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Biophysical techniques

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Biophotonics. For the spontaneous low-level emission of photons from living tissues, see Biophoton.

Biophotonics

The term biophotonics denotes a combination of biology and photonics, with photonics being the science and technology of generation, manipulation, and detection of photons, quantum units of light. Photonics is related to electronics and photons. Photons play a central role in information technologies such as fiber optics the way electrons do in electronics. Biophotonics can also be described as the "development and application of optical techniques, particularly imaging, to the study of biological molecules, cells and tissue". Bioelectromagnetics. Biological phenomena[edit] Short-lived electrical events called action potentials occur in several types of animal cells which are called excitable cells, a category of cell include neurons, muscle cells, and endocrine cells, as well as in some plant cells.

Bioelectromagnetics

These action potentials are used to facilitate inter-cellular communication and activate intracellular processes. The physiological phenomena of action potentials are possible because voltage-gated ion channels allow the resting potential caused by electrochemical gradient on either side of a cell membrane to resolve. Calcium imaging. Calcium imaging is a scientific technique usually carried out in research which is designed to show the calcium (Ca2+) status of a cell, tissue or medium.

Calcium imaging

Calcium imaging techniques take advantage of so-called calcium indicators, fluorescent molecules that can respond to the binding of Ca2+ ions by changing their fluorescence properties. Two main classes of calcium indicators exist: chemical indicators and genetically encoded calcium indicators (GECI). Calcium imaging can be used to optically probe intracellular calcium in living animals.[1] This technique has allowed studies of neuronal activity in hundreds of neurons and glial cells within neuronal circuits.

Chemical indicators[edit] This group of indicators includes fura-2, indo-1, fluo-3, fluo-4, Calcium Green-1. These dyes are generally used with the chelator carboxyl groups masked as acetoxymethyl esters, in order to render the molecule lipophilic and to allow easy entrance into the cell. Calorimetry. Chromatography. Pictured is a sophisticated gas chromatography system.

Chromatography

This instrument records concentrations of acrylonitrile in the air at various points throughout the chemical laboratory. Automated fraction collector and sampler for chromatographic techniques Chromatography (/ˌkroʊməˈtɒɡrəfi/; from Greek χρῶμα chroma "color" and γράφειν graphein "to write"[1]) is the collective term for a set of laboratory techniques for the separation of mixtures. The mixture is dissolved in a fluid called the mobile phase, which carries it through a structure holding another material called the stationary phase.

The various constituents of the mixture travel at different speeds, causing them to separate. Chromatography may be preparative or analytical. Circular dichroism. Physical principles[edit] Circular polarization of light[edit] Interaction of circularly polarized light with matter[edit] The rotational strength has also been determined theoretically, We see from these two equations that in order to have non-zero , the electric and magnetic dipole moment operators (

Circular dichroism

Computational chemistry. Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems.

Computational chemistry

It uses methods of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids. Its necessity arises from the fact that — apart from relatively recent results concerning the hydrogen molecular ion (see references therein for more details) — the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. Cryobiology. Dual-polarization interferometry. Instrumentation[edit] The technique is quantitative and real-time (10 Hz) with a dimensional resolution of 0.01 nm.[2] Applications[edit] A novel application for dual-polarization interferometry emerged in 2008, where the intensity of light passing through the waveguide is extinguished in the presence of crystal growth.

Dual-polarization interferometry

This has allowed the very earliest stages in protein crystal nucleation to be monitored.[3] Later versions of dual-polarization interferometers also have the capability to quantify the order and disruption in birefringent thin films.[4] This has been used, for example, to study the formation of lipid bilayers and their interaction with membrane proteins.[5][6] Electrophysiology. "Current Clamp" is a common technique in electrophysiology.

Electrophysiology

This is a whole-cell current clamp recording of a neuron firing due to it being depolarized by current injection Definition and scope[edit] Classical electrophysiological techniques[edit] Electrophysiology is the science and branch of physiology that pertains to the flow of ions in biological tissues and, in particular, to the electrical recording techniques that enable the measurement of this flow. Electron microscope. Diagram of a transmission electron microscope An electron microscope (EM) is a type of microscope that uses an electron beam to illuminate a specimen and produce a magnified image.

