Embedding Environment Research Articles

Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir.

In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this Letter, we show a novel approach where the latest version of the adaptive resolution scheme (AdResS), with noninteracting tracers as particles' reservoir, is combined with a fluctuating hydrodynamics (FHD) solver. The resulting algorithm, supported by a solid mathematical model, allows for a physically consistent exchange of matter and energy between the particle domain and its fluctuating continuum reservoir. Numerical tests are performed to show the validity of the algorithm. Differently from previous algorithms of the same kind, the current approach allows for simulations where, in addition to density fluctuations, also thermal fluctuations can be accounted for, thus large complex molecular systems, as, for example, hydrated biological membranes in a thermal field, can now be efficiently treated.

Pushing the limits: Efficient wavefunction methods for excited states in complex systems using frozen-density embedding.

Frozen density embedding (FDE) is an embedding method for complex environments that is simple for users to set up. It reduces the computation time by dividing the total system into small subsystems and approximating the interaction by a functional of their densities. Its combination with wavefunction methods is, however, limited to small- or medium-sized molecules because of the steep scaling in computation time of these methods. To mitigate this limitation, we present a combination of the FDE approach with pair natural orbitals (PNOs) in the TURBOMOLE software package. It combines the uncoupled FDE (FDEu) approach for excitation energy calculations with efficient implementations of second-order correlation methods in the ricc2 and pnoccsd programs. The performance of this combination is tested for tetraazaperopyrene (TAPP) molecular crystals. It is shown that the PNO truncation error on environment-induced shifts is significantly smaller than the shifts themselves and, thus, that the local approximations of PNO-based wavefunction methods can without the loss of relevant digits be combined with the FDE method. Computational wall times are presented for two TAPP systems. The scaling of the wall times is compared to conventional supermolecular calculations and demonstrates large computational savings for the combination of FDE- and PNO-based methods. Additionally, the behavior of excitation energies with the system size is investigated. It is found that the excitation energies converge quickly with the size of the embedding environment for the TAPPs investigated in the current study.

StigLD: Stigmergic Coordination in Linked Systems

While current Semantic Web technologies are well-suited for data publication and integration, the design and deployment of dynamic, autonomous and long-lived multi-agent systems (MAS) on the Web is still in its infancy. Following the vision of hypermedia MAS and Linked Systems, we propose to use a value-passing fragment of Milner’s Calculus to formally specify the generic hypermedia-driven behaviour of Linked Data agents and the Web as their embedding environment. We are specifically interested in agent coordination mechanisms based on stigmergic principles. When considering transient marker-based stigmergy, we identify the necessity of generating server-side effects during the handling of safe and idempotent agent-initiated resource requests. This design choice is oftentimes contested with an imprecise interpretation of HTTP semantics, or with rejecting environments as first-class abstractions in MAS. Based on our observations, we present a domain model and a SPARQL function library facilitating the design and implementation of stigmergic coordination between Linked Data agents on the Web. We demonstrate the efficacy our of modelling approach in a Make-to-Order fulfilment scenario involving transient stigmergy and negative feedback as well as by solving a problem instance from the (time constrained) Trucks World domain as presented in the fifth International Planning Competition.

A Lightweight Face Recognition Model based on MobileFaceNet for Limited Computation Environment

The face recognition method based on deep convolutional neural network is difficult to deploy in the embedding devices. In this work, we optimize the MobileFaceNet face recognition network MobileFaceNet so as to deploy it in embedding environment. Firstly, we reduce the model parameters by reducing the number of layers in MobileFaceNet. Then, the h-ReLU6 activation function is used to replace PReLU in the original model. Finally, the effective channel attention module efficient channel attention is introduced to obtain the importance of each feature channel by learning. After the optimization, the MobileFaceNet parameters are compressed to 3.4 MB,which is smaller than the original model (4.9 MB), and the mAPs reach 98.52%, 97.54% and 91.33% on the test sets of LFW, VGGFace2 and the self-built database, respectively, and the recognition time is about 85 ms/photo. It shows that the proposed method achieves a good balance between the model complexity and model performance.

