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Reliable and robust convergence to the electronic ground state within density functional theory (DFT) Kohn-Sham (KS) calculations remains a thorny issue in many systems of interest. In such cases, charge sloshing can delay or completely hinder the convergence. Here, we use an approach based on transforming the time-dependent DFT equations to imaginary time, followed by imaginary-time evolution, as a reliable alternative to the self-consistent field (SCF) procedure for determining the KS ground state. We discuss the theoretical and technical aspects of this approach and show that the KS ground state should be expected to be the long-imaginary-time output of the evolution, independent of the exchange-correlation functional or the level of theory used to simulate the system. By maintaining self-consistency between the single-particle wave functions (orbitals) and the electronic density throughout the determination of the stationary state, our method avoids the typical difficulties encountered in SCF. To demonstrate dependability of our approach, we apply it to selected systems which struggle to converge with SCF schemes. In addition, through the van Leeuwen theorem, we affirm the physical meaningfulness of imaginary-time TDDFT, justifying its use in certain topics of statistical mechanics such as in computing imaginary-time path integrals. Copyright © 2019 American Chemical Society.

We introduce a method to carry out zero-temperature calculations within density functional theory (DFT) but without relying on the Born-Oppenheimer (BO) approximation for the ionic motion. Our approach is based on the finite-temperature many-body path-integral formulation of quantum mechanics by taking the zero-temperature limit and treating the imaginary-time propagation of the electronic variables in the context of DFT. This goes beyond the familiar BO approximation and is limited from being an exact treatment of both electrons and ions only by the approximations involved in the DFT component. We test our method in two simple molecules, H2 and benzene. We demonstrate that the method produces a difference from the results of the BO approximation which is significant for many physical systems, especially those containing light atoms such as hydrogen; in these cases, we find that the fluctuations of the distance from its equilibrium position, due to the zero-point motion, is comparable to the interatomic distances. The method is suitable for use with conventional condensed-matter approaches and currently is implemented on top of the periodic pseudopotential code siesta. © 2018 American Physical Society.

The current understanding of epigenetic signaling assigns a central role to post-translational modifications that occur in the histone tails. In this context, it has been proposed that methylation of K9 and phosphorylation of S10 in the tail of histone H3 represent a binary switch that controls its reversible association to heterochromatin protein 1 (HP1). To test this hypothesis, we performed a comprehensive molecular dynamics study in which we analyzed a crystallographically defined complex that involves the HP1 chromodomain and an H3 tail peptide. Microsecond-long simulations show that the binding of the trimethylated K9 H3 peptide in the aromatic cage of HP1 is only slightly affected by S10 phosphorylation, because the modified K9 and S10 do not interact directly with one another. Instead, the phosphate group of S10 seems to form a persistent intramolecular salt bridge with R8, an interaction that can provoke a major structural change and alter the hydrogen-bonding regime in the H3-HP1 complex. These observations suggest that interactions between adjacent methyl-lysine and phosphoserine side chains do not by themselves provide a binary switch in the H3-HP1 system, but arginine-phosphoserine interactions, which occur in both histones and nonhistone proteins in the context of a conserved RKS motif, are likely to serve a key regulatory function. Biophys J

We use the results of first-principles electronic structure calculations and a strong coupling perturbation approach, together with general theoretical arguments, to illustrate the differences in super-exchange interactions between the copper-oxides and iron-pnictides. We provide a possible explanation for the two magnetic ground states within the same theoretical foundation. Contrary to the emerging view that magnetic order in the iron-pnictides is of itinerant nature, we argue that the observed magnetic moment is small because of frustration introduced by the electrons of the Fe orbitals as they compete to impose their preferred magnetic ordering. © 2009 Elsevier Ltd. All rights reserved.

We present density functional theory (DFT) results on the structural, electronic, and optical properties of Cu-flavonoid complexes for molar ratios 1:1, 1:2, and 1:3. We find that the preferred chelating site is close to the 4-oxo group and in particular the 3-4 site followed by the 3'-4' dihydroxy group in ring B. For the Cu-quercetin complexes, the large bathochromic shift of the first absorbance band upon complexation, which is in good agreement with experimental UV-vis spectra, results from the reduction of the electronic. energy gap. The HOMO states for these complexes are characterized by pi-bonding between the Cu d orbitals and the C, 0 p orbitals except for the case of 1:1. complex (spin minority), which corresponds to sigma-type bonds. The LUMO states are attributed to the contribution of Cu pz orbitals. Consequently, the main features of the first optical absorption maxima are essentially due to pi -> pi* transitions, while the 1:1 complex exhibits also sigma -> pi* transitions. Our optical absorption calculations based on time-dependent DFT demonstrate that the 1: 1 complex is responsible for the spectroscopic features at pH 5.5, whereas the 1:2 complex is mainly the one responsible for the characteristic spectra at pH 7.4. These theoretical predictions explain in detail the behavior of the optical absorption for the Cu-flavonoid complexes observed in experiments and are thus useful in elucidating the complexation mechanism and antioxidant activity of flavonoids. Journal of Physical Chemistry B

We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the translocation process. Based on these results, we construct a phenomenological model which incorporates the statistical and dynamical features of the translocation process and predicts a power-law dependence of the translocation time on the polymer length with an exponent alpha approximate to 1.2. The actual value of the exponent from the simulations is alpha=1.28 +/- 0.01, which is in excellent agreement with experimental measurements of DNA translocation through a nanopore, and is not sensitive to the choice of parameters in the simulation. The mechanism behind the emergence of such a robust exponent is related to the interplay between the longitudinal and transversal dynamics of both translocated and untranslocated segments. The connection to the macroscopic picture involves separating the contributions from the blob shrinking and shifting processes, which are both essential to the translocation dynamics.

The recently discovered FeAs-based superconductors show intriguing behavior and unusual dynamics of electrons and holes which occupy the Fed orbitals and As4s and 4p orbitals. Starting from the atomic limit, we carry out a strong-coupling expansion to derive an effective Hamiltonian that describes the electron and hole behaviors. The hopping and the hybridization parameters between the Fed and Ass and p orbitals are obtained by fitting the results of our density-functional-theory calculations to a tight-binding model with nearest-neighbor interactions and a minimal orbital basis. We find that the effective Hamiltonian, in the strong on-site Coulomb-repulsion limit, operates on three distinct subspaces coupled through Hund's rule. The three subspaces describe different components (or subsystems): (a) one spanned by the d x2 - y2 Fe orbital, (b) one spanned by the degenerate atomic Fe orbitals dxz and dyz, and (c) one spanned by the atomic Fe orbitals dxy and d z2. Each of these Hamiltonians is an extended t- t′ -J- J′ model and is characterized by different coupling constants and filling factors. For the case of the undoped material the second subspace alone prefers a ground state characterized by a spin-density-wave order similar to that observed in recent experimental studies, while the other two subspaces prefer an antiferromagnetic order. We argue that the observed spin-density-wave order minimizes the ground-state energy of the total Hamiltonian. © 2008 The American Physical Society.

In this paper, shear deformation at high strain rates is modeled within the framework of discrete dislocation plasticity. The method of discrete dislocation plasticity is extended to incorporate the temperature rise induced by moving dislocations. Also, the stress and displacement fields of a screw dislocation on inclined planes in a periodic structure are developed. The influence on the temperature rise on various micro-mechanical processes is discussed.