Electron microscope

An EM has greater resolving power than a light microscope and can reveal the structure of smaller objects because electrons have wavelengths about 100,000 times shorter than visible light photons. They can achieve better than 50 pm resolution[1] and magnifications of up to about 10,000,000x whereas ordinary, non-confocal light microscopes are limited by diffraction to about 200 nm resolution and useful magnifications below 2000x.

The electron microscope uses electrostatic and electromagnetic lenses to control the electron beam and focus it to form an image. Fluorescence spectroscopy. Fluorescence spectroscopy (also known as fluorometry or spectrofluorometry) is a type of electromagnetic spectroscopy which analyzes fluorescence from a sample.

Fluorescence spectroscopy

It involves using a beam of light, usually ultraviolet light, that excites the electrons in molecules of certain compounds and causes them to emit light; typically, but not necessarily, visible light. A complementary technique is absorption spectroscopy. Devices that measure fluorescence are called fluorometers or fluorimeters. Theory[edit] Main article: Fluorescence Molecules have various states referred to as energy levels. In fluorescence spectroscopy, the species is first excited, by absorbing a photon, from its ground electronic state to one of the various vibrational states in the excited electronic state. Force spectroscopy. Force spectroscopy is a set of techniques for the study of the binding forces between individual molecules.[1][2] These methods can be used to measure the mechanical properties of single polymer molecules or proteins, or individual chemical bonds. The name "force spectroscopy", although widely used in the scientific community, is somewhat misleading, because there is no true matter-radiation interaction.[3]

Gel electrophoresis. Digital image of 3 plasmid restriction digests run on a 1% w/v agarose gel, 3 volt/cm, stained with ethidium bromide. The DNA size marker is a commercial 1 kbp ladder. The position of the wells and direction of DNA migration is noted. Gel electrophoresis is a method for separation and analysis of macromolecules (DNA, RNA and proteins) and their fragments, based on their size and charge. Isothermal titration calorimetry. Mass spectrometry. SIMS mass spectrometer, model IMS 3f. Orbitrap mass spectrometer. Mass spectrometry (MS) is an analytical chemistry technique that helps identify the amount and type of chemicals present in a sample by measuring the mass-to-charge ratio and abundance of gas-phase ions.[1] A mass spectrum (plural spectra) is a plot of the ion signal as a function of the mass-to-charge ratio.

The spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical structures of molecules, such as peptides and other chemical compounds. Mass spectrometry works by ionizing chemical compounds to generate charged molecules or molecule fragments and measuring their mass-to-charge ratios. In a typical MS procedure, a sample, which may be solid, liquid, or gas, is ionized, for example by bombarding it with electrons.

Microscale thermophoresis. Microscopy. Microscopy is the technical field of using microscopes to viewing objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of microscopy: optical, electron, and scanning probe microscopy. Atomic force microscopy. An atomic force microscope on the left with controlling computer on the right. Block diagram of atomic force microscope using beam deflection detection.

Neuroimaging. Para-sagittal MRI of the head in a patient with benign familial macrocephaly. Neuroimaging includes the use of various techniques to either directly or indirectly image the structure, function/pharmacology of the nervous system. Neutron spin echo. Neutron spin echo spectroscopy is an inelastic neutron scattering technique invented by Ferenc Mezei in the 1970s, and developed in collaboration with John Hayter.[1] In recognition of his work and in other areas, Mezei was awarded the first Walter Haelg Prize in 1999. The spin echo spectrometer possesses an extremely high energy resolution (roughly one part in 100,000). Additionally, it measures the density-density correlation (or intermediate scattering function) F(Q,t) as a function of momentum transfer Q and time.

Other neutron scattering techniques measure the dynamic structure factor S(Q,ω), which can be converted to F(Q,t) by a Fourier transform, which may be difficult in practice. For weak inelastic features S(Q,ω) is better suited, however, for (slow) relaxations the natural representation is given by F(Q,t). Optical tweezers. Magnetic tweezers. Magnetic tweezers (MT) are scientific instruments for the manipulation and characterization of biomolecules or polymers. Patch clamp. Nuclear magnetic resonance spectroscopy of proteins. Small-angle X-ray scattering. Spectrophotometry. Colorimetry. Spectroscopy. Circular dichroism. Nuclear magnetic resonance spectroscopy.

Differential centrifugation. X-ray crystallography.