The Lanczos Algorithm in Molecular Dynamics: Calculation of Spectral Densities

Author(s):  
Giorgio Moro ◽  
Jack H. Freed
2018 ◽  
Vol 84 (3) ◽  
Author(s):  
A. Panarese ◽  
D. Bruno ◽  
P. Tolias ◽  
S. Ratynskaia ◽  
S. Longo ◽  
...  

Spectral densities of plasma fluctuations are calculated for the thermal case using classical molecular dynamics (MD) assuming Coulomb interactions and a short-range cutoff radius. The aim of the calculation is to verify limits and performances of such calculations in the light of possible generalizations, e.g. collisional or non-ideal plasmas. Results are presented for ideal, collisionless, fully ionized thermal plasmas. Comparison with the analytical theory reveals a generally satisfactory agreement with possibility for improvement when more strict numerical parameters are used albeit with a strong increase in computational cost. The largest deviations have been observed in the vicinity of the weakly damped eigenmodes. The agreement is strong in other parts of the spectrum, where Landau damping is prominent, and overcomes the effects stemming from the excess collisionality and coupling as well as from the exclusion of short-range collisions.


1993 ◽  
Vol 60 (2) ◽  
pp. 358-365 ◽  
Author(s):  
R. Vale´ry Roy ◽  
P. D. Spanos

Spectral densities of the response of nonlinear systems to white noise excitation are considered. By using a formal solution of the associated Fokker-Planck-Kolmogorov equation, response spectral densities are represented by formal power series expansion for large frequencies. The coefficients of the series, known as the spectral moments, are determined in terms of first-order response statistics. Alternatively, a J-fraction representation of spectral densities can be achieved by using a generalization of the Lanczos algorithm for matrix tridiagonalization, known as the “recursion method.” Sequences of rational approximations of increasing order are obtained. They are used for numerical calculations regarding the single-well and double-well Duffing oscillators, and Van der Pol type oscillators. Digital simulations demonstrate that the proposed approach can be quite reliable over large variations of the system parameters. Further, it is quite versatile as it can be used for the determination of the spectrum of the response of a broad class of randomly excited nonlinear oscillators, with the sole prerequisite being the availability, in exact or approximate form, of the stationary probability density of the response.


2021 ◽  
Author(s):  
Sayan Maity ◽  
Vangelis Daskalakis ◽  
Marcus Elstner ◽  
Ulrich Kleinekathöfer

Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born–Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.


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