Failure of density-matrix minimization methods for linear-scaling density-functional theory using the Kohn penalty-functional

Accepted versio

Fuel optimum stochastic attitude control

Numerical solution of stochastic Hamilton-Jacobi equation for fuel optimal spacecraft attitude control syste

Preconditioned iterative minimization for linear-scaling electronic structure calculations

Linear-scaling electronic structure methods are essential for calculations on large systems. Some of these approaches use a systematic basis set, the completeness of which may be tuned with an adjustable parameter similar to the energy cut-off of plane-wave techniques. The search for the electronic ground state in such methods suffers from an ill-conditioning which is related to the kinetic contribution to the total energy and which results in unacceptably slow convergence. We present a general preconditioning scheme to overcome this ill-conditioning and implement it within our own first-principles linear-scaling density functional theory method. The scheme may be applied in either real space or reciprocal space with equal success. The rate of convergence is improved by an order of magnitude and is found to be almost independent of the size of the basis

Ab initio diffusional potential energy surface for CO chemisorption on Pd{110} at high coverage: Coupled translation and rotation

[[abstract]]The ground statepotential energy surface for CO chemisorption across Pd{110} has been calculated using density functional theory with gradient corrections at monolayer coverage. The most stable site corresponds well with the experimental adsorption heat, and it is found that the strength of binding to sites is in the following order: pseudo-short-bridge>atop>long-bridge>hollow. Pathways and transition states for CO surfacediffusion, involving a correlation between translation and orientation, are proposed and discussed.[[notice]]補正完畢[[journaltype]]國外[[booktype]]紙本[[countrycodes]]US

Prediction of GABARAP interaction with the GABA type A receptor.

We have performed docking simulations on GABARAP interacting with the GABA type A receptor using SwarmDock. We have also used a novel method to study hydration sites on the surface of these two proteins; this method identifies regions around proteins where desolvation is relatively easy, and these are possible locations where proteins can bind each other. There is a high degree of consistency between the predictions of these two methods. Moreover, we have also identified binding sites on GABARAP for other proteins, and listed possible binding sites for as yet unknown proteins on both GABARAP and the GABA type A receptor intracellular domain

Single-molecule and super-resolved imaging deciphers membrane behavior of onco-immunogenic CCR5

The ability of tumors to establish a pro-tumorigenic microenvironment is an important point of investigation in the search for new therapeutics. Tumors form microenvironments in part by the “education” of immune cells attracted via chemotactic axes such as that of CCR5-CCL5. Further, CCR5 upregulation by cancer cells, coupled with its association with pro-tumorigenic features such as drug resistance and metastasis, has suggested CCR5 as a therapeutic target. However, with several conformational “pools” being reported, phenotypic investigations must be capable of unveiling conformational heterogeneity. Addressing this challenge, we performed super-resolution structured illumination microscopy (SIM) and single molecule partially TIRF-coupled HILO (PaTCH) microscopy of CCR5 in fixed cells. SIM data revealed a non-random spatial distribution of CCR5 assemblies, while Intensity-tracking of CCR5 assemblies from PaTCH images indicated dimeric sub-units independent of CCL5 perturbation. These biophysical methods can provide important insights into the structure and function of onco-immunogenic receptors and many other biomolecules

Making tea: a human centred approach to designing a pervasive smart lab notebook

The methodology used to design a useful and workable laboratory electronic notebook is described along with some of the technology needed to implement the smart lab systems

Role of spin in the calculation of Hubbard U and Hund's J parameters from first principles

The density functional theory (DFT)+$U$ method is a pragmatic and effective approach for calculating the ground-state properties of strongly-correlated systems, and linear response calculations are widely used to determine the requisite Hubbard parameters from first principles. We provide a detailed treatment of spin within this linear response approach, demonstrating that the conventional Hubbard $U$ formula, unlike the conventional DFT+$U$ corrective functional, incorporates interactions that are off-diagonal in the spin indices and places greater weight on one spin channel over the other. We construct alternative definitions for Hubbard and Hund's parameters that are consistent with the contemporary DFT+$U$ functional, expanding upon the minimum-tracking linear response method. This approach allows Hund's $J$ and spin-dependent $U$ parameters to be calculated with the same ease as for the standard Hubbard $U$. Our methods accurately reproduce the experimental band gap, local magnetic moments, and the valence band edge character of manganese oxide, a canonical strongly-correlated system. We also apply our approach to a complete series of transition-metal complexes [M(H$_2$O)$_6$]$^{n+}$ (for M = Ti to Zn), showing that Hubbard corrections on oxygen atoms are necessary for preserving bond lengths, and demonstrating that our methods are numerically well-behaved even for near-filled subspaces such as in zinc. However, spectroscopic properties appear beyond the reach of the standard DFT+$U$ approach. Collectively, these results shed new light on the role of spin in the calculation of the corrective parameters $U$ and $J$, and point the way towards avenues for further development of DFT+$U$-type methods