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Biology Monte Carlo Method
Biology Monte Carlo methods (BioMOCA) have been developed at the University of Illinois at Urbana-Champaign to simulate ion transport in an electrolyte environment through ion channels or nano-pores embedded in membranes. It is a 3-D particle-based Monte Carlo simulator for analyzing and studying the ion transport problem in ion channel systems or similar nanopores in wet/biological environments. The system simulated consists of a protein forming an ion channel (or an artificial nanopores like a Carbon Nano Tube, CNT), with a membrane (i.e. lipid bilayer) that separates two ion baths on either side. BioMOCA is based on two methodologies, namely the Boltzmann transport Monte Carlo (BTMC)C. Jacoboni, P. Lugli, The Monte Carlo Method for Semiconductor Device Simulation, Springer Verlag, New York (1989) and particle-particle-particle-mesh (P3M).R. Hockney, J. Eastwood, Computer Simulation Using Particles, McGraw-Hill, New York (1981) The first one uses Monte Carlo method to solve the Bo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Monte Carlo Methods
Monte Carlo methods, or Monte Carlo experiments, are a broad class of computational algorithms that rely on repeated random sampling to obtain numerical results. The underlying concept is to use randomness to solve problems that might be deterministic in principle. They are often used in physical and mathematical problems and are most useful when it is difficult or impossible to use other approaches. Monte Carlo methods are mainly used in three problem classes: optimization, numerical integration, and generating draws from a probability distribution. In physics-related problems, Monte Carlo methods are useful for simulating systems with many coupled degrees of freedom, such as fluids, disordered materials, strongly coupled solids, and cellular structures (see cellular Potts model, interacting particle systems, McKean–Vlasov processes, kinetic models of gases). Other examples include modeling phenomena with significant uncertainty in inputs such as the calculation of risk in b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nanopore
A nanopore is a pore of nanometer size. It may, for example, be created by a pore-forming protein or as a hole in synthetic materials such as silicon or graphene. When a nanopore is present in an electrically insulating membrane, it can be used as a single-molecule detector. It can be a biological protein channel in a high electrical resistance lipid bilayer, a pore in a solid-state membrane or a hybrid of these – a protein channel set in a synthetic membrane. The detection principle is based on monitoring the ionic current passing through the nanopore as a voltage is applied across the membrane. When the nanopore is of molecular dimensions, passage of molecules (e.g., DNA) cause interruptions of the "open" current level, leading to a "translocation event" signal. The passage of RNA or single-stranded DNA molecules through the membrane-embedded alpha-hemolysin channel (1.5 nm diameter), for example, causes a ~90% blockage of the current (measured at 1 M KCl solution). It m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scattering Rate
A formula may be derived mathematically for the rate of scattering when a beam of electrons passes through a material. The interaction picture Define the unperturbed Hamiltonian by H_0, the time dependent perturbing Hamiltonian by H_1 and total Hamiltonian by H. The eigenstates of the unperturbed Hamiltonian are assumed to be : H=H_0+H_1\ : H_0 , k\rang = E(k), k\rang In the interaction picture, the state ket is defined by : , k(t)\rang _I= e^ , k(t)\rang_S= \sum_ c_(t) , k'\rang By a Schrödinger equation, we see : i\hbar \frac , k(t)\rang_I=H_, k(t)\rang_I which is a Schrödinger-like equation with the total H replaced by H_. Solving the differential equation, we can find the coefficient of n-state. : c_(t) =\delta_ - \frac \int_0^t dt' \;\lang k', H_1(t'), k\rang \, e^ where, the zeroth-order term and first-order term are :c_^=\delta_ :c_^=- \frac \int_0^t dt' \;\lang k', H_1(t'), k\rang \, e^ The transition rate The probability of finding , k'\rang is found by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Collision
In physics, a collision is any event in which two or more bodies exert forces on each other in a relatively short time. Although the most common use of the word ''collision'' refers to incidents in which two or more objects collide with great force, the scientific use of the term implies nothing about the magnitude of the force. Some examples of physical interactions that scientists would consider collisions are the following: * When an insect lands on a plant's leaf, its legs are said to collide with the leaf. * When a cat strides across a lawn, each contact that its paws make with the ground is considered a collision, as well as each brush of its fur against a blade of grass. * When a boxer throws a punch, their fist is said to collide with the opponents body. * When an astronomical object merges with a black hole, they are considered to collide. Some colloquial uses of the word collision are the following: * A traffic collision involves at least one automobile. * A mid-air ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scattering
Scattering is a term used in physics to describe a wide range of physical processes where moving particles or radiation of some form, such as light or sound, are forced to deviate from a straight trajectory by localized non-uniformities (including particles and radiation) in the medium through which they pass. In conventional use, this also includes deviation of reflected radiation from the angle predicted by the law of reflection. Reflections of radiation that undergo scattering are often called ''diffuse reflections'' and unscattered reflections are called ''specular'' (mirror-like) reflections. Originally, the term was confined to light scattering (going back at least as far as Isaac Newton in the 17th century). As more "ray"-like phenomena were discovered, the idea of scattering was extended to them, so that William Herschel could refer to the scattering of "heat rays" (not then recognized as electromagnetic in nature) in 1800. John Tyndall, a pioneer in light scattering researc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Momentum
