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Leiden Classical

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Leiden Classical

Leiden Classical is a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student! Classical Dynamics is used for describing the motion of a variety of different macroscopic objects.

Leiden Classical project URL; http://boinc.gorlaeus.net/

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Leiden Classical studies several different areas in the field of Classical Dynamics. The following is a short summery of each area.

Classical Dynamics Theory

Classical DynamicsClassical mechanics (commonly confused with Newtonian mechanics, which is a sub-field thereof) is used for describing the motion of macroscopic objects, from projectiles to parts of machinery, as well as astronomical objects, such as spacecraft, planets, stars, and galaxies. It produces very accurate results within these domains, and is one of the oldest and largest subjects in science and technology.

Besides this, many related specialties exist, dealing with gases, liquids, and solids, and so on. Classical mechanics is enhanced by special relativity for objects moving with high velocity, approaching the speed of light,general relativity is employed to handle gravitation at a deeper level, and quantum mechanics handles the wave-particle duality of atoms and molecules. Read more about this here.

Solar System Dynamics

Solar System DynamicsA numerical model of the solar system is a set of mathematical equations, which, when solved, give the approximate positions of the planets as a function of time. Attempts to create such a model established the more general field of celestial mechanics. The results of this simulation can be compared with past measurements to check for accuracy and then be used to predict future positions. Its main use therefore is in preparation of almanacs.Read more about this here.

Celestial Dynamics

Celestial Dynamics Celestial mechanics is the branch of astrophysics that deals with the motions of celestial objects. The field applies principles of physics, historically classical mechanics, to astronomical objects such as stars and planets to produce ephemeris data. Orbital mechanics (astrodynamics) is a sub-field which focuses on the orbits of artificial satellites. Read more about this here.

Molecular Dynamics

Molecular Dynamics Molecular dynamics (MD) is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics, giving a view of the motion of the atoms. Because molecular systems generally consist of a vast number of particles, it is impossible to find the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. It represents an interface between laboratory experiments and theory, and can be understood as a "virtual experiment". MD probes the relationship between molecular structure, movement and function. Molecular dynamics is a multidisciplinary method. Its laws and theories stem from mathematics, physics, and chemistry, and it employs algorithms from computer science and information theory. It was originally conceived within theoretical physics in the late 1950s, but is applied today mostly in materials science and bio-molecules. Read more about this here.

Force-fields between Atoms and Molecules

The Lennard-Jones potential

John Lennard-JonesA pair of neutral atoms or molecules is subject to two distinct forces in the limit of large separation and small separation: an attractive force at long ranges (van der Waals force, or dispersion force) and a repulsive force at short ranges (the result of overlapping electron orbitals, referred to as Pauli repulsion from Pauli exclusion principle). The Lennard-Jones potential (also referred to as the L-J potential, 6-12 potential or, less commonly, 12-6 potential) is a simple mathematical model that represents this behavior. It was proposed in 1924 by John Lennard-Jones. Read more about this here.

Basic molecular force-fields

Theoretical studies of biological molecules permit the study of the relationships between structure, function and dynamics at the atomic level. Since many of the problems that one would like to address in biological systems involve many atoms, it is not yet feasible to treat these systems using quantum mechanics. However, the problems become much more tractable when turning to empirical potential energy functions, which are much less computationally demanding than quantum mechanics; but this comes at a cost. Numerous approximations are introduced which lead to certain limitations. Read more about this here.

Well known Molecular Force-fields

Molecular Force-fieldsIn the context of molecular mechanics, a force field (also called a force-field) refers to the functional form and parameter sets used to describe the potential energy of a system of particles (typically but not necessarily atoms). Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical calculations. "All-atom" force fields provide parameters for every atom in a system, including hydrogen, while "united-atom" force fields treat the hydrogen and carbon atoms in methyl and methylene groups as a single interaction center. "Coarse-grained" force fields, which are frequently used in long-time simulations of proteins, provide even more abstracted representations for increased computational efficiency. Read more about this here.

Water Potentials

Water PotentialsWater molecular models have been developed in order to help discover the structure of water. They are useful given the basis that if the (known but hypothetical) model (that is, computer water) can successfully predict the physical properties of liquid water then the (unknown) structure of liquid water is determined. They involve orienting electrostatic effects and Lennard-Jones sites that may or may not coincide with one or more of the charged sites. Read more about this here.

Cool video about Quantum Tunneling

In quantum mechanics, quantum tunneling is a micro nanoscopic phenomenon in which a particle violates the principles of classical mechanics by penetrating or passing through a potential barrier or impedance higher than the kinetic energy of the particle. A barrier, in terms of quantum tunnelling, may be a form of energy state analogous to a "hill" or incline in classical mechanics, which classically suggests that passage through or over such a barrier would be impossible without sufficient energy.

 

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