The Qualitative Thesis

The Qualitative Thesis says that if you leave open P, then you are sure of if P, then Q just in case you are sure of the corresponding material conditional. We argue the Qualitative Thesis provides compelling reasons to accept a thesis that we call Conditional Locality, which says, roughly, the interpretation of an indicative conditional depends, in part, on the conditional’s local embedding environment. In the first part of the paper, we present an argument—due to Ben Holguín—showing that, without Conditional Locality, the Qualitative Thesis is in tension with a margin for error principle on rational sureness. We show Conditional Locality reconciles the Qualitative Thesis with the margin for error principle. In the second part, we argue the full range of data supports what we call the Strong Qualitative Thesis. Without Conditional Locality, the Strong Qualitative Thesis has unacceptable consequences. But with Conditional Locality, it is tenable.

Fluorescence–Phosphorescence Manipulation and Atom Probe Observation of Fully Inorganic Silver Quantum Clusters: Imitating from and Behaving beyond Organic Hosts

AbstractSilver quantum clusters (Ag QCs) have attracted great attention due to their unique electronic structure and molecule‐like photoluminescence (PL). Applications in catalysis, biology, and optoelectronics have already been realized, however, the understanding of PL mechanism and direct observation of Ag QCs still remain challenging. Here, fully inorganic Ag QCs well stabilized in the borate glass with simultaneous excellent chemical stability, tunable PL emission, and high quantum yield are prepared. And the PL properties of Ag QCs respond drastically to changes of the embedding environment, displaying pronounced fluorescence to phosphorescence (F‐P) switching. Combining the structural and spectral analysis, it is found that the F‐P switching is triggered by the Ag QCs aggregation and [BO3]→[BO4]− conversion of the borate network. Using atom probe tomography enables to quantitatively characterize the evolution of Ag QCs at an atomic level, which reveals that Ag QCs consisting of less than 20 atoms are responsible for the observed PL.

Active Basal Plane Catalytic Activity via Interfacial Engineering for a Finely Tunable Conducting Polymer/MoS2 Hydrogen Evolution Reaction Multilayer Structure

The fixation of the catalyst interface is an important consideration for the design of practical applications. However, the electronic structure of MoS2 is sensitive to its embedding environment, and the catalytic performance of MoS2 catalysts may be altered significantly by the type of binding agents and interfacial structure. Interfacial engineering is an effective method for designing efficient catalysts, arising from the close contact between different components, which facilitates charge transfer and strong electronic interactions. Here, we have developed a layer-by-layer (LbL) strategy for the preparation of interfacial MoS2-based catalyst structures with two types of conducting polymers on various substrates. We demonstrate how the assembled partners in the LbL structure can significantly impact the electronic structures in MoS2. As the number of bilayers grows, using polypyrrole as a binder remarkably increases the catalytic efficacy as compared to using polyaniline. On the one hand, the ratio of S22- (or S2-), which is related to the remaining active hydrogen evolution reaction (HER) species, is further increased. On the other hand, density functional theory calculations indicate that the interfacial charge transport from the conducting polymers to MoS2 may boost the HER activity of the interfacial structure of the conducting polymer/MoS2 by decreasing the adsorption free energy of the intermediate H* at the S sites in the basal plane of MoS2. The optimized catalytic efficacy of the (conducting polymer/MoS2)n assembly peaks is obtained with 16 assembly cycles. In preparing interfacial catalytic structures, the LbL-based strategy exhibits several key advantages, including the flexibility of choosing assembly partners, the ability to fine-tune the structures with precision at the nanometer scale, and planar homogeneity at the centimeter scale. We expect that this LbL-based catalyst immobilization strategy will contribute to the fundamental understanding of the scalability and control of highly efficient electrocatalysts at the interface for practical applications.

Graphene and Carbon Nanotubes for Electronics Nanopackaging

In recent years, the aggressive downscaling of electronic components has led to highly dense and power-hungry devices. With Moores law expected to soon reach its physical limit, there is a pressing need to significantly improve the efficiency and performance not only of nanodevices, but also of the embedding environment in which such nanodevices are integrated. In this context, key for improving the performance and for reducing both system cost and size is electronics packaging. However, electronics packaging at the nanoscale (i.e., nanopackaging) is currently facing several technological challenges, as in such scale conventional materials present intrinsic physical limitations. To address this, it becomes necessary to replace these latter with novel alternatives, such as low-dimensional carbon-based nanomaterials. Carbon nanotubes (CNTs) and graphene (materials with 1D and 2D dimensionality, respectively) have the potential to be successfully integrated into traditional silicon-based electronics as well as with beyond-silicon electronics, and their unique electrical, thermal, mechanical, and optical properties could be key enablers for significant performance improvements. In this short review we describe why these nanomaterials are very promising for electronics nanopackaging, and we outline the key application areas, mainly interconnects, thermal management, and flexible devices.