In Newtonian mechanics, momentum (more specifically linear momentum or translational momentum) is the product of the mass and velocity of an object. It is a vector quantity, possessing a magnitude and a direction. If is an object's mass and is its velocity (also a vector quantity), then the object's momentum is : \mathbf = m \mathbf. In the International System of Units (SI), the unit of measurement of momentum is the kilogram metre per second (kg⋅m/s), which is equivalent to the newton-second. Newton's second law of motion states that the rate of change of a body's momentum is equal to the net force acting on it. Momentum depends on the frame of reference, but in any inertial frame it is a ''conserved'' quantity, meaning that if a closed system is not affected by external forces, its total linear momentum does not change. Momentum is also conserved in special relativity (with a modified formula) and, in a modified form, in electrodynamics, quantum mechanics, quan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Diffusion
Molecular diffusion, often simply called diffusion, is the thermal motion of all (liquid or gas) particles at temperatures above absolute zero. The rate of this movement is a function of temperature, viscosity of the fluid and the size (mass) of the particles. Diffusion explains the net flux of molecules from a region of higher concentration to one of lower concentration. Once the concentrations are equal the molecules continue to move, but since there is no concentration gradient the process of molecular diffusion has ceased and is instead governed by the process of self-diffusion, originating from the random motion of the molecules. The result of diffusion is a gradual mixing of material such that the distribution of molecules is uniform. Since the molecules are still in motion, but an equilibrium has been established, the result of molecular diffusion is called a "dynamic equilibrium". In a phase with uniform temperature, absent external net forces acting on the particles, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lennard-Jones
Sir John Edward Lennard-Jones (27 October 1894 – 1 November 1954) was a British mathematician and professor of theoretical physics at the University of Bristol, and then of theoretical science at the University of Cambridge. He was an important pioneer in the development of modern computational chemistry and theoretical chemistry. Early life and education Lennard-Jones was born on 27 October 1894 at Leigh, Lancashire, the eldest son of Mary Ellen and Hugh Jones, an insurance agent. He was educated at Leigh Grammar School, going on to study at the University of Manchester, graduating in 1915 with a first-class honours degree in mathematics. Career Lennard-Jones is well known among scientists for his work on molecular structure, valency and intermolecular forces. Much research of these topics over several decades grew from a paper he published in 1929. His theories of liquids and of surface catalysis also remain influential. He wrote few, albeit influential, papers. His m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Structures
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of molecule, i.e. they can be understood as approximately local and hence transferable properties. Determination The molecular geometry can be determined by various spectroscopic methods and diffraction methods. IR, microwave and Raman spectroscopy can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques. X-ray crystallography, neutron diffraction and electron diffraction can give molecular s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Siegfried Selberherr
Siegfried Selberherr (* 3. August 1955 in Klosterneuburg) is an Austrian scientist in the field of microelectronics. He is a professor at the Institute for Microelectronics of the Technische Universität Wien (TU Wien). His primary research interest is in modeling and simulation of physical phenomena in the field of microelectronics. Biography Since 1988 Siegfried Selberherr is a chair professor for software technology of microelectronic systems at the TU Wien. He studied electrical engineering at the TU Wien, where he received the degree of Diplom-Ingenieur and the doctoral degree in technical sciences in 1978 and 1981, respectively, and the Habilitation in 1984. Afterwards he was a visiting researcher with the Bell-Labs for some time. Between 1996 and 2020 Prof. Selberherr was a Distinguished Lecturer of the IEEE Electron Devices Society. For many years, Prof. Selberherr was a leader of the Institute for Microelectronics at the TU Wien (now this Institute is headed by his you ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Poisson Equation
Poisson's equation is an elliptic partial differential equation of broad utility in theoretical physics. For example, the solution to Poisson's equation is the potential field caused by a given electric charge or mass density distribution; with the potential field known, one can then calculate electrostatic or gravitational (force) field. It is a generalization of Laplace's equation, which is also frequently seen in physics. The equation is named after French mathematician and physicist Siméon Denis Poisson. Statement of the equation Poisson's equation is \Delta\varphi = f where \Delta is the Laplace operator, and f and \varphi are real or complex-valued functions on a manifold. Usually, f is given and \varphi is sought. When the manifold is Euclidean space, the Laplace operator is often denoted as and so Poisson's equation is frequently written as \nabla^2 \varphi = f. In three-dimensional Cartesian coordinates, it takes the form \left( \frac + \frac + \frac \right)\varph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobic
In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, thus, prefer other neutral molecules and nonpolar solvents. Because water molecules are polar, hydrophobes do not dissolve well among them. Hydrophobic molecules in water often cluster together, forming micelles. Water on hydrophobic surfaces will exhibit a high contact angle. Examples of hydrophobic molecules include the alkanes, oils, fats, and greasy substances in general. Hydrophobic materials are used for oil removal from water, the management of oil spills, and chemical separation processes to remove non-polar substances from polar compounds. Hydrophobic is often used interchangeably with lipophilic, "fat-loving". However, the two terms are not synonymous. While hydrophobic substances are usually lipophilic, there are exceptions, suc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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