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 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.

Geometric effect on the vortex configuration and motion in mesoscopic superconducting cylinders

2015 ◽  
Vol 29 (03) ◽  
pp. 1550009 ◽  
Author(s):  
Shan-Shan Wang ◽  
Guo-Qiao Zha
Keyword(s):  
Phase Transitions ◽  
Vortex Dynamics ◽  
Axial Symmetry ◽  
Time Dependent ◽  
Vortex Matter ◽  
Ginzburg Landau ◽  
Geometric Effect ◽  
Multiply Connected ◽  
Vortex States ◽  
Ginzburg Landau Equations

Based on the time-dependent Ginzburg–Landau equations, we study numerically the vortex configuration and motion in mesoscopic superconducting cylinders. We find that the effects of the geometric symmetry of the system and the noncircular multiply-connected boundaries can significantly influence the steady vortex states and the vortex matter moving. For the square cylindrical loops, the vortices can enter the superconducting region in multiples of 2 and the vortex configuration exhibits the axial symmetry along the square diagonal. Moreover, the vortex dynamics behavior exhibits more complications due to the existed centered hole, which can lead to the vortex entering from different edges and exiting into the hole at the phase transitions.

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