bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconfiguring droplet interface bilayer networks through sacrificial membranes
Authors: Challita Elio J. , Makhoul-Mansour Michelle M. , Freeman Eric C.
Published: June 2018

The droplet interface bilayer platform allows for the fabrication of stimuli-responsive microfluidic materials, using phospholipids as an organic surfactant in water-in-oil mixtures. In this approach, lipid-coated droplets are adhered together in arranged networks, forming lipid bilayer membranes with embedded transporters and establishing selective exchange pathways between neighboring aqueous subcompartments. The resulting material is a biologically inspired droplet-based material that exhibits emergent properties wherein different droplets accomplish different functions, similar to multicellular organisms. These networks have been successfully applied towards biomolecular sensing and energy harvesting applications. However, unlike their source of inspiration, these droplet structures are often static. This limitation not only renders the networks unable to adapt or modify their structure and function after formation but also limits their long term use as passive ionic exchange between neighboring droplet pairs may initiate immediately after the membranes are established. This work addresses this shortcoming by rupturing selected sacrificial membranes within the collections of droplets to rearrange the remaining droplets into new configurations, redirecting the droplet-droplet exchange pathways. This is accomplished through electrical shocks applied between selected droplets. Experimental outcomes are compared to predictions provided by a coupled mechanical-electrical model for the droplet networks, and then advanced configurations are proposed using this model.
A flow-pulse adsorption-microcalorimetry system for studies of adsorption processes on powder catalysts
Authors: You Rui , Li Zhaorui , Zeng Hongyu , Huang Weixin
Published: June 2018

A pulse chemisorption system combining a Tian-Calvet microcalorimeter (Setaram Sensys EVO 600) and an automated chemisorption apparatus (Micromeritics Autochem II 2920) was established to accurately measure differential adsorption heats of gas molecules’ chemisorption on solid surfaces in a flow-pulse mode. Owing to high sensitivity and high degree of automation in a wide range of temperatures from −100 to 600 °C, this coupled system can present adsorption heats as a function of adsorption temperature and adsorbate coverage. The functions of this system were demonstrated by successful measurements of CO adsorption heats on Pd surfaces at various temperatures and also at different CO coverages by varying the CO concentration in the pulse dose. Key parameters, including adsorption amounts, integral adsorption heats, and differential adsorption heats of CO adsorption on a Pd/CeO2 catalyst, were acquired. Our adsorption-microcalorimetry system provides a powerful technique for the investigation of adsorption processes on powder catalysts.
Composition susceptibility and the role of one, two, and three-body interactions in glass forming alloys: Cu50Zr50 vs Ni50Al50
Authors: Tang Chunguang , Harrowell Peter
Published: June 2018

In this paper, we compare the composition fluctuations and interaction potentials of a good metallic glass former, Cu50Zr50, and a poor glass former, Ni50Al50. The Bhatia-Thornton correlation functions are calculated. Motivated by the observation of chemical ordering at the NiAl surface, we derive a new property, R^cn(q), corresponding to the linear susceptibility of concentration to a perturbation in density. We present a direct comparison of the potentials for the two model alloys using a 2nd order density expansion, and establish that the one-body energy plays a crucial role in stabilizing the crystal relative to the liquid in both alloys but that the three-body contribution to the heat of fusion is significantly larger in NiAl than CuZr.
Spin-hall-active platinum thin films grown via atomic layer deposition
Authors: Schlitz Richard , Amusan Akinwumi Abimbola , Lammel Michaela , Schlicht Stefanie , Tynell Tommi , Bachmann Julien , Woltersdorf Georg , Nielsch Kornelius , Goennenwein Sebastian T. B. , Thomas Andy
Published: June 2018

We study the magnetoresistance of yttrium iron garnet/Pt heterostructures in which the Pt layer was grown via atomic layer deposition (ALD). Magnetotransport experiments in three orthogonal rotation planes reveal the hallmark features of spin Hall magnetoresistance. To estimate the spin transport parameters, we compare the magnitude of the magnetoresistance in samples with different Pt thicknesses. We check the spin Hall angle and the spin diffusion length of the ALD Pt layers against the values reported for high-quality sputter-deposited Pt films. The spin diffusion length of 1.5 nm agrees well with that of platinum thin films reported in the literature, whereas the spin Hall magnetoresistance Δρ/ρ=2.2×10−5 is approximately a factor of 20 smaller compared to that of our sputter-deposited films. Our results demonstrate that ALD allows fabricating spin-Hall-active Pt films of suitable quality for use in spin transport structures. This work provides the basis to establish conformal ALD coatings for arbitrary surface geometries with spin-Hall-active metals and could lead to 3D spintronic devices in the future.
Thermodynamic limitations on the temperature sensitivity of cell-membrane ion channels: Trouble with enthalpy uncertainty
Authors: Zheltikov A. M.
Published: June 2018

Energy exchange between a thermodynamic ensemble of heat- and cold-activated cell-membrane ion channels and the surrounding heat reservoir is shown to impose fundamental limitations on the performance of such channels as temperature-controlled gates for thermal cell activation. Analysis of unavoidable thermodynamic internal-energy fluctuations caused by energy exchange between the ion channels and the heat bath suggests that the resulting enthalpy uncertainty is too high for a robust ion-current gating by a single ion channel, implying that large ensembles of ion channels are needed for thermal cell activation. We argue, based on this thermodynamic analysis, that, had thermosensitive cell-membrane ion channels operated individually, rather than as large ensembles, robust thermal cell activation would have been impossible because of thermodynamic fluctuations.
Effect of turbulent flow on an atmospheric-pressure AC powered gliding arc discharge
Authors: Kong Chengdong , Gao Jinlong , Zhu Jiajian , Ehn Andreas , Aldén Marcus , Li Zhongshan
Published: June 2018

