Full rate constant matrix contraction method for obtaining branching ratio of unimolecular decomposition

The branching ratio of unimolecular decomposition can be evaluated by solving the rate equations. Recent advances in automated reaction path search methods have enabled efficient construction of the rate equations based on quantum chemical calculations. However, it is still difficult to solve the rate equations composed of hundreds or more elementary steps. This problem is especially serious when elementary steps that occur in highly different timescales coexist. In this article, we introduce an efficient approach to obtain the branching ratio from a given set of rate equations. It has been derived from a recently proposed rate constant matrix contraction (RCMC) method, and termed full‐RCMC (f‐RCMC). The f‐RCMC gives the branching ratio without solving the rate equations. Its performance was tested numerically for unimolecular decomposition of C₃H₅ and C₄H₅. Branching ratios obtained by the f‐RCMC precisely reproduced the values obtained by numerically solving the rate equations. It took about 95 h to solve the rate equations of C₄H₅ consisting of 234 elementary steps. In contrast, the f‐RCMC gave the branching ratio in less than 1 s. The f‐RCMC would thus be an efficient alternative of the conventional kinetic simulation approach. © 2016 Wiley Periodicals, Inc.     

GPU‐accelerated direct numerical simulations of decaying compressible turbulence employing a GKM‐based solver

Gas Kinetic Method‐based flow solvers have become popular in recent years owing to their robustness in simulating high Mach number compressible flows. We evaluate the performance of the newly developed analytical gas kinetic method (AGKM) by Xuan et al. in performing direct numerical simulation of canonical compressible turbulent flow on graphical processing unit (GPU)s. We find that for a range of turbulent Mach numbers, AGKM results shows excellent agreement with high order accurate results obtained with traditional Navier–Stokes solvers in terms of key turbulence statistics. Further, AGKM is found to be more efficient as compared with the traditional gas kinetic method for GPU implementation. We present a brief overview of the optimizations performed on NVIDIA K20 GPU and show that GPU optimizations boost the speedup up‐to 40x as compared with single core CPU computations. Hence, AGKM can be used as an efficient method for performing fast and accurate direct numerical simulations of compressible turbulent flows on simple GPU‐based workstations. Copyright © 2016 John Wiley & Sons, Ltd.     

A mathematical and physical Study of multiscale deconvolution models of turbulence

This work presents a rigorous analysis of mathematical and physical properties for solutions of multiscale deconvolution turbulence models. We show that solutions of these models exactly conserve model quantities for the integral invariants of fundamental physical importance: kinetic energy, helicity, and (in two dimensions) enstrophy. The kinetic energy conservation is the key that allows us to next apply the phenomenology of homogeneous, isotropic turbulence to establish the existence of a model energy cascade and, in particular, that the cascade exhibits enhanced energy dissipation in a secondary accelerated cascade, which ends at the model's microscale (which we establish is larger than the Kolmogorov microscale). We also prove that the model dissipates energy at the same rate as true turbulent flow, ～ O(U³ ∕ L), independent of Reynolds number. Lastly, we prove the existence of global attractors for the model solutions; the proof of which also shows that solutions are actually one degree of regularity higher than previously known. Copyright © 2012 John Wiley & Sons, Ltd.     

Novel Azobenzene-Functionalized Polyelectrolytes of Different Substituted Head Groups 2: Control of Surface Wetting in Self-Assembled Multilayer Films

A novel set of light-responsive polyelectrolytes has been developed and studied, to control and tune surface wettability by introducing various types of substituted R head-groups of azo polyelectrolytes in self-assembled multilayer (SAMU) films. As part of a larger project to develop polymer surfaces where one can exert precise control over properties important to proteins and cells in contact, photo-reversibly, we describe here how one can tune quite reliably the contact angle of a biocompatible SAMU, containing a photo-reversible azo chromophore for eventual directed cell growth. The azo polyelectrolytes described here have different substituted R head-group pairs of shorter-ionized hydrophilic COOH and SO₃H, shorter non-ionized hydrophobic H and OC₂H₅, and larger non-ionized hydrophobic octyl C₈H₁₇ and C₈F₁₇, and were employed as polyanions to fabricate the SAMU onto silicon substrates by using the counter-charge polycation PDAC. The prepared SAMU films were primarily characterized by measurement of their contact angles with water. The surface wetting properties of the thin films were found to be dependent on the type of substituted R-groups of the azo polyelectrolytes through their degree of ionization, size, hydrophobicity/hydrophilicity, solubility, conformation, and inter-polymeric association and intra-polymeric aggregation. All these factors appeared to be inter-related, and influenced variations in hydrophobic/hydrophilic character to different extents of aggregates/non-aggregates in solution because of solvation effects of the azo polyanions, and were thus manifested when adsorbed as thin films via the SAMU deposition process. For example, one interesting observation is significantly higher contact angles of 79° for SAMU films of larger octyl R groups of PAPEA-C₈F₁₇ and PAPEA-C₈H₁₇ than for others with contact angles of 64° observed for non-polar R-groups of OC₂H₅ and H. Furthermore, lower contact angle values of 59° for SAMU films with polar R-groups of COOH and SO₃H relative to that of non-polar R-groups are in accordance with their expected order of the hydrophilicity or hydrophobicity. It is possible that the large octyl groups are more effective in shielding the ionic functional groups on the substrate surface, and contributed less to the water drop-molecule interactions with ionic groups of the PDAC and/or AA groups. In addition, higher hydrophobicity of the SAMU films may be due to the incorporation of bulky and hydrophobic groups in these polyelectrolytes, which can produce aggregates on the surfaces of the SAMU films. Through understanding and controlling the complex aggregation behavior of the different substituted R-groups of these azo polyelectrolytes, and hence their adsorption on substrates, it appears possible to finely tune the surface energy of these biocompatible films over a wide range, enhance the photo-switching capabilities of the SAMU films, and tailor other surface properties for the development and application of new devices in diverse areas of microfluidics, specialty coatings, sensors, and biomedical sciences.     