A Scalable Interfacial Engineering Strategy for a Finely Tunable, Homogeneous MoS2/rGO‐Based HER Catalytic Structure

AbstractThe electronic structures and catalytic efficacies of molybdenum disulfide (MoS2)‐based catalysts are sensitive to embedding environment. In order to develop a finely tunable strategy, a “layer‐by‐layer and Nafion capping” strategy for the scalable preparation of interfacial (MoS2)‐based catalytic structures is developed. The study shows that the assembly partner influences the electronic structures of the Zn&N co‐doped (MoS2) (Zn‐N‐(MoS2)) catalysts. Poly(allylamine hydrochloride) (PAH) decreases the catalytic efficacy, whereas when PAH‐rGO (rGO [reduced graphene oxide]) is the assembly partner, effective interfacial catalysts are prepared. The superior catalytic efficacy of (PAH‐rGO/Zn‐N‐(MoS2))n can be attributed to the fact that rGO effectively activates the basal plane S2− as the active sites. The catalytic efficacy of the multilayers at 16 assembly cycles due to a balance between the number of active sites and low resistance. After capping with Nafion layer, the interfacial catalysts exhibit high stability. Compared with the widely used drop‐casting methods, the layer‐by‐layer strategy possesses unique benefits, including fine‐tune the structures, free choice of the partner, and planar homogeneity. It is expected that this layer‐by‐layer catalyst immobilization strategy will benefit fundamental understandings regarding the finely controlled scalable interfacial immobilization of catalysts with superior efficacy, and assist in promoting the practical utilization of various catalysts.

Special Issue on Advanced Material Driven Design of Machine Tools

Special Issue on Advanced Material Driven Design of Machine Tools

Towards a transferable design of solid-state embedding models on the example of a rutile TiO2 (110) surface.

In this work, we present general and robust transferable principles for the construction of quantum-mechanically treated clusters in a solid-state embedding (SSE) approach, beyond the still prevalent trial and error approach. Thereby, we probe the quality of different cluster shapes on the accuracy of chemisorption energies of small molecules and small polaron formation energies at the rutile TiO2 (110) surface as test cases. Our analyses show that at least the binding energies and electronic structures in the form of the density of states tend to be quite robust already for small, nonoptimal cluster shapes. In contrast to that, the description of polaron formation can be dramatically influenced by the employed cluster geometry possibly leading to an erroneous energetic ordering or even to a wrong prediction of the polaronic states themselves. Our findings show that this is mainly caused by an inaccurate description of the Hartree potential at boundary and surrounding atoms, which are insufficiently compensated by the embedding environment. This stresses the importance of the cluster size and shape for the accuracy of general-purpose SSE models that do not have to be refitted for each new chemical question. Based on these observations, we derive some general design criteria for solid state embedded clusters.

Functional Extrapolations to Tame Unbound Anions in Density-Functional Theory Calculations.

Standard flavors of density-functional theory (DFT) calculations are known to fail in describing anions, due to large self-interaction errors. The problem may be circumvented using localized basis sets of reduced size, leaving no variational flexibility for the extra electron to delocalize. Alternatively, a recent approach exploiting DFT evaluations of total energies on electronic densities optimized at the Hartree-Fock (HF) level has been reported, showing that the self-interaction-free HF densities are able to lead to an improved description of the additional electron, returning affinities in close agreement with the experiments. Nonetheless, such an approach can fail when the HF densities are too inaccurate. Here, an alternative approach is presented, in which an embedding environment is used to stabilize the anion in a bound configuration. Similar to the HF case, when computing total energies at the DFT level on these corrected densities, electron affinities in very good agreement with experiments can be recovered. The effect of the environment can be evaluated and removed by an extrapolation of the results to the limit of vanishing embedding. Apart from the definition of the domain of the embedding potential, the approach is free from parameters and it can be easily applied to DFT calculations with delocalized basis sets, e.g., plane waves, for which alternative approaches are either not viable or more computationally demanding. The proposed extrapolation strategy can be thus applied also to extended systems, as often studied in condensed-matter physics and materials science, and we illustrate how the embedding environment can be exploited to determine the energy of an adsorbing anion, here a chloride ion on a metal surface, whose charge configuration would be incorrectly predicted by standard density functionals.