A high-power gliding arc (GA) discharge was generated in a turbulent air flow driven by a 35 kHz alternating current electric power supply. The effects of the flow rate on the characteristics of the GA discharge were investigated using combined optical and electrical diagnostics. Phenomenologically, the GA discharge exhibits two types of discharge, i.e., glow type and spark type, depending on the flow rates and input powers. The glow-type discharge, which has peak currents of hundreds of milliamperes, is sustained at low flow rates. The spark-type discharge, which is characterized by a sharp current spike of several amperes with duration of less than 1 μs, occurs more frequently as the flow rate increases. Higher input power can suppress spark-type discharges in moderate turbulence, but this effect becomes weak under high turbulent conditions. Physically, the transition between glow- and spark-type is initiated by the short cutting events and the local re-ignition events. Short cutting events occur owing to the twisting, wrinkling, and stretching of the plasma columns that are governed by the relatively large vortexes in the flow. Local re-ignition events, which are defined as re-ignition along plasma columns, are detected in strong turbulence due to increment of the impedance of the plasma column and consequently the internal electric field strength. It is suggested that the vortexes with length scales smaller than the size of the plasma can penetrate into the plasma column and promote mixing with surroundings to accelerate the energy dissipation. Therefore, the turbulent flow influences the GA discharges by ruling the short cutting events with relatively large vortexes and the local re-ignition events with small vortexes.
Symbolic recurrence plots to analyze dynamical systems
Authors: Caballero-Pintado M. Victoria , Matilla-García Mariano , Ruiz Marín Manuel
Published: June 2018

This paper, based on the concept of symbolic correlation integral, introduces a set of symbolic recurrence plots and associated invariant measures, which are independent of the distance parameter, serving as a tool for quantifying the dynamic structure. These new measures allow the study of transient behavior, coexistence of attractors, bifurcations, and structural change. The final user does not have to choose the free distance parameter. An empirical application to electrocardiography data illustrates the use of symbolic recurrence measures.
Probing charge transfer during metal-insulator transitions in graphene-LaAlO3/SrTiO3 systems
Authors: Aliaj I. , Sambri A. , Miseikis V. , Stornaiuolo D. , di Gennaro E. , Coletti C. , Pellegrini V. , Miletto Granozio F. , Roddaro S.
Published: June 2018

Two-dimensional electron systems (2DESs) at the interface between LaAlO3 (LAO) and SrTiO3 (STO) perovskite oxides display a wide class of tunable phenomena ranging from superconductivity to metal-insulator transitions. Most of these effects are strongly sensitive to surface physics and often involve charge transfer mechanisms, which are, however, hard to detect. In this work, we realize hybrid field-effect devices where graphene is used to modulate the transport properties of the LAO/STO 2DES. Different from a conventional gate, graphene is semimetallic and allows us to probe charge transfer with the oxide structure underneath the field-effect electrode. In LAO/STO samples with a low initial carrier density, graphene-covered regions turn insulating when the temperature is lowered to 3 K, but conduction can be restored in the oxide structure by increasing the temperature or by field effect. The evolution of graphene’s electron density is found to be inconsistent with a depletion of LAO/STO, but it rather points to a localization of interfacial carriers in the oxide structure.
Electronic behaviour of Au-Pt alloys and the 4f binding energy shift anomaly in Au bimetallics- X-ray spectroscopy studies
Authors: Wang Dongniu , Cui Xiaoyu , Xiao Qunfeng , Hu Yongfeng , Wang Zhiqiang , Yiu Y. M. , Sham T. K.
Published: June 2018

The electronic structure and charge redistribution of 6s conduction charge and 5d charge in Au and Pt alloys, Au9Pt and AuPt9 have been investigated using a charge compensation model. It is found that, both the Au and Pt 4f binding energy (BE) exhibits a negative shift in the alloys relatively to the pure metal in apparent disagreement with electroneutrality considerations (Au is the most electronegative metallic element); more interestingly, the negative Au 4f BE shift in Au-Pt alloy is in contrast to previous observations for a large number of Au bimetallic systems with more electropositive hosts in which the more electropositive the host„ the more positive the Au 4f BE shift. This anomaly is counter intuitive to electronegativity considerations. This dilemma was resolved by the charge compensation model in which both electronegativity and charge neutrality can be satisfied and the overall charge flow δ, onto Au is small and positive and δ arises from charge flow of 6s conduction charge, Δnc onto Au site, which is partially compensated by the depletion of 6d charge Δnd at the Au site (δ = Δnc+ Δnd ∼0.1 >0). The much larger Coulomb interaction between 4f and 5d than that between 4f and 6s results in positive 4f BE shifts. The Au 4f BE shift in Au-Pt alloys together with 193Au Mössbauer data were used in the charge compensation model analysis which shows that the model is still valid in that the Au 4f shift in Au-Pt alloy arises from mainly conduction charge gain with little depletion of d charge at the Au site. The model also works for Pt. The Au and Pt 5d character in the alloys have been examined with valence band spectra which show both maintain their d characteristic in dilute alloys with Pt d piling up at the Fermi level, and the top of the Au valence band being pushed toward the Fermi level; this is confirmed with DFT densities of state calculations. When Pt is diluted in Au, it gains d charge as evident from the reduction in whiteline intensity at the Pt L3-edge XANES. What emerges from this work is a picture in which the s-d charge compensation in Au bimetallic alloys is triggered by electronegativity difference between Au and the host. For Au-Pt and Au-Pd systems, the difference in electronegativity is very small, conduction charge transfer dominates, and the Au 4f shift is negative whereas in most Au bimetallics, the larger the electronegativity difference, the larger the compