Hydrogenated Nanocrystalline Silicon Thin Films Prepared by Hot-Wire Method with Varied Process Pressure

Hydrogenated nanocrystalline silicon films were prepared by hot-wire method at low substrate temperature (200∘C) without hydrogen dilution of silane (SiH4). A variety of techniques, including Raman spectroscopy, low angle X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, atomic force microscopy (AFM), and UV-visible (UV-Vis) spectroscopy, were used to characterize these films for structural and optical properties. Films are grown at reasonably high deposition rates (>15 Å/s), which are very much appreciated for the fabrication of cost effective devices. Different crystalline fractions (from 2.5% to 63%) and crystallite size (3.6–6.0 nm) can be achieved by controlling the process pressure. It is observed that with increase in process pressure, the hydrogen bonding in the films shifts from Si–H to Si–H2 and (Si–H2)n complexes. The band gaps of the films are found in the range 1.83–2.11 eV, whereas the hydrogen content remains <9 at.% over the entire range of process pressure studied. The ease of depositing films with tunable band gap is useful for fabrication of tandem solar cells. A correlation between structural and optical properties has been found and discussed in detail

Orbital overlap effects in electron transfer reactions across a metal nanowire/electrolyte solution interface

In this paper, we report on calculations of the orbital overlap between Fe(III) and Cr(III) aquacomplexes and different electrode surfaces: Cu(111), Ag (111), Au(111), Pt(111), and corresponding monatomic wires. The electronic structure of the monocrystalline surfaces and nanowires are described in terms of the electronic spillover and density of electronic states at the Fermi level obtained from periodic density functional theory (DFT) calculations. The transmission coefficients (κ) characterizing the first stage of outer-sphere electron transfer for the reduction of aquacomplexes are calculated on the basis of Landau–Zener theory as a function of electrode–reactant separation; the electronic transmission coefficients for the [Cr(H2O)6]3+/2+ redox couple were found to be smaller than those for [Fe(H2O)6]3+/2+. Two different intervals can be clearly distinguished for Cu, Au and Pt: “a catalytic region”, where κ(wire) > κ(Me slab) and “an inhibition region”, where κ(wire) < κ(Me slab). A similar behavior exhibits the coupling constant estimated for a hydrogen atom adsorbed at the Au(111) surface and the Au monatomic wire. These effects originate from some specific features of electronic density profile for metal nanowires: at short distances the electronic density of nanowires is higher compared with the (111) metal surfaces, while at larger separations it decreases more sharply.Fil: Nazmutdinov, Renat R.. Kazan National Research Technological University; RusiaFil: Berezin, Alexander S.. Kazan National Research Technological University; RusiaFil: Soldano, Germán. Universitat Ulm; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Schmickler, Wolfgang. Universitat Ulm; Alemani

A statistical learning strategy for closed-loop control of fluid flows

This work discusses a closed-loop control strategy for complex systems utilizing scarce and streaming data. A discrete embedding space is first built using hash functions applied to the sensor measurements from which a Markov process model is derived, approximating the complex system’s dynamics. A control strategy is then learned using reinforcement learning once rewards relevant with respect to the control objective are identified. This method is designed for experimental configurations, requiring no computations nor prior knowledge of the system, and enjoys intrinsic robustness. It is illustrated on two systems: the control of the transitions of a Lorenz’63 dynamical system, and the control of the drag of a cylinder flow. The method is shown to perform well

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.Comment: 19 page

Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C

Cells utilise specialized polymerases from the Primase-Polymerase (Prim-Pol) superfamily to maintain genome stability. Prim-Pol’s function in genome maintenance pathways including replication, repair and damage tolerance. Mycobacteria contain multiple Prim-Pols required for lesion repair, including Prim-PolC that performs short gap repair synthesis during excision repair. To understand the molecular basis of Prim-PolC’s gap recognition and synthesis activities, we elucidated crystal structures of pre- and post-catalytic complexes bound to gapped DNA substrates. These intermediates explain its binding preference for short gaps and reveal a distinctive modus operandi called Synthesis-dependent Template Displacement (STD). This mechanism enables Prim-PolC to couple primer extension with template base dislocation, ensuring that the unpaired templating bases in the gap are ushered into the active site in an ordered manner. Insights provided by these structures establishes the molecular basis of Prim-PolC’s gap recognition and extension activities, while also illuminating the mechanisms of primer extension utilised by closely related Prim-Pols