Investigation of Water Loss from Pipes Located in Various Relief Features of Iaşi County

Abstract Water losses are present in all water supply system pipes. Their parameters and value vary depending on the constructional and functional features of the pipes (diameter, material, pressure, embedding environment, location, position etc.). The phenomenon is present in all water supply systems networks in Romania as well as globally. The water supply pipes within the regional water supply system are located in areas with diversified relief, from plateaus and hills to plains. The studies and researches were carried out in the geographical placement area of the Timişeşti-Iaşi pipeline. The geographic area studied is enclosed in Siret and Prut hydrographic basins. The paper aims to establish a correlation between the detection methods of water leaks from pipes and the areal relief features in Iaşi County. At the same time, it is highlighted the impact of the variation of the geographical relief characteristics on the water loss management on different type of pipes.

Social behaviour as an emergent property of embodied curiosity: a robotics perspective.

Social interaction is an extremely complex yet vital component in daily life. We present a bottom-up approach for the emergence of social behaviours from the interaction of the curiosity drive, i.e. the intrinsic motivation to learn as much as possible, and the embedding environment of an agent. Implementing artificial curiosity algorithms in robots that explore human-like environments results in the emergence of a hierarchical structure of learning and behaviour. This structure resembles the sequential emergence of behavioural patterns in human babies, culminating in social behaviours, such as face detection, tracking and attention-grabbing facial expressions. These results suggest that an embodied curiosity drive may be the progenitor of many social behaviours if satiated by a social environment. This article is part of the theme issue 'From social brains to social robots: applying neurocognitive insights to human-robot interaction'.

Solvent-Aware Interfaces in Continuum Solvation.

Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key ingredient of continuum models is the choice of the solute cavity, i.e., the definition of the sharp or smooth boundary between the regions of space occupied by the quantum-mechanical (QM) system and the continuum embedding environment. The cavity, which should really reflect the region of space accessible to the degrees of freedom of the environmental components (the solvent), is usually defined by an exclusion approach in terms of the degrees of freedom of the system (the solute), typically, the atomic position of the QM system or its electronic density. Although most of the solute-based approaches developed lead to models with comparable and high accuracy when applied to small organic molecules, they can introduce significant artifacts when complex systems are considered. As an example, condensed-matter simulations often deal with supports that present open structures, i.e., low-density materials that have regions of space in which a continuum environment could penetrate, while a real solvent would not be able to. Similarly, unphysical pockets of continuum solvent may appear in systems featuring multiple molecular components, e.g., when dealing with hybrid QM/continuum approaches to solvation that involve introducing explicit solvent molecules around the solvated system. Here, we introduce a solvent-aware approach to eliminate the unphysical effects where regions of space smaller than the size of a single solvent molecule could still be filled with a continuum environment. We do this by defining a smoothly varying solute cavity that overcomes several of the limitations of straightforward solute-based definitions. This new approach applies to any smooth local definition of the continuum interface, it being based on the electronic density or the atomic positions of the QM system. It produces boundaries that are continuously differentiable with respect to the QM degrees of freedom, leading to accurate forces and/or Kohn-Sham potentials. The additional parameters involved in the solvent-aware interfaces can be set according to geometrical principles or can be converged to improve accuracy in complex multicomponent systems. Benchmarks on semiconductor substrates and on explicit water substrates confirm the flexibility and the accuracy of the approach and provide a general set of parameters for condensed-matter systems featuring open structures and/or explicit liquid components.

Ring-opening attachment as an explanation for the long lifetime of the octafluorooxolane anion.

