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Molecular Models Of DNA
Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid ( DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either ''in vivo'' or ''in vitro''. These representations include closely packed spheres ( CPK models) made of plastic, metal wires for ''skeletal models'', graphic computations and animations by computers, artistic rendering. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions ''in vivo''. The more advanced, computer-based molecular models of DNA involve molecular dynamics simulations and quantum mechanics computations of vibro-rotations, delocalized molecular orbitals (MOs), electric dipole moments, hydrogen-bonding, and so on. ''DNA molecular dynamics modeling'' involves simulating deoxyribonucleic acid ( ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nanoscopic Scale
The nanoscopic scale (or nanoscale) usually refers to structures with a length scale applicable to nanotechnology, usually cited as 1–100 nanometers (nm). A nanometer is a billionth of a meter. The nanoscopic scale is (roughly speaking) a lower bound to the mesoscopic scale for most solids. For technical purposes, the nanoscopic scale is the size at which fluctuations in the averaged properties (due to the motion and behavior of individual particles) begin to have a significant effect (often a few percent) on the behavior of a system, and must be taken into account in its analysis. The nanoscopic scale is sometimes marked as the point where the properties of a material change; above this point, the properties of a material are caused by 'bulk' or 'volume' effects, namely which atoms are present, how they are bonded, and in what ratios. Below this point, the properties of a material change, and while the type of atoms present and their relative orientations are still importan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Histone
In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 90 micrometers (0.09 mm) of 30 nm diameter chromatin fibers. There are five families of histones which are designated H1/H5 (linker histones), H2, H3, and H4 (core histones). The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer. The tight wrapping of DNA around histones ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation tends to exist within any given population as a result of genetic mutation and recombination. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or more rare within a population. The evolutionary pressures that determine whether a characteristic is common or rare within a population constantly change, resulting in a change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms, and molecules. The theory of evolution by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromosome
A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are the histones. These proteins, aided by chaperone proteins, bind to and condense the DNA molecule to maintain its integrity. These chromosomes display a complex three-dimensional structure, which plays a significant role in transcriptional regulation. Chromosomes are normally visible under a light microscope only during the metaphase of cell division (where all chromosomes are aligned in the center of the cell in their condensed form). Before this happens, each chromosome is duplicated ( S phase), and both copies are joined by a centromere, resulting either in an X-shaped structure (pictured above), if the centromere is located equatorially, or a two-arm structure, if the centromere is located distally. The joined copies are now called si ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell (biology)
The cell is the basic structural and functional unit of life forms. Every cell consists of a cytoplasm enclosed within a membrane, and contains many biomolecules such as proteins, DNA and RNA, as well as many small molecules of nutrients and metabolites.Cell Movements and the Shaping of the Vertebrate Body in Chapter 21 of Molecular Biology of the Cell '' fourth edition, edited by Bruce Alberts (2002) published by Garland Science. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos. It is also common to describe small molecules such as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anharmonicity
In classical mechanics, anharmonicity is the deviation of a system from being a harmonic oscillator. An oscillator that is not oscillating in harmonic motion is known as an anharmonic oscillator where the system can be approximated to a harmonic oscillator and the anharmonicity can be calculated using perturbation theory. If the anharmonicity is large, then other numerical techniques have to be used. In reality all oscillating systems are anharmonic, but most approximate the harmonic oscillator the smaller the amplitude of the oscillation is. As a result, oscillations with frequencies 2\omega and 3\omega etc., where \omega is the fundamental frequency of the oscillator, appear. Furthermore, the frequency \omega deviates from the frequency \omega_0 of the harmonic oscillations. See also intermodulation and combination tones. As a first approximation, the frequency shift \Delta \omega=\omega-\omega_0 is proportional to the square of the oscillation amplitude A: :\Delta \omeg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Harmonic Oscillator
In classical mechanics, a harmonic oscillator is a system that, when displaced from its Mechanical equilibrium, equilibrium position, experiences a restoring force ''F'' Proportionality (mathematics), proportional to the displacement ''x'': \vec F = -k \vec x, where ''k'' is a positive coefficient, constant. If ''F'' is the only force acting on the system, the system is called a simple harmonic oscillator, and it undergoes simple harmonic motion: sinusoidal oscillations about the equilibrium point, with a constant amplitude and a constant frequency (which does not depend on the amplitude). If a frictional force (Damping ratio, damping) proportional to the velocity is also present, the harmonic oscillator is described as a damped oscillator. Depending on the friction coefficient, the system can: * Oscillate with a frequency lower than in the Damping ratio, undamped case, and an amplitude decreasing with time (Damping ratio, underdamped oscillator). * Decay to the equilibrium p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Computing
DNA computing is an emerging branch of unconventional computing which uses DNA, biochemistry, and molecular biology hardware, instead of the traditional electronic computing. Research and development in this area concerns theory, experiments, and applications of DNA computing. Although the field originally started with the demonstration of a computing application by Len Adleman in 1994, it has now been expanded to several other avenues such as the development of storage technologies, nanoscale imaging modalities, synthetic controllers and reaction networks, etc. A brief history of DNA computing and molecular programming Leonard Adleman of the University of Southern California initially developed this field in 1994. — The first DNA computing paper. Describes a solution for the directed Hamiltonian path problem. Also available here: Adleman demonstrated a proof-of-concept use of DNA as a form of computation which solved the seven-point Hamiltonian path problem. Since the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantum Computing
Quantum computing is a type of computation whose operations can harness the phenomena of quantum mechanics, such as superposition, interference, and entanglement. Devices that perform quantum computations are known as quantum computers. Though current quantum computers may be too small to outperform usual (classical) computers for practical applications, larger realizations are believed to be capable of solving certain computational problems, such as integer factorization (which underlies RSA encryption), substantially faster than classical computers. The study of quantum computing is a subfield of quantum information science. There are several models of quantum computation with the most widely used being quantum circuits. Other models include the quantum Turing machine, quantum annealing, and adiabatic quantum computation. Most models are based on the quantum bit, or "qubit", which is somewhat analogous to the bit in classical computation. A qubit can be in a 1 or 0 quantum s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Vibrational Circular Dichroism
Vibrational circular dichroism (VCD) is a spectroscopic technique which detects differences in attenuation of left and right circularly polarized light passing through a sample. It is the extension of circular dichroism spectroscopy into the infrared and near infrared ranges. Because VCD is sensitive to the mutual orientation of distinct groups in a molecule, it provides three-dimensional structural information. Thus, it is a powerful technique as VCD spectra of enantiomers can be simulated using ''ab initio'' calculations, thereby allowing the identification of absolute configurations of small molecules in solution from VCD spectra. Among such quantum computations of VCD spectra resulting from the chiral properties of small organic molecules are those based on density functional theory (DFT) and gauge-including atomic orbitals (GIAO). As a simple example of the experimental results that were obtained by VCD are the spectral data obtained within the carbon-hydrogen (C-H) stretchin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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