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  • atoms
  • The popular Prentice Hall sets for general and organic chemistry utilize Molymod atoms and bond links and may be upgraded or customized with additional model parts. (sigmaaldrich.com)
  • John Dalton represented compounds as aggregations of circular atoms, and although Johann Josef Loschmidt did not create physical models, his diagrams based on circles are two-dimensional analogues of later models. (wikipedia.org)
  • The concept of the chemical bond as a direct link between atoms can be modelled by linking balls (atoms) with sticks/rods (bonds). (wikipedia.org)
  • Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass. (wikipedia.org)
  • It is typically modeled using a 6-12 Lennard-Jones potential, which means that attractive forces fall off with distance as r−6 and repulsive forces as r−12, where r represents the distance between two atoms. (wikipedia.org)
  • In the field of computational chemistry, energy minimization (also called energy optimization, geometry minimization, or geometry optimization) is the process of finding an arrangement in space of a collection of atoms where, according to some computational model of chemical bonding, the net inter-atomic force on each atom is acceptably close to zero and the position on the potential energy surface (PES) is a stationary point (described later). (wikipedia.org)
  • In chemistry, the CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models. (wikipedia.org)
  • Their models represented atoms by faceted hardwood balls, painted in different bright colors to indicate the respective chemical elements. (wikipedia.org)
  • AM1 is an attempt to improve the MNDO model by reducing the repulsion of atoms at close separation distances. (wikipedia.org)
  • Crick and Wa
  • Models encompass a wide range of degrees of precision and engineering: some models such as J.D. Bernal's water are conceptual, while the macromodels of Pauling and Crick and Watson were created with much greater precision. (wikipedia.org)
  • atomic
  • As one of our main research lines, we model enzymatic activity addressing not only the atomic (and electronic) detailed mechanism but also suggesting mutations for changes in activity, substrate specificity, etc. (bsc.es)
  • doi:10.1063/1.1770803 Walter L. Koltun (1965), Space filling atomic units and connectors for molecular models. (wikipedia.org)
  • atomistic
  • Physical models of atomistic systems have played an important role in understanding chemistry and generating and testing hypotheses. (wikipedia.org)
  • Structural
  • Docking is among a number of structural bioinformatics strategies trying to understand molecular recognition, both to understand structure to function relationships in macromolecules, and to derive tools useful in fields like drug design. (bsc.es)
  • From the very early stages of structural studies of DNA by X-ray diffraction and biochemical means, molecular models such as the Watson-Crick nucleic acid double helix model were successfully employed to solve the 'puzzle' of DNA structure, and also find how the latter relates to its key functions in living cells. (wikipedia.org)
  • Structural information is generated from X-ray diffraction studies of oriented DNA fibers with the help of molecular models of DNA that are combined with crystallographic and mathematical analysis of the X-ray patterns. (wikipedia.org)
  • closely packed spheres
  • The symmetrical arrangement of closely packed spheres informed theories of molecular structure in the late 1800s, and many theories of crystallography and solid state inorganic structure used collections of equal and unequal spheres to simulate packing and predict structure. (wikipedia.org)
  • These representations include closely packed spheres (CPK models) made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. (wikipedia.org)
  • explicitly
  • An extension of AM1 is SemiChem Austin Model 1 (SAM1), which is implemented in the AMPAC program and which explicitly treats d-orbitals. (wikipedia.org)
  • structures
  • After the development of X-ray crystallography as a tool for determining crystal structures, many laboratories built models based on spheres. (wikipedia.org)
  • Although such initial studies of DNA structures with the help of molecular models were essentially static, their consequences for explaining the in vivo functions of DNA were significant in the areas of protein biosynthesis and the quasi-universality of the genetic code. (wikipedia.org)
  • Supercoiling, packing with histones in chromosome structures, and other such supramolecular aspects also involve in vivo DNA topology which is even more complex than DNA molecular geometry, thus turning molecular modeling of DNA into an especially challenging problem for both molecular biologists and biotechnologists. (wikipedia.org)
  • The Molecular Modeling Database (MMDB) is a database of experimentally determined three-dimensional biomolecular structures and hosted by the National Center for Biotechnology Information. (wikipedia.org)
  • theoretical
  • Professor Krylov leads the iOpenShell lab, a research group focused on theoretical modeling of open shell and electronically excited species. (wikipedia.org)
  • typically
  • The dihedral or torsional terms typically have multiple minima and thus cannot be modeled as harmonic oscillators, though their specific functional form varies with the implementation. (wikipedia.org)
  • peptide
  • I am interested in molecular modeling of Antigenic peptide of M Leprae and its interaction with T cell CD4+ with the MHCII complex .I have chosen an antigenic peptide of 12k obtained from field trials in India.Is there any other proven antigenic peptide of m-lepray?If so what is the amino acid sequence? (bio.net)
  • systems
  • Coordinate systems: how to describe 3-D molecular structure. (warwick.ac.uk)
  • In this article, " molecular model " will primarily refer to systems containing more than one atom and where nuclear structure is neglected. (primidi.com)
  • The energy minimization method is useful to obtain a static picture for comparing between states of similar systems, while molecular dynamics provides information about the dynamic processes with the intrinsic inclusion of temperature effects. (wikipedia.org)
  • Biology
  • The 150 credits should include a minimum of 20 credits within the fields of Mathematics, Numerical Analysis and Computer Sciences, 5 of these must be within the fields of Numerical Analysis and Computer Sciences, 20 credits of Chemistry, possibly including courses in Chemical Measuring Techniques and 20 credits of Biotechnology or Molecular Biology. (kth.se)
  • A total of 20 university credits (hp) in Biotechnology or Molecular Biology. (kth.se)
  • software
  • http://biotech.isCool.net or http://www.ahpcc.unm.edu/~aroberts or http://www.arc.unm.edu/~aroberts This site allows easy access to hyperlinks and free software for the biochemist, biophysicist and molecular biologist. (bio.net)
  • Physical Models
  • The construction of physical models is often a creative act, and many bespoke examples have been carefully created in the workshops of science departments. (wikipedia.org)