Octafluorooxalane, C4F8O, has recently attracted attention as a possible replacement of SF6 in high voltage insulation, and its reactivity with respect to free-electron attachment was investigated by mass spectrometry. The most intense signal peaks at 0.9 eV and corresponds to the parent anion, C4F8O-; fragments stemming from complex breakup reactions are detected starting above ∼1.6 eV. Since parent anions in free-electron attachment are normally associated with threshold attachment or an embedding environment allowing excess energy deposition, this observation is highly unusual. Based on density functional calculations, it was nevertheless interpreted as attachment followed by intermolecular-vibrational-relaxation. Here, electron-attachment to octafluorooxalane is studied computationally. First, the electron affinity (EA) is characterized using density functionals and ab initio methods. Moreover, the negative vertical EA is estimated by extrapolating electron binding energies computed in the vicinity of C4F8O- to the geometry of neutral octafluorooxalane. Then, alternative explanations for the 0.9 eV peak are considered. Specifically, a ring-opening reaction that yields a distonic isomer of C4F8O- is identified. Our analysis reveals that the chain isomer possesses many conformers, all of which are considerably more stable than the ring isomer, and that the time scale for the unimolecular ring opening reaction is significantly faster than 1 μs. Thus, at the experimental energy, the ring isomer of C4F8O- is predicted to convert practically completely into the chain isomer, and we argue that the long lifetime and the peak position are effectively determined by the properties of the ring-opening transition state.

Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties.

The UV-vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV-vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua-p-Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV-vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical-computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc.

Optimal Coefficient Quantization in Optimal-NTF <inline-formula> <tex-math notation="LaTeX">$\Delta \!\Sigma $ </tex-math> </inline-formula> Modulators

Strategies for the adaptation of $\Delta \!\Sigma $ modulators ( $\Delta \!\Sigma $ Ms) to the embedding environment with respect to the ability of the latter to remove quantization noise have recently been introduced. They rely on formal optimization techniques to deliver finely tuned values for the coefficients of the $\Delta \!\Sigma \text{M}$ internal filters. However, in digital $\Delta \!\Sigma $ Ms, coefficients will necessarily be quantized to short wordlengths, the shorter the better, cost-wise. Unfortunately, this can severely hinder optimality. In this brief, a strategy is proposed to re-use the very optimization framework to minimize the effects of coefficient quantization. The technique is discussed by a practical design example based on a $\Delta \!\Sigma \text{M}$ for a wideband fractional- ${N}$ phase locked loop (PLL).

Improved Electrostatic Embedding for Fragment-Based Chemical Shift Calculations in Molecular Crystals.

Fragment-based methods predict nuclear magnetic resonance (NMR) chemical shielding tensors in molecular crystals with high accuracy and computational efficiency. Such methods typically employ electrostatic embedding to mimic the crystalline environment, and the quality of the results can be sensitive to the embedding treatment. To improve the quality of this embedding environment for fragment-based molecular crystal property calculations, we borrow ideas from the embedded ion method to incorporate self-consistently polarized Madelung field effects. The self-consistent reproduction of the Madelung potential (SCRMP) model developed here constructs an array of point charges that incorporates self-consistent lattice polarization and which reproduces the Madelung potential at all atomic sites involved in the quantum mechanical region of the system. The performance of fragment- and cluster-based 1H, 13C, 14N, and 17O chemical shift predictions using SCRMP and density functionals like PBE and PBE0 are assessed. The improved embedding model results in substantial improvements in the predicted 17O chemical shifts and modest improvements in the 15N ones. Finally, the performance of the model is demonstrated by examining the assignment of the two oxygen chemical shifts in the challenging γ-polymorph of glycine. Overall, the SCRMP-embedded NMR chemical shift predictions are on par with or more accurate than those obtained with the widely used gauge-including projector augmented wave (GIPAW) model.

Stabilization of activated fragments by shell‐wise construction of an embedding environment

An activated fragment which is structurally unstable when considered isolated can be stabilized through binding to a suitable molecular environment; for instance, to a transition-metal fragment. The metal fragment may be designed in a shell-wise build-up of a surrounding molecular environment. However, adding more and more atoms in a consecutive fashion soon leads to a combinatorial explosion of structures, which is unfeasible to handle without automation. Here, we present a fully automated and parallelized framework that constructs such an embedding environment atom-wise. Molecular realizations of such an environment are constructed based on simple heuristic rules intended to screen a sufficiently large portion of the possible compound space and are then subsequently optimized by electronic structure methods. (Constrained-optimized) structures are then evaluated with respect to a scoring function, for which we choose here the concept of gradient-driven molecule construction. This concept searches for structure modifications that reduce the forces on all atoms. We develop and analyze our approach at the example of CO2 activation by reproducing a known compound and mapping out possible alternative structures and their effect on the stabilization of a (bent) CO2 ligand. For all generated structures, the nuclear gradient on the activated fragment and its coordination energy are evaluated to steer the design process. © 2017 Wiley Periodicals, Inc.