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  • 1
    Electronic Resource
    Electronic Resource
    Hierarchical characterization of energy landscapes using Gaussian packet states (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 9844-9857 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present a new method for exploring multidimensional energy landscapes by using Gaussian packets to characterize metastable states. Focusing on spatial scaling properties of the energy function, we derive nonlinear self-consistent packet equations which determine the parameters of these Gaussian packets. This provides a unique definition of the thermodynamic properties of metastable states and a computational prescription for their calculation. The packet equations allow bifurcation and enable us to follow the "trajectories'' of states as functions of temperature and to determine the hierarchical relationships between states. The method is demonstrated on simple one-dimensional models and on Lennard-Jones six-, seven-, and eight-atom microclusters. We find that the microcluster state trajectories that are connected to lowest zero-temperature energy conformations are also connected to the lowest free-energy trajectories up to their destabilization temperatures. That is, the global minima have a "strong scaling'' property that can accelerate searches for global minima by scale-dependent annealing methods. © 1994 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468485
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  • 2
    Electronic Resource
    Electronic Resource
    Finding transition states using contangency curves (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 10099-10104 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present a new method for approximating reaction paths and transition states of conformational transitions in polyatomic systems. The method uses the quasi-harmonic properties of the metastable state to construct a bi-Gaussian model for the energy landscape. Its reaction path is approximated by the equipotential contour cotangency (contangency) curve which connects the two equilibrium states with the saddle point lying between them. Unlike the reaction path, the contangency curve has an explicit analytic definition which makes it a useful starting point for conventional reaction path calculations. The method is illustrated for the conformational transition between the chair and twisted-boat isomers of cyclohexane. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.474043
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  • 3
    Electronic Resource
    Electronic Resource
    Macrostates of classical stochastic systems (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 9986-10007 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The thermodynamic and dynamic properties of a stochastic system can be determined from the underlying microscopic description once appropriate macroscopic states ("macrostates'') have been identified. Macrostates correspond to temperature-dependent regions of conformation space that are effectively isolated by potential energy barriers. However, there is no rigorous procedure for defining them and they are generally specified by ad hoc temperature-independent prescriptions. This is inadequate for complicated multidimensional systems like proteins. Here we provide a rigorous definition of macrostates of diffusive stochastic systems by relating the eigenfunction expansion of the Smoluchowski equation to a macrostate expansion via a "Minimum Uncertainty Condition.'' We develop a general computational bootstrap procedure for identifying macrostates in multiple dimensions and computing their thermal and dynamic properties. This employs nonlinear "characteristic packet equations'' to identify anisotropic Gaussian packets that provide a coarse-grained representation of the equilibrium probability distribution. These provide starting points for a variational method for calculating transition rates between macrostates and for a perturbative method for describing relaxations within macrostates. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472830
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  • 4
    Electronic Resource
    Electronic Resource
    Variational calculation of macrostate transition rates (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 1670-1686 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We develop the macrostate variational method (MVM) for computing reaction rates of diffusive conformational transitions in multidimensional systems by a variational coarse-grained "macrostate" decomposition of the Smoluchowski equation. MVM uses multidimensional Gaussian packets to identify and focus computational effort on the "transition region," a localized, self-consistently determined region in conformational space positioned roughly between the macrostates. It also determines the "transition direction" which optimally specifies the projected potential of mean force for mean first-passage time calculations. MVM is complementary to variational transition state theory in that it can efficiently solve multidimensional problems but does not accommodate memory-friction effects. It has been tested on model 1- and 2-dimensional potentials and on the 12-dimensional conformational transition between the isoforms of a microcluster of six-atoms having only van der Waals interactions. Comparison with Brownian dynamics calculations shows that MVM obtains equivalent results at a fraction of the computational cost. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476882
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  • 5
    Electronic Resource
    Electronic Resource
    Erratum: "Variational calculation of macrostate transition rates" [J. Chem. Phys. 109, 1670 (1998)] (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 4975-4975 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.478394
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  • 6
    Electronic Resource
    Electronic Resource
    Erratum: "Macrostates of classical stochastic systems" [J. Chem. Phys. 105, 9986 (1996)] (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 4975-4975 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.478393
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  • 7
    Electronic Resource
    Electronic Resource
    Wrong policy? (1994)
    [s.l.] : Nature Publishing Group
    Nature 372 (1994), S. 214-214 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] SIR - In a recent leading article on genome databases (Nature 371, 363; 1994) you comment: "The fear that this asym-metry [between the contributions to and uses of databases by industrial and academic scientists] would become a problem is partly why Nature resolved ... not to make the submission of ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/372214c0
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  • 8
    Electronic Resource
    Electronic Resource
    An RNA-binding protein associated with Src through its SH2 and SH3 domains in mitosis (1994)
    [s.l.] : Nature Publishing Group
    Nature 368 (1994), S. 867-871 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] NIH3T3 fibroblasts and NIH3T3-derived c-Src overexpressor cells were arrested in mitosis (Fig. 1). To stabilize tyrosine phos-phorylation, some cells were briefly (10 min) treated with protein tyrosine phosphatase (FTP) inhibitors before lysis. Mitotic, but not unsynchronized, NIH3T3 cells ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/368867a0
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  • 9
    Electronic Resource
    Electronic Resource
    Regulation of focal adhesion-associated protein tyrosine kinase by both cellular adhesion and oncogenic transformation (1992)
    [s.l.] : Nature Publishing Group
    Nature 358 (1992), S. 690-692 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Earlier studies showed that tyrosine phosphorylation of pp120 can be induced by plating NIH3T3 cells on either plasma fibronectin or on anti-integrin antibody, but not on nonspecific substrates such as poly-L-lysine or concanavalin A (ref. 2). These studies excluded the possibility of pp120 being ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/358690a0
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  • 10
    Electronic Resource
    Electronic Resource
    Induction by E1A oncogene expression of cellular susceptibility to lysis by TNF (1987)
    [s.l.] : Nature Publishing Group
    Nature 330 (1987), S. 581-583 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Cell lines were cloned from foci isolated after transfecting NIH 3T3 cells with plasmics expressing v-src (pMvsrc) (ref. 7), human bladder carcinoma activated ras (T24-6) or human c-Ha-ras (ras Cl-2) (S. Yokoyama, personal communication), poly-oma middle T or large T antigens (pPyMTl, pLT214) (ref. ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/330581a0
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