Symplectic quaternion scheme for biophysical molecular dynamics

Massively parallel biophysical molecular dynamics simulations, coupled with efficient methods, promise to open biologically significant time scales for study. In order to promote efficient fine-grained parallel algorithms with low communication overhead, the fast degrees of freedom in these complex systems can be divided into sets of rigid bodies. Here, a novel Hamiltonian form of a minimal, nonsingular representation of rigid body rotations, the unit quaternion, is derived, and a corresponding reversible, symplectic integrator is presented. The novel technique performs very well on both model and biophysical problems in accord with a formal theoretical analysis given within, which gives an explicit condition for an integrator to possess a conserved quantity, an explicit expression for the conserved quantity of a symplectic integrator, the latter following and in accord with Calvo and Sanz-Sarna, Numerical Hamiltonian Problems (1994), and extension of the explicit expression to general systems with a flat phase space

Anisotropy of Mechanical Properties of Pinctada margaritifera Mollusk Shell

The research was co-financed by the European Union from the resources of the European Social Fund (Project No.WND-POWR.03.02.00-00-I043/16), the DAAD program. A.C. acknowledges project CGL2017-85118-P of the Spanish Ministerio de Ciencia e Innovaciónfor funding.The mechanical properties such as compressive strength and nanohardness were investigated for Pinctada margaritifera mollusk shells. The compressive strength was evaluated through a uniaxial static compression test performed along the load directions parallel and perpendicular to the shell axis, respectively, while the hardness and Young modulus were measured using nanoindentation. In order to observe the crack propagation, for the first time for such material, the in-situ X-ray microscopy (nano-XCT) imaging (together with 3D reconstruction based on the acquired images) during the indentation tests was performed. The results were compared with these obtained during the micro-indentation test done with the help of conventional Vickers indenter and subsequent scanning electron microscopy observations. The results revealed that the cracks formed during the indentation start to propagate in the calcite prism until they reach a ductile organic matrix where most of them are stopped. The obtained results confirm a strong anisotropy of both crack propagation and the mechanical strength caused by the formation of the prismatic structure in the outer layer of P. margaritifera shell.The research was co-financed by the European Union from resources of the European Social Fund (Project No.WND-POWR.03.02.00-00-I043/16)

Evolution of epitaxial semiconductor nanodots and nanowires from supersaturated wetting layers

In this tutorial we review recent progress in the design and growth of epitaxial semiconductor nanostructures in lattice-mismatched material systems. We focus on the Ge on Si model system after pointing out the similarities to III–V and other growth systems qualitatively as well as quantitatively. During material deposition, the first layers of the epitaxial film wet the surface before the formation of strain-driven three-dimensional nanostructures. In particular, we stress that the supersaturation of the wetting layer (WL), whose relevance is often neglected, plays a key role in determining the nucleation and growth of nanodots (NDs), nanodot-molecules and nanowires (NWs). At elevated growth temperatures the Ge reservoir in the planar, supersaturated WL is abruptly consumed and generates NDs with highly homogeneous sizes – a process mainly driven by elastic energy minimization. Furthermore, the careful control of the supersaturated Ge layer allows us to obtain perfectly site-controlled, ordered NDs or ND-molecules on pit-patterned substrates for a broad range of pit-periods. At low growth temperatures subtle interplays between surface energies of dominant crystal facets in the system drive the material transfer from the supersaturated WL into the elongating NWs growing horizontally, dislocation- and catalyst-free on the substrate surface. Due to the similarities in the formation of nanostructures in different epitaxial semiconductor systems we expect that the observation of the novel growth phenomena described in this Tutorial Review for Ge/Si should be relevant for other lattice-mismatched heterostructure systems, too

Optical properties of individual site-controlled Ge quantum dots

We report photoluminescence (PL) experiments on individual SiGe quantum dots (QDs) that were epitaxially grown in a site-controlled fashion on pre-patterned Si(001) substrates. We demonstrate that the PL line-widths of single QDs decrease with excitation power to about 16 meV, a value that is much narrower than any of the previously reported PL signals in the SiGe/Si heterosystem. At low temperatures, the PL-intensity becomes limited by a 25 meV high potential-barrier between the QDs and the surrounding Ge wetting layer (WL). This barrier impedes QD filling from the WL which collects and traps most of the optically excited holes in this type-II heterosystem. This work was supported by the Austrian Science Funds (FWF) via Schrödinger Scholarship J3328-N19 and the Project Nos. F2502-N17 and F2512-N17 of SFB025: IRON. M.G. and O.G.S. acknowledge support from the Center for Advancing Electronics Dresden, CfAED. T.T. was supported by the ICR-KU International Short-term Exchange Program for Young Researchers. The authors thank T. Fromherz and F. Hackl for helpful discussions