An approach to locating delayed activities in software processes

Activity is now playing a vital role in software processes. To ensure the high-level efficiency of software processes, a key point is to locate those activities that own bigger resource occupation probabilities with respect to average execution time, called delayed activities, and then improve them. To this end, we firstly propose an approach to locating delayed activities in software processes. Furthermore, we present a case study, which exhibits the high-level efficiency of the approach, to concretely illustrate this new solution. Some beneficial analysis and reasonable modification are developed in the end

Approximate policy iteration: A survey and some new methods

We consider the classical policy iteration method of dynamic programming (DP), where approximations and simulation are used to deal with the curse of dimensionality. We survey a number of issues: convergence and rate of convergence of approximate policy evaluation methods, singularity and susceptibility to simulation noise of policy evaluation, exploration issues, constrained and enhanced policy iteration, policy oscillation and chattering, and optimistic and distributed policy iteration. Our discussion of policy evaluation is couched in general terms and aims to unify the available methods in the light of recent research developments and to compare the two main policy evaluation approaches: projected equations and temporal differences (TD), and aggregation. In the context of these approaches, we survey two different types of simulation-based algorithms: matrix inversion methods, such as least-squares temporal difference (LSTD), and iterative methods, such as least-squares policy evaluation (LSPE) and TD (λ), and their scaled variants. We discuss a recent method, based on regression and regularization, which rectifies the unreliability of LSTD for nearly singular projected Bellman equations. An iterative version of this method belongs to the LSPE class of methods and provides the connecting link between LSTD and LSPE. Our discussion of policy improvement focuses on the role of policy oscillation and its effect on performance guarantees. We illustrate that policy evaluation when done by the projected equation/TD approach may lead to policy oscillation, but when done by aggregation it does not. This implies better error bounds and more regular performance for aggregation, at the expense of some loss of generality in cost function representation capability. Hard aggregation provides the connecting link between projected equation/TD-based and aggregation-based policy evaluation, and is characterized by favorable error bounds.National Science Foundation (U.S.) (No.ECCS-0801549)Los Alamos National Laboratory. Information Science and Technology InstituteUnited States. Air Force (No.FA9550-10-1-0412

Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme

Biomolecular function is realized by recognition, and increasing evidence shows that recognition is determined not only by structure but also by flexibility and dynamics. We explored a biomolecular recognition process that involves a major conformational change – protein folding. In particular, we explore the binding-induced folding of IA3, an intrinsically disordered protein that blocks the active site cleft of the yeast aspartic proteinase saccharopepsin (YPrA) by folding its own N-terminal residues into an amphipathic alpha helix. We developed a multi-scaled approach that explores the underlying mechanism by combining structure-based molecular dynamics simulations at the residue level with a stochastic path method at the atomic level. Both the free energy profile and the associated kinetic paths reveal a common scheme whereby IA3 binds to its target enzyme prior to folding itself into a helix. This theoretical result is consistent with recent time-resolved experiments. Furthermore, exploration of the detailed trajectories reveals the important roles of non-native interactions in the initial binding that occurs prior to IA3 folding. In contrast to the common view that non-native interactions contribute only to the roughness of landscapes and impede binding, the non-native interactions here facilitate binding by reducing significantly the entropic search space in the landscape. The information gained from multi-scaled simulations of the folding of this intrinsically disordered protein in the presence of its binding target may prove useful in the design of novel inhibitors of aspartic proteinases