Developed in the Project COMPLEX DEVELOPMENT OF TEACHING MATERIALS FOR MOLECULAR BIONICS BSC AND INFOBIONICS MSC COURSES WITHIN CONSORTIUM
Consortium leader: Pázmány Péter Catholic University, Faculty of Information Technology, www.itk.ppke.hu
Members: Semmelweis University NORDEX Cultural and Trading Ltd.
Press: PPKE ITK, Budapest 2011
Contributing editor: Ágnes Bércesné Novák
Edited by: Balázs Balogh, András Budinszky, György Cserey, Ildikó Csurgayné, Árpád Csurgay, Péter Földesy, Tamás Freund, Dániel Györffy, György Karmos, Kristóf Iván, Szabolcs Káli, Imre Kalló, József Laczkó, János Levendovszky, Zsolt Liposits, Péter Mátyus, András Oláh, Sándor Pongor, Zoltán Vidnyánszky, Péter Závodszky
Compiled by: Balázs Balogh, András Budinszky, Éva Bankó, Dóra Bihary, Bence Borbély, László Csanády, György Cserey, Richárd Csercsa, Ildikó Csurgayné, Balázs Dombóvári, György Erőss, Richárd Fiáth, Péter Földesy, Tamás Freund, Viktor Gál, Péter Gál, Zoltán Gáspári, Zsolt Gelencsér, Miklós Gyöngy, Dániel Györffy, Domonkos Horváth, Imre Kalló, Szabolcs Káli, Kristóf Iván, György Karmos, Péter Katona, Péter Kerekes, István Kóbor, Kraszimir Kolev, Lajos R. Kozák, Gábor Krajsovszky, Ákos Kusnyerik, József Laczkó, Zsolt Liposits, Raymund Machovich, Péter Mátyus, Tamás Molnár, András Oláh, Sándor Pongor, Róbert Tibold, Attila Tihanyi, Dávid Tisza, Kálmán Tornai, Gergely Treplán, László Tretter, István Ulbert, Zoltán Vidnyánszky, Péter Závodszky
Expert Proofreaders: Endre Barta, Péter Fürjesi, László Füstöss, Sándor György, Erik Hrabovszky, Gyula Kovács, Lóránt Kovács, János Makó, András Poppe, András Szilágyi, Balázs Ujfalussy, András Varró, Lucia Wittner, Géza Zboray
English Language Proofreader: Márton Péri
The Faculty of Information Technology (PPCU FIT) of Pázmány Péter Catholic University, together with Semmelweis University (SU) were the first universities in Hungary to launch the Molecular Bionics BSc in the year 2008. From February 2012 on the new infobionics MSc is going to be launched, which is probably the first in the world with these curricula and profile.
The TÁMOP-4.1.208/2/A/KMR-2009-006* grant in years 2010–2011 made it possible to standardize the professional content of the molecular bionics and infobionics courses, and to develop the teaching material in a fairly detailed way. These materials are written in English and published on the World Wide Web, so they are available free of charge to all interested parties – in order to make the learning process of these new disciplines easier.
The work, led by the leading professors of the two universities, resulted in the preparation of the teaching materials of seventeen courses in English, having at least 12 slide presentations for each. More than 12,000 slides organized in lectures have already been placed in the World Wide Web. All the completed learning materials written by almost 50 widely known and respected researchers and professors are listed in Table 1.
Digital- and neural based signal processing and kiloprocessor arrays
Electrophysiological methods for the study of the nervous- and muscular system
Introduction to bioinformatics
Introduction to biophysics
Introduction to functional neurobiology and additional animation
Modeling neurons and networks
Neural interfaces and prostheses
Neuromorph movement control
Organic- and biochemistry
Physics for nanobiotechnology
VLSI design methodologies
World of molecules
In addition, to help the individuals learning the new concepts in the curricula both in English and in Hungarian, the participants developed a glossary of the main notions in English, a bilingual dictionary in English and Hungarian and completed these dictionaries with a bilingual glossary of the keywords (These last two are more appropriate to be used in connection with the lecture slide shows). This “Glossary of key notions of Bionics and beyond” with more than 2500 headwords, may be used during all phases of the learning process.
I would like to express our gratitude to all Authors, Professionals; Proofreaders, language and teaching Experts and other Participants who provided their assistance.
IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997).
XML on-line corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata
updates compiled by A. Jenkins. ISBN 0-9678550-9-8. doi:10.1351/goldbook
MathWorld --A Wolfram Web Resource: http://mathworld.wolfram.com
http://cnx.org/content#subject/Mathematics and Statistics
Chapter 2. Glossary
13C-NMR (Carbon-13 NMR) → ~ an application of nuclear magnetic resonance (NMR) spectroscopy to the 13C isotope of carbon within the molecules of a substance, in order to determine the structure of its molecules.
1H-NMR → ~an application of nuclear magnetic resonance (NMR) spectroscopy with respect to hydrogen-1 nuclei within the molecules of a substance, in order to determine the structure of its molecules. In other words: proton NMR
2DGE → Two-dimensional gel electrophoresis: Laboratory method for separating elements of a complex mixture of proteins. The first dimension is usually IEF and the second one is SDS-PAGE.