First-principles molecular-dynamics simulations of a hydrous silica melt: Structural properties and hydrogen diffusion mechanism

We use {\it ab initio} molecular dynamics simulations to study a sample of liquid silica containing 3.84 wt.% H$_2$O.We find that, for temperatures of 3000 K and 3500 K,water is almost exclusively dissolved as hydroxyl groups, the silica network is partially broken and static and dynamical properties of the silica network change considerably upon the addition of water.Water molecules or free O-H groups occur only at the highest temperature but are not stable and disintegrate rapidly.Structural properties of this system are compared to those of pure silica and sodium tetrasilicate melts at equivalent temperatures. These comparisons confirm the picture of a partially broken tetrahedral network in the hydrous liquid and suggest that the structure of the matrix is as much changed by the addition of water than it is by the addition of the same amount (in mole %) of sodium oxide. On larger length scales, correlations are qualitatively similar but seem to be more pronounced in the hydrous silica liquid. Finally, we study the diffusion mechanisms of the hydrogen atoms in the melt. It turns out that HOSi$_2$ triclusters and SiO dangling bonds play a decisive role as intermediate states for the hydrogen diffusion.Comment: 25 pages, 18 figures. submitte

Photoluminescence investigation of strictly ordered Ge dots grown on pit-patterned Si substrates

We investigate the optical properties of ordered Ge quantum dots (QDs) by means of micro-photoluminescence spectroscopy (PL). These were grown on pit-patterned Si(001) substrates with a wide range of pit-periods and thus inter QD-distances (425–3400 nm). By exploiting almost arbitrary inter-QD distances achievable in this way we are able to choose the number of QDs that contribute to the PL emission in a range between 70 and less than three QDs. This well-defined system allows us to clarify, by PL-investigation, several points which are important for the understanding of the formation and optical properties of ordered QDs. We directly trace and quantify the amount of Ge transferred from the surrounding wetting layer (WL) to the QDs in the pits. Moreover, by exploiting different pit-shapes, we reveal the role of strain-induced activation energy barriers that have to be overcome for charge carriers generated outside the dots. These need to diffuse between the energy minimum of the WL in and between the pits, and the one in the QDs. In addition, we demonstrate that the WL in the pits is already severely intermixed with Si before upright QDs nucleate, which further enhances intermixing of ordered QDs as compared to QDs grown on planar substrates. Furthermore, we quantitatively determine the amount of Ge transferred by surface diffusion through the border region between planar and patterned substrate. This is important for the growth of ordered islands on patterned fields of finite size. We highlight that the Ge WL-facets in the pits act as PL emission centres, similar to upright QDs

Molecular dynamics in shape space and femtosecond vibrational spectroscopy of metal clusters

We introduce a method of molecular dynamics in shape space aimed at metal clusters. The ionic degrees of freedom are described via a dynamically deformable jellium with inertia parameters derived from an incompressible, irrotational flow. The shell correction method is used to calculate the electronic potential energy surface underlying the dynamics. Our finite temperature simulations of Ag_14 and its ions, following the negative to neutral to positive scheme, demonstrate the potential of pump and probe ultrashort laser pulses as a spectroscopy of cluster shape vibrations.Comment: Latex/Revtex, 4 pages with 3 Postscript figure

Controlling the energy flow in nonlinear lattices: a model for a thermal rectifier

We address the problem of heat conduction in 1-D nonlinear chains; we show that, acting on the parameter which controls the strength of the on site potential inside a segment of the chain, we induce a transition from conducting to insulating behavior in the whole system. Quite remarkably, the same transition can be observed by increasing the temperatures of the thermal baths at both ends of the chain by the same amount. The control of heat conduction by nonlinearity opens the possibility to propose new devices such as a thermal rectifier.Comment: 4 pages with figures included. Phys. Rev. Lett., to be published (Ref. [10] corrected