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Coarse-Grained Molecular Dynamics (Hardcover)
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Coarse-Grained Molecular Dynamics (Hardcover)
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The book entitled Coarse-Grained Molecular Dynamics Simulations
provides an overview of the most used coarse-grained (CG)
techniques and their applications on different systems. The CG
methods offer results for larger systems over a long period of time
that are not obtainable with the all-atom description of these
systems. The thermodynamics-based, structural-based and force
matching methods for constructing potentials, used in the building
of effective CG models, are discussed in the first part of the
book. In this part also is highlighted some significant application
of the coarse-grained molecular dynamics simulations in
biochemistry and medicine. The rest of the book gives a detailed
description of different CG models, constructed for specific
molecules and systems. Proteins and peptides, topic of part 2 of
the book, are scientifically interesting objects, as well as, for
their medical importance as potential drugs. Most of the current
docking procedures are focused on all-atoms conformational
adjustments and fail to reproduce large-scale protein motion.
CABS-dock, which employs a coarse-grained representation of
proteins, is one of the very few tools that allow unrestrained
docking with large conformational freedom of the receptor. Another
CG technique used for a description of protein folding and dynamics
is the G?-like model in which each amino acid residue is
represented as a single unified atom, and either an attractive or a
repulsive interaction is defined between any two residues. In this
part of the book are also shown interesting investigations of
interactions of proteins with lipid bilayers on CG level. Computer
modelling of very large bimolecular systems, such as long DNA and
RNA cannot reach the all-atom resolution in a foreseeable future
and this necessitates the development of CG approximations. Part 3
of the book present different CG models used for prediction of
structures, solution properties and dynamics of DNAs and RNAs. The
last part of the book, Coarse-Grained Models for Lipids, collect a
big selection of researches in the area. The fundamental building
blocks of all cell membranes are phospholipids. Phospholipid
molecules can demonstrate more than one micellar structures, which
play important role in drug delivery systems as well as in
biological systems. The use of CG models in exploring a variety of
structural and dynamic properties of large molecular systems built
from lipid molecules is discussed in details. The CG-MD technique
can provide a good approximation based on the selection of the
interaction parameters, as well as filling the gap between
theoretical and experimentally determined results. Although CG-MD
has provided valuable information for understanding the different
phenomenon, there is still limits in its application, but the
continuous theoretical developments guarantee the fast progress of
this area.
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