-specific channels within the rod cell membrane which are naturally open to influx of Na+ in the dark, and due to the effect of hyperpolarisation, the inner synatic body sends a nerve signal to other neurons in the Retina. Finally the light-induced lowering of calcium levels aids recovery of excited neurons to a passive, "dark" state and the cycle starts again upon detection of light. The photoreceptors of cone cells are also seven a-helical receptors with 11-cis-retinal as their chromophore. The detection range varies from green to red as the three nonpolar hydroxyl-containing residues near retinal are sequentially replaced with polar ones.

Cataract: A cataract is a clouding that develops in the crystalline lens of the eye or in its envelope, varying in degree from slight to complete opacity and obstructing the passage of light. A senile cataract, occurring in the elderly, is characterized by an initial opacity in the lens, subsequent swelling of the lens and final shrinkage with complete loss of transparency. Macular degeneration: Age-related macular degeneration (AMD) is a medical condition which usually affects older adults and results in a loss of vision in the center of the visual field (the macula) because of damage to the retina. It occurs in dry and wet forms. It is a major cause of blindness and visual impairment in older adults (>50 years). Macular degeneration can make it difficult or impossible to read or recognize faces, although enough peripheral vision remains to allow other activities of daily life.

Human ear:
As a wave reaches its peak in the cochlea, the outer hair cells near this peak give a small, physical push to enhance the movement of the basilar membrane. Much like a carpet on a floor being pushed into folds, the basilar membrane's folds act as an amplifier and cause the endolymph in the tympanic canal (high in potassium with a positive charge) to squirt towards the hairs of the inner hair cells which have a negative charge (in the form of calcium crystals). The hairs are deflected and very small channels open up near the tips of the hairs. The potassium atoms in the endolymph flow through these small channels, being propelled by their charges. This action is called depolarization - a positive change in the voltage across a cell's membrane.

Decibles: The decibel (dB) is a logarithmic unit that indicates the ratio of a physical quantity (usually power or intensity) relative to a specified or implied reference level. A ratio in decibels is ten times the logarithm to base 10 of the ratio of two power quantities.[1] A decibel is one tenth of a bel, a seldom-used unit. It is shown as: 10 log I/I

Ultrasound:
Ultrasound is cyclic sound pressure with a frequency greater than the upper limit of human hearing. Ultrasound is thus not separated from "normal" (audible) sound based on differences in physical properties, only the fact that humans cannot hear it. Although this limit varies from person to person, it is approximately 20 kilohertz (20,000 hertz) in healthy, young adults. The production of ultrasound is used in many different fields, typically to penetrate a medium and measure the reflection signature or supply focused energy. The reflection signature can reveal details about the inner structure of the medium, a property also used by animals such as bats for hunting. The most well known application of ultrasound is its use in sonography to produce pictures of fetuses in the human womb. There are a vast number of other applications as well.

Doppler effect:
The relative changes in frequency can be explained as follows. When the source of the waves is moving toward the observer, each successive wave crest is emitted from a position closer to the observer than the previous wave. Therefore each wave takes slightly less time to reach the observer than the previous wave. Therefore the time between the arrival of successive wave crests at the observer is reduced, causing an increase in the frequency. While they are travelling, the distance between successive wave fronts is reduced; so the waves "bunch together". Conversely, if the source of waves is moving away from the observer, each wave is emitted from a position farther from the observer than the previous wave, so the arrival time between successive waves is increased, reducing the frequency. The distance between successive wave fronts is increased, so the waves "spread out".