O(N)Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

We propose a new strategy to solve the Tkatchenko-Scheffler Many-Body Dispersion (MBD) model’s equations. Our approach overcomes the original O(N**3) computational complexity that limits its applicability to large molecular systems within thecontext of O(N) Density Functional Theory (DFT). First, in order to generate the required frequency-dependent screenedpolarizabilities, we introduce an efficient solution to the Dyson-like self-consistent screening equations. The scheme reducesthe number of variables and, coupled to a DIIS extrapolation, exhibits linear-scaling performances. Second, we apply astochastic Lanczos trace estimator resolution to the equations evaluating the many-body interaction energy of coupled quantumharmonic oscillators. While scaling linearly, it also enables communication-free pleasingly-parallel implementations. As the resulting O(N) stochastic massively parallel MBD approach is found to exhibit minimal memory requirements, it opens up the possibility of computing accurate many-body van der Waals interactions of millions-atoms’ complex materials and solvated biosystems with computational times in the range of minutes.

O(N)Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

We propose a new strategy to solve the Tkatchenko-Scheffler Many-Body Dispersion (MBD) model’s equations. Our approach overcomes the original O(N**3) computational complexity that limits its applicability to large molecular systems within thecontext of O(N) Density Functional Theory (DFT). First, in order to generate the required frequency-dependent screenedpolarizabilities, we introduce an efficient solution to the Dyson-like self-consistent screening equations. The scheme reducesthe number of variables and, coupled to a DIIS extrapolation, exhibits linear-scaling performances. Second, we apply astochastic Lanczos trace estimator resolution to the equations evaluating the many-body interaction energy of coupled quantumharmonic oscillators. While scaling linearly, it also enables communication-free pleasingly-parallel implementations. As the resulting O(N) stochastic massively parallel MBD approach is found to exhibit minimal memory requirements, it opens up the possibility of computing accurate many-body van der Waals interactions of millions-atoms’ complex materials and solvated biosystems with computational times in the range of minutes.

The Role of Graphene Monolayers in Enhancing the Yield of Bacteriorhodopsin Photostates for Optical Memory Applications

Bacteriorhodopsin (bR) is a photoactive protein that has gained increasing importance as a tool for optical memory storage due to its remarkable photochemical and thermal stability. The two stable photostates (bR and Q) obtained during the bR photocycle are appropriate to designate the binary bit 0 and 1, respectively. Such devices, however, have limited success due to a low quantum yield of the Q state. Many studies have used genetic and chemical modification as optimization strategies to increase the yield of the Q state. Nonetheless, this compromises the overall photochemical stability of bR. This paper introduces a unique way of stabilizing the conformations of bacteriorhodopsin and, thereby, the bR and Q photostates through adsorption onto graphene. All-atom molecular dynamics (MD) simulations with NAMD and CHARMM force fields have been used here to understand the interactive events at the interface of the retinal chromophore within bR and a single-layer graphene sheet. Based on the stable RMSD (~4.5 Å), secondary structure, interactive van der Waals energies (~3000 kcal/mol) and electrostatic energies (~2000 kcal/mol), it is found that the adsorption of bR onto graphene can stabilize its photochemical behavior. Furthermore, the optimal adsorption distance for bR is found to be ~4.25 Å from the surface of graphene, which is regulated by a number of interfacial water molecules and their hydrogen bonds. The conformations of the key amino acids around the retinal chromophore that are responsible for the proton transport are also found to be dependent on the adsorption of bR onto graphene. The quantity and lifetime of the salt bridges also indicate that more salt bridges were formed in the absence of graphene, whereas more were broken in the presence of it due to conformational changes. Finally, the analysis on the retinal dihedrals (C11 = C12-C13 = C14, C12-C13 = C14-C15, C13 = C14-C15 = NZ and C14-C15 = NZ-CE) show that bacteriorhodopsin in the presence of graphene exhibits increased stability and larger dihedral energy values.

Macroscale adhesion of gecko setae reflects nanoscale differences in subsurface composition

Surface energies are commonly used to determine the adhesion forces between materials. However, the component of surface energy derived from long-range forces, such as van der Waals forces, depends on the material's structure below the outermost atomic layers. Previous theoretical results and indirect experimental evidence suggest that the van der Waals energies of subsurface layers will influence interfacial adhesion forces. We discovered that nanometre-scale differences in the oxide layer thickness of silicon wafers result in significant macroscale differences in the adhesion of isolated gecko setal arrays. Si/SiO 2 bilayer materials exhibited stronger adhesion when the SiO 2 layer is thin (approx. 2 nm). To further explore how layered materials influence adhesion, we functionalized similar substrates with an octadecyltrichlorosilane monolayer and again identified a significant influence of the SiO 2 layer thickness on adhesion. Our theoretical calculations describe how variation in the SiO 2 layer thickness produces differences in the van der Waals interaction potential, and these differences are reflected in the adhesion mechanics. Setal arrays used as tribological probes provide the first empirical evidence that the ‘subsurface energy’ of inhomogeneous materials influences the macroscopic surface forces.

Forces that Drive the Self-assembly of Metallic Dots on Semiconductor Substrates

ABSTRACTThe scaling and ordering of metallic nanoclusters on semiconductor substrates has been explored computationally. Numerical techniques were implemented to calculate the total electrostatic and van der Waals energies for systems containing multiple disks. Observations show that interactions in charge clouds beneath the metallic disks led to an electrostatic repulsive force. Attraction was observed due to the van der Waals energy. An energy barrier exists for disk coalescence. This work suggests the potential of double layer charges in the development of large-scale nanodot systems that require precise control over both dot location and size.