Carrier removal by implanted IONS in GaAs

Abstract

A model for calculation of the range distribution of energetic ions with taking into account the channeling effect is proposed. The measurement of the depth distributions of boron ions in silicon crystals implanted at 13.6 and 91 MeV revealed significant difference between the measured and the calculated range profiles when the channeling effects have not been included in the calculation. In spite of deminishing the critical angles of channeling with growing ion energy the probability of the capture of ions into the channeling regime is significant in case of high energy implantation even when the incident angles are 7–10° off the main crystallographic directions.     

Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD‐based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907‐atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc.     

A Luminescent Metal–Organic Framework Thermometer with Intrinsic Dual Emission from Organic Lumophores

A new mixed‐ligand metal–organic framework (MOF), ZnATZ‐BTB, has been constructed as a luminescent ratiometric thermometer by making use of the intrinsic dual emission at cryogenic temperatures. Its twofold interpenetrated network promotes the Dexter energy transfer (DET) between the mixed organic lumophores. The temperature‐dependent luminescent behavior arises from the thermal equilibrium between two separated excited states coupled by DET, which is confirmed by Boltzmann distribution fitting. The small excited‐state energy gap allows ZnATZ‐BTB to measure and visualize cryogenic temperatures (30–130 K) with significantly high relative sensitivity (up to 5.29 % K^?1 at 30 K). Moreover, it is the first example of a ratiometric MOF thermometer the dual emitting sources of which are widely applicable mixed organic ligands, opening up new opportunities for designing such devices.     

Free energy and states of fractional-order hereditariness

Complex materials, often encountered in recent engineering and material sciences applications, show no complete separations between solid and fluid phases. This aspect is reflected in the continuous relaxation time spectra recorded in cyclic load tests. As a consequence the material free energy cannot be defined in a unique manner yielding a significative lack of knowledge of the maximum recoverable work that can extracted from the material. The non-uniqueness of the free energy function is removed in the paper for power-laws relaxation/creep function by using a recently proposed mechanical analogue to fractional-order hereditariness.     

First stereoselective total synthesis of decytospolides A and B

The first synthesis of bioactive decytospolides A and B adopting an oxa-Michael addition as the key step is reported.     

Catalytic hydrolysis of phosphodiesters by nucleophilic ions in gemini micellar media

The catalytic hydrolysis of bis(4‐nitrophenyl)phosphate (BNPP) and bis(2,4‐dinitrophenyl)phosphate (BDNPP) catalyzed by α‐nucleophiles in gemini micellar media was investigated at 27 °C. The cationic gemini surfactants, i.e., alkanediyl‐α‐ω‐bis(hydroxyethylmethylhexadecylammonium bromide) (16‐s‐16 MEA 2Br^?, where s = 4 and 6) were used. Nucleophilic reactivity of α‐nucleophiles such as hydroperoxide (HOO^?), acetohydroxamate (AHA^?), and butane 2,3‐dione monoximate ions (BDMO^?) were compared. The kinetic rate data were treated by applying the pseudophase model. The cationic gemini surfactants show unusual rate acceleration toward the cleavage of phosphodiesters with nucleophiles. These studies reveal that the hydroperoxide ion shows the highest catalytic activity reported so far with an unprecedented acceleration rate, 10⁷ times faster than that of the uncatalyzed reaction. The possible mechanism for the BNPP and BDNPP cleavage promoted by α‐nucleophiles is proposed on the basis of kinetic analysis. Copyright © 2014 John Wiley & Sons, Ltd.