(2R)-amino-5-phosphonovaleric acid (APV) → A chemical compound exerting antagonistic effects on NMDA receptors.
2’s complement code → The bit with the highest digit is the sign. In the case of a positive number, binary numbers fill the bit positions in a way that the imaginary binary point follows the bit positions kept for representation. In the case of a negative number, we represent the absolute value the same way, then we invert every bit piece by piece, then we add 1 (binary) to the result.
6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) → A chemical compound exerting antagonistic effects on AMPA and/or kainate receptors.
Ab initio → It is a Latin term meaning “from the beginning” and is derived from the Latin ab ~ from + initio. Ab initio simulation is based on the numerical solution of the fundamental physical laws.
Ab initio QM methods → Ab initio methods are QM calculations independent of any experiment other than the determination of fundamental constants. The methods are based on the use of the full Schroedinger equation to treat all the electrons of a chemical system. In practice, approximations are necessary to restrict the complexity of the electronic wavefunction and to make its calculation possible.
ABC transporter → ATP binding cassette protein, integral plasma membrane protein that consists of two domains (each of 6 transmembrane segments) and 2 loops (each containing an ATP-binding site) and that uses the energy of ATP for the transport of variety of hydrophobic substances (the A1 subtype is a specific carrier of membrane cholesterol to HDL)
Abduction → To draw away a limb from a position near or parallel to the median axis of the body
Absolute addressing mode → In the address part of the instruction, the real and exact address of the operand can be found. The address might be of the memory or one of the registers of the processor. In the case of register addressing, we need a smaller address part than in the case of memory addressing.
Absolute error → Specifies what the biggest error of the measured value could be.
Absolute refractory period (ARP) → No stimulus can evoke a response.
Absolute value, phase → A complex number can be viewed as a point or position vector in a two-dimensional Cartesian coordinate system. In angle notation (often used in electronics) to represent a phasor with absolute value (or modulus or magnitude) of r and the argument or phase of z is the angle to the real axis.
Absorbance → Absorbance is the logarithm of the intensity of the incident light divided by the intensity of the light transmitted through the sample.
Absorption → Absorption of electromagnetic radiation is the way by which the energy of a photon is taken up by matter, typically the electrons of an atom. Thus, the electromagnetic energy is transformed to other forms of energy for example, to heat.
Absorption (biology:digestion) → passage across intestinal cell membranes of the products of digestion
Absorption spectrum → is a plot of wavelength of incident light versus the amount of absorbed light. Organic molecules show absorption spectra in both the IR and UV spectrum.
Abutment → The abutment is a connection point between two structures. In case of the bone anchored hearing apparatus (BAHA) the abutment connects the sound processor and the titanium implant and transfers sound vibrations from the processor to the implant.
Abzymes → Molecules with enzymatic activity. They produced by some organism immunized by the transition state of a given reaction. Abzymes will catalyze this reaction.
AC (alternatign current) → In alternating current, the movement of electric charge periodically reverses direction.
Acausal → Acausality is a system property. A system is acausal if it is dependent on the future and past values of it’s input.
ACC → anterior cingulate cortex
Acceleration → The acceleration, or rate of change of velocity, is the derivative of the velocity with respect to time (the second derivative of the position with respect to time). Acceleration can arise from a change with time of the magnitude of the velocity or of the direction of the velocity or both. If only the magnitude of the velocity decreases, this is sometimes referred to as deceleration, but generally any change in the velocity with time, including deceleration, is simply referred to as acceleration.
Acceptor level, atoms → An energy level in a semiconductor that results from the presence of acceptor atoms.
Accumulation → An elementary operation, summing up the input values from the accumulator’s reset time til the actual input sample.
Accuracy → It is the degree of exactness which the final product corresponds to the measurement standard.
Acetylcholine → The neurotransmitter used both in the peripheral and central nervous system acting through metabotropic (muscarin-type) and ionotropic (nicotin-.type) receptors.
Acid → ~ is a molecular entity or chemical species capable of donating a hydron (proton) (see Brønsted acid) or capable of forming a covalent bond with an electron pair (see Lewis acid).
Acid amides → Amides of carboxylic acids, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the –C(=O)NH2 group including its carbon atom.
Acid dissociation constant → ~ (Ka) is a constant that establishes the ratio of products to reactants for weak acid at equilibrium. Usually the negative logarithm form (pKa) is used. The equilibrium constant Kan for splitting off the nth proton from a charged or uncharged acid, to be defined. pKa also defines the strength of the conjugate base of an acid. The higher the pKa value of the conjugate acid is, the stronger the base is.
Acid halides (acyl halides) → ~ are compounds consisting of an acyl group bonded to halogen.
Acid nitriles → Nitriles of carboxylic acids, having the structure RC≡N where the suffix includes the carbon atom of the –CN. However, carbonitrile is not a class name for nitriles.
