scholarly journals Linear response theory in the continuum for deformed nuclei: Green's function vs time-dependent Hartree-Fock with the absorbing boundary condition

2005 ◽  
Vol 71 (2) ◽  
Author(s):  
Takashi Nakatsukasa ◽  
Kazuhiro Yabana
Keyword(s):  
Boundary Condition ◽  
Linear Response ◽  
Linear Response Theory ◽  
Time Dependent ◽  
Absorbing Boundary Condition ◽  
Response Theory ◽  
Absorbing Boundary ◽  
Deformed Nuclei ◽  
Hartree Fock ◽  
The Continuum

scholarly journals Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory

2019 ◽  
Author(s):  
Bang-Chieh Huang ◽  
Chi-Hong Chang-Chein ◽  
Lee-Wei Yang
Keyword(s):  
Equilibrium State ◽  
Linear Response ◽  
Signal Propagation ◽  
Linear Response Theory ◽  
Time Dependent ◽  
Response Theory ◽  
Functional Sites ◽  
Allosteric Sites ◽  
Intramolecular Communication ◽  
Non Equilibrium

ABSTRACTIt has been an established idea in recent years that protein is a physiochemically connected network. Allostery, understood in this new context, is a manifestation of residue communicating between remote sites in this network, and hence a rising interest to identify functionally relevant communication pathways and the frequent communicators within. Previous studies rationalized the coupling between functional sites and experimentally observed allosteric sites by theoretically discovered high positional/velocity/thermal correlations between these sites. However, for one to systematically discover previously unobserved allosteric sites in any receptor/enzyme providing the position of functional (orthosteric) sites, these high correlations may not be able to identify remote allosteric sites because of a number of false-positives while many of those are located in proximity to the functional site. Also, whether allosteric sites should be found in equilibrium or non-equilibrium state of a protein to be more biologically relevant is not clear, neither is the directionality preference of aforementioned propagating signals. In this study, we devised a time-dependent linear response theory (td-LRT) integrating intrinsic protein dynamics and perturbation forces that excite protein’s temporary reconfiguration at the non-equilibrium state, to describe atom-specific time responses as the propagating mechanical signals and discover that the most frequent remote communicators can be important allosteric sites, mutation of which would deteriorate the hydride transfer rate in DHFR by 2 to 3 orders. The preferred directionality of the signal propagation can be inferred from the asymmetric connection matrix (CM), where the coupling strength between a pair of residues is suggested by their communication score (CS) in the CM, which is found consistent with experimentally characterized nonadditivity of double mutants. Also, the intramolecular communication centers (ICCs), having high CSs, are found evolutionarily conserved, suggesting their biological importance.

scholarly journals CONTINUUM COUPLING AND PAIR CORRELATION IN WEAKLY BOUND DEFORMED NUCLEI

2009 ◽  
Vol 18 (10) ◽  
pp. 2015-2019 ◽  
Author(s):  
HIROSHI OBA ◽  
MASAYUKI MATSUO
Keyword(s):  
Boundary Condition ◽  
Green's Function ◽  
Pair Correlation ◽  
Function Technique ◽  
Coordinate Space ◽  
Weakly Bound ◽  
Deformed Nuclei ◽  
Numerical Examples ◽  
Hartree Fock ◽  
The Continuum

We formulate a new Hartree-Fock-Bogoliubov method applicable to weakly bound deformed nuclei using the coordinate-space Green's function technique. An emphasis is put on treatment of quasiparticle states in the continuum, on which we impose the correct boundary condition of the asymptotic out-going wave. We illustrate this method with numerical examples.

Linear Response Theory and the Time-Dependent Ginzburg-Landau Equations

1971 ◽  
Vol 3 (5) ◽  
pp. 1625-1630 ◽  
Author(s):  
A. Houghton ◽  
K. Maki
Keyword(s):  
Linear Response ◽  
Linear Response Theory ◽  
Time Dependent ◽  
Response Theory ◽  
Ginzburg Landau ◽  
Ginzburg Landau Equations

scholarly journals Analysis of the window dissipation formula on the basis of linear response theory

1987 ◽  
Vol 475 (3) ◽  
pp. 557-568 ◽  
Author(s):  
Thomas Døssing ◽  
Jørgen Randrup
Keyword(s):  
Linear Response ◽  
Linear Response Theory ◽  
Response Theory
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