Results 211 to 220 of about 744,325 (256)

Normal mode analysis and applications in biological physics

Journal of Physics: Condensed Matter, 2010
Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies. The use of normal modes in the study of these motions is often extremely fruitful since many of the functional motions of large proteins can be described using just a few normal modes which are ...
Eric C, Dykeman, Otto F, Sankey
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Multiscale Coarse-Graining via Normal Mode Analysis

Journal of Chemical Theory and Computation, 2012
A multiscale coarse-graining method called the normal-mode analysis based fluctuation matching (NMA-FM) is developed for constructing coarse-grained models of biomolecular systems. In the framework of normal-mode analysis, an arbitrary fine-grained model can be systematically converted to a more coarse-grained model, while the crucial low-frequency ...
Xia, Fei, Lu, Lanyuan
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Normal Mode Analysis of Polytheonamide B

Journal of the Physical Society of Japan, 2007
Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating D- and L-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis.
Takaharu Mori, Hironori Kokubo, Hirofumi Shimizu, Masayuki Iwamoto, Shigetoshi Oiki, Yuko Okamoto   +5 more
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Normal mode analysis of the image potential

Solid State Communications, 1978
Abstract A classical normal mode analysis has been made of the surface and bulk plasmon contributions to the image potential of a point charge source outside a metallic half-space. It is shown that the two contributions add up to give a result obtained earlier by direct solution of the hydrodynamic model equations for the charge density fluctuations.
P. Summerside, J. Mahanty
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Normal Mode Analysis

2005
Normal mode theory and harmonic potential approximations Konrad Hinsen All-atom normal mode calculations of large molecular systems using iterative methods Liliane Mouawad and David Perahia The Gaussian network model: Theory and applications A.J. Radar, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar Normal mode analysis of macromolecules: from enzyme ...
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Gradient-based direct normal-mode analysis

The Journal of Chemical Physics, 2005
A formulation of a direct, iterative method for obtaining the lowest eigenvalues and eigenvectors of a Hessian matrix is presented. Similar to the iterative schemes in electronic structure configuration interaction calculations (methods due to Lanczos, Davidson, and others), the mass-weighted Hessian matrix K is not constructed explicitly; instead, its
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Normal mode analysis of a model semirigid polymer

The Journal of Chemical Physics, 2011
Dynamic and structural properties of biological polymers are important to their function but it is difficult to obtain information on molecular flexibility at an atomic level. This paper describes how a normal mode analysis can be used to describe the equilibrium and nonequilibrium properties of complex polymer systems such as DNA in solution.
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DNA nanotube formation based on normal mode analysis

Nanotechnology, 2012
Ever since its inception, a popular DNA motif called the cross tile has been recognized to self-assemble into addressable 2D templates consisting of periodic square cavities. Although this may be conceptually correct, in reality certain types of cross tiles can only form planar lattices if adjacent tiles are designed to bind in a corrugated manner, in ...
PengFei, Qian, Sangjae, Seo, Junghoon, Kim, Seungjae, Kim, Byeong Soo, Lim, Wing Kam, Liu, Bum Joon, Kim, Thomas Henry, LaBean, Sung Ha, Park, Moon Ki, Kim   +9 more
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Normal mode analysis of protein dynamics

Current Opinion in Structural Biology, 1994
Abstract Notable recent developments in the use of normal mode methods to study protein dynamics include the use of quasiharmonic descriptions in crystallographic and NMR refinement protocols, and the development of techniques that can be applied to disordered systems (such as liquids) that do not oscillate about a single minimum. Harmonic models can
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Vibrattonal spectrum and normal-mode analysis of 1,3- cyclohexadiene

Journal of Molecular Structure, 1969
Abstract The IR and Raman spectra of 1,3-cyclohexadiene have been obtained. A vibrational assignment based both on the vapour IR rotational band shapes and Raman depolarization data is given. The assignment is supported by a zero-order frequency calculation, performed by means of a valence force field previously obtained for cyclohexene 4 , which
C. di Lauro, NETO, NATALE, CALIFANO, SALVATORE   +2 more
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