Solvation dynamics in polar solvents and imidazolium ionic liquids: failure of linear response approximations

Large scale computer simulations of different fluorophore-solvent systems reveal when and why linear response theory applies to time-dependent fluorescence measurements.

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Hybrid MPI and OpenMP parallel implementation of large-scale linear-response time-dependent density functional theory with plane-wave basis set

Electronic Structure ◽

10.1088/2516-1075/abfd1f ◽

2021 ◽

Author(s):

Lingyun Wan ◽

Xiaofeng Liu ◽

Jie Liu ◽

Xinming Qin ◽

Wei Hu ◽

...

Keyword(s):

Density Functional Theory ◽

Plane Wave ◽

Linear Response ◽

Density Functional ◽

Large Scale ◽

Parallel Implementation ◽

Time Dependent ◽

Basis Set ◽

Functional Theory ◽

Dependent Density

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Dynamic Fields and Response Properties

Quantum Theory for Chemical Applications ◽

10.1093/oso/9780190920807.003.0023 ◽

2020 ◽

pp. 473-554

Author(s):

Jochen Autschbach

Keyword(s):

Absorption Coefficient ◽

Linear Response ◽

Optical Rotation ◽

Polarized Light ◽

Linear Response Theory ◽

Time Dependent ◽

Electronic Transitions ◽

Orbital Theory ◽

Response Properties ◽

Set Up

It is shown how electronic transitions can be induced by the interaction with an electromagnetic wave of a suitable frequency. The rate of a transition between two electronic states induced by a time-dependent field is derived. The transition rate expression is used to calculate the absorption coefficient due to electronic transitions. The differential absorption coefficient for left and right circular polarized light is specific to chiral molecules and has different signs for a pair of enantiomers. The discussion then shifts to general functions describing the response of an atom or molecule to an external. The ideas developed thus far are then applied to the dynamic polarizability, molecular linear response functions in general, and the optical rotation. Linear response theory is set up within time-dependent molecular orbital theory. The Chapter concludes with a discussion of non-linear response properties and two-photon absorption.

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Atomic transport via point defects in crystals V. Equivalence of kinetic and linear response theories

Proceedings of the Royal Society of London Series A - Mathematical and Physical Sciences ◽

10.1098/rspa.1987.0124 ◽

1987 ◽

Vol 413 (1845) ◽

pp. 429-441 ◽

Cited By ~ 1

Keyword(s):

Kinetic Theory ◽

Point Defects ◽

Linear Response ◽

Transport Coefficients ◽

Linear Response Theory ◽

Time Dependent ◽

Defects In Crystals ◽

Response Functions ◽

Atomic Transport ◽

Solute Atoms

Earlier papers in this series have presented a general formulation of the kinetic theory of isothermal atomic transport via point defects. This has been used to derive expressions for the macroscopic transport coefficients and to analyse the response to time-dependent fields in terms of parameters characterizing the defects and their interaction with solute atoms, etc. In this paper it is shown that these transport coefficients and response functions are invariant with respect to a class of transformations of the quantities representing the defect displacements in all the transitions considered. In this way the exact equivalence of these results of kinetic theory to corresponding results of the linear response theory of Allnatt and Okamura is demonstrated.

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Combining non-equilibrium simulations and coarse-grained modelling allows for a fine-grained decomposition of solvation dynamics

Physical Chemistry Chemical Physics ◽

10.1039/c6cp06282b ◽

2016 ◽

Vol 18 (45) ◽

pp. 30954-30960 ◽

Cited By ~ 5

Author(s):

Michael Schmollngruber ◽

Daniel Braun ◽

Othmar Steinhauser

Keyword(s):

Ionic Liquids ◽

Stokes Shift ◽

Time Dependent ◽

Coarse Grained ◽

Solvation Dynamics ◽

Fine Grained ◽

Non Equilibrium

The time-dependent Stokes shift is shown to be a localized and short-ranged effect in ionic liquids.

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

10.1101/677617 ◽

2019 ◽

Cited By ~ 2

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.

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A linear response theory based method for prediction of large scale protein conformational changes upon ligand binding

10.1101/2021.03.09.434598 ◽

2021 ◽

Author(s):

Rajat Punia ◽

Gaurav Goel

Keyword(s):

Ligand Binding ◽

Conformational Change ◽

Linear Response ◽

Large Scale ◽

Normal Modes ◽

Linear Response Theory ◽

Conformational Space ◽

Small Scale ◽

Excitation Temperature

ABSTRACTPrediction of ligand-induced protein conformational transitions is a challenging task due to a large and rugged conformational space, and limited knowledge of probable direction(s) of structure change. These transitions can involve a large scale, global (at the level of entire protein molecule) structural change and occur on a timescale of milliseconds to seconds, rendering application of conventional molecular dynamics simulations prohibitive even for small proteins. We have developed a computational protocol to efficiently and accurately predict these ligand-induced structure transitions solely from the knowledge of protein apo structure and ligand binding site. Our method involves a series of small scale conformational change steps, where at each step linear response theory is used to predict the direction of small scale global response to ligand binding in the protein conformational space (dLRT) followed by construction of a linear combination of slow (low frequency) normal modes (calculated for the structure from the previous step) that best overlaps with dLRT. Protein structure is evolved along this direction using molecular dynamics with excited normal modes (MDeNM) wherein excitation energy along each normal mode is determined by excitation temperature, mode frequency, and its overlap with dLRT. We show that excitation temperature (ΔT) is a very important parameter that allows limiting the extent of structural change in any one step and develop a protocol for automated determination of its optimal value at each step. We have tested our protocol for three protein–ligand systems, namely, adenylate Kinase – di(adenosine-5’)pentaphosphate, ribose binding protein – β-D-ribopyranose, and DNA β-glucosyltransferase – uridine-5’-diphosphate, that incorporate important differences in type and range of structural changes upon ligand binding. We obtain very accurate prediction for not only the structure of final protein–ligand complex (holo-structure) having a large scale conformational change, but also for biologically relevant intermediates between the apo and the holo structures. Moreover, most relevant set of normal modes for conformational change at each step are an output from our method, which can be used as collective variables for determination of free energy barriers and transition timescales along the identified pathway.

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