Action potential → A short-lasting event in which the membrane potential of the cell rapidly rises and falls, following a stereotyped trajectory. In neurons, they play a central role in cell-to-cell communication. An ~ is typically generated in the initial segment of the axon (hillock) and propagates along the axon, and at the axon terminals it is transmitted to other neurons through synapses.
Action quantum → „The explanation of the second universal constant of the radiation law was not so easy. Because it represents the product of energy and time, I described it as the ~ of action ... the ~, appeared suitable for obtaining a simple explanation for a series of noteworthy observations during the action of light.” (from Nobel Lecture of Planck)
Activated complex → The ~ is the assembly of atoms (charged or neutral) which corresponds to the maximum in the potential energy profile (or the saddle point on the potential energy surface) describing the transformation of reactant(s) into product(s) in a single step reaction with the vibrations and rotations appropriate to the reaction conditions (temperature, pressure, solvent, etc.).
Activation → ~ is a process of the opening of gates by membrane depolarization in a voltage-gated ion channel.
Activation controlled reaction, energy controlled reaction → A reaction where the rate of the transformation of reactants determine the rate of the overall reaction. Reactions with high activation energy are usually activation controlled.
Activation energy → A minimal energy that a particle must posses for a reaction to occur.
Activation function → The function which is evaluated by the neuron for the input arguments
Activation gate → Part of an ion channel that reacts to membrane potential change such that it allows the channel to open if the membrane is depolarized.
Active electrode → Electrodes are integrated with the input amplifier, to reduce noise
Active pixel sensor → The photosensitive device’s signal is amplified in each pixel.
Active site → A site of the enzyme where the catalysis occurs. It is responsible for the substrate binding and the reaction itself.
Active transport → Ion transport through the cell membrane when energy is needed. The necessary energy comes from adenosine triphosphate (ATP) dephosphorylation.
Activity → A term describing the concentration of a solution taking into account the non-ideality of it. It approaches the molar concentration as the dilution approaches infinity.
Activity coefficient → A term giving the relation between the molar concentration and activity. It approaches one at infinite dilution.
Actuator → ~ is a mechanical device for moving or controlling a mechanism or system. It is operated by a source of energy, usually in the form of an electric current, and converts that energy into some kind of motion.
Adaptive architecutre → An architecture, which adapts its free parameters to the environment
Addition reaction → A reaction in which two or more molecular entities reacting with each other resulting in a single reaction product containing all atoms of all components. In this reaction, two new chemical bonds are formed and the net bond multiplicity is reduced at least in one of the reactants. The reverse process is called an elimination reaction.
Additive name → ~ is the formal assembly of names for the components of a compound without loss of atoms or groups of atoms from any component.
Additive tree → The distance between any pair of leaves is the sum of distances between those leaves and the first node they share on the tree
Adduction → To pull a limb to the midline in frontal plane
Ad-Hoc Networks → It is a local area network that is built spontaneously as devices connect. The individual network nodes forward packets to and from each other.
Adiabatic process → A process with no energy transfer.
Adipocyte → The parenchymal cell of adipose tissue
Aerobic process → A metabolic process that requires the presence of oxygen
Afferent → Neurons that carry signals from receptors toward the central nervous system; pathway providing input to a brain region
Affine gap penalty → Using a higher gap opening penalty and lower gap extending penalty for similarity scoring
Affinity chromatography → A method for protein isolation based on protein-protein interaction.
AFM, Atomic Force Microscope → ~ is one of the foremost tools for imaging, measuring, and manipulating matter at the nanoscale. The information is gathered by “feeling” the surface with a mechanical probe. Piezoelectric elements that facilitate tiny but accurate and precise movements on (electronic) command enable the very precise scanning.
Afterglow of the Big Bang → The universe underwent inflation in the past. We find today an `afterglow’ (cosmological constant 2.7 K.)
Afterhyperpolarization → A period after an action potential during which the membrane potential is more negative than usual
Agonist → A molecule, which evokes identical or very similar responses through the receptor as the natural ligand.
Alcohols → ~ are compounds in which a hydroxy group, –OH, is attached to a saturated carbon atom.
Aldehydes → ~ are compounds RC(=O)H , in which a carbonyl group is bonded to one hydrogen atom and to one R group.
Aliasing → It refers to an effect that causes different signals to become indistinguishable when sampled
Alicyclic compounds → ~ are aliphatic compounds having a carbocyclic ring structure which may be saturated or unsaturated, but may not be a benzenoid or other aromatic system.
Aliphatic compounds → ~ are acyclic or cyclic, saturated or unsaturated carbon compounds, excluding aromatic compounds.
Alkanes → ~ are acyclic (branched or unbranched) hydrocarbons having the general formula CnH2n+2. ~ are consisting entirely of hydrogen atoms and saturated carbon atoms.
Alkenes → ~ are acyclic (branched or unbranched) hydrocarbons having one carbon–carbon double bond and the general formula CnH2n. Acyclic branched or unbranched hydrocarbons having more than one double bond are as called alkadienes, alkatrienes, etc.