An official website of the United States government
DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman’s path integral formalism of quantum mechanics. The flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.
more »
« less
Theoretical assessment of the nuclear quantum effects on polymer crystallinity via perturbation theory and dynamics
As seen in experiments with poly(3‐hexylthiophene), substitution of hydrogen with deuterium on the main chain alone decreases crystallinity. To understand this effect, a general formalism for analysis of the dipole moments and polarizabilities incorporating quantum nuclei, is developed. The formalism, based on quantum dynamics of the proton/deuteron and on the perturbative analysis of the dipole interaction energy, accounts for the anharmonicity of a potential energy surface and for the anisotropy of molecular dipole moments. The formalism is implemented within the Discrete Variable Representation and the Density Functional Theory describing, respectively, the quantum proton/deuteron on the thiophene ring and the electronic structure of the 27‐atom model polymer chain, embedded into a larger crystalline environment. The isotope effect is mainly attributed to the differences in the zero‐point energy of the CH/CD bonds and to the isotope‐dependence of the dipole‐dipole inter‐chain interactions.
more »
« less
- Award ID(s):
- 1655740
- PAR ID:
- 10075804
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- International Journal of Quantum Chemistry
- Volume:
- 118
- Issue:
- 20
- ISSN:
- 0020-7608
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The elucidation of the detailed mechanism used by F 0 to convert proton gradient to torque and rotational motion presents a major puzzle despite significant biophysical and structural progress. Although the conceptual model has advanced our understanding of the working principles of such systems, it is crucial to explore the actual mechanism using structure-based models that actually reproduce a unidirectional proton-driven rotation. Our previous work used a coarse-grained (CG) model to simulate the action of F 0 . However, the simulations were based on a very tentative structural model of the interaction between subunit a and subunit c. Here, we again use a CG model but with a recent cryo-EM structure of cF 1 F 0 and also explore the proton path using our water flooding and protein dipole Langevin dipole semimacroscopic formalism with its linear response approximation version (PDLD/S-LRA) approaches. The simulations are done in the combined space defined by the rotational coordinate and the proton transport coordinate. The study reproduced the effect of the protomotive force on the rotation of the F 0 while establishing the electrostatic origin of this effect. Our landscape reproduces the correct unidirectionality of the synthetic direction of the F 0 rotation and shows that it reflects the combined electrostatic coupling between the proton transport path and the c-ring conformational change. This work provides guidance for further studies in other proton-driven mechanochemical systems and should lead (when combined with studies of F 1 ) to a complete energy transduction picture of the F 0 F 1 -ATPase system.more » « less
-
Nuclear response theory beyond the one-loop approximation is formulated for the case of finite temperature. For this purpose, the time blocking approximation to the time-dependent part of the in-medium nucleon-nucleon interaction amplitude is adopted for the thermal (imaginary-time) Green's function formalism. We found that introducing a soft blocking, instead of a sharp blocking at zero temperature, brings the Bethe-Salpeter equation to a single frequency variable equation also at finite temperatures. The method is implemented self-consistently in the framework of Quantum Hadrodynamics and designed to connect the high-energy scale of heavy mesons and the low-energy domain of nuclear medium polarization effects in a parameter-free way. In this framework, we investigate the temperature dependence of dipole spectra in the even-even nuclei $$^{48}$$Ca and $$^{100,120,132}$$Sn with a special focus on the giant dipole resonance's width problem and on the low-energy dipole strength distribution.more » « less
-
We present a novel theoretical formulation for performing quantum dynamics in terms of moments within the single-particle description. By expressing the quantum dynamics in terms of increasing orders of moments, instead of single-particle wave functions as generally done in time-dependent density functional theory, we describe an approach for reducing the high computational cost of simulating the quantum dynamics. The equation of motion is given for the moments by deriving analytical expressions for the first-order and second-order time derivatives of the moments, and a numerical scheme is developed for performing quantum dynamics by expanding the moments in the Taylor series as done in classical molecular dynamics simulations. We propose a few numerical approaches using this theoretical formalism on a simple one-dimensional model system, for which an analytically exact solution can be derived. The application of the approaches to an anharmonic system is also discussed to illustrate their generality. We also discuss the use of an artificial neural network model to circumvent the numerical evaluation of the second-order time derivatives of the moments, as analogously done in the context of classical molecular dynamics simulations.more » « less
-
Significant advances in Penning trap measurements of atomic masses and mass ratios of the proton, deuteron, triton, helion, and alpha-particle have occurred in the last five years. These include a measurement of the mass of the deuteron against 12C with 8.5 × 10−12 fractional uncertainty; resolution of vibrational levels of H2+ as mass and the application of a simultaneous measurement technique to the H2+/D+ cyclotron frequency ratio, yielding a deuteron/proton mass ratio at 5 × 10−12; new measurements of HD+/3He+, HD+/T+, and T+/3He+ leading to a tritium beta-decay Q-value with an uncertainty of 22 meV, and atomic masses of the helion and triton at 13 × 10−12; and a new measurement of the mass of the alpha-particle against 12C at 12 × 10−12. Some of these results are in strong disagreement with previous values in the literature. Their impact in determining a precise proton/electron mass ratio and electron atomic mass from spectroscopy of the HD+ molecular ion is also discussed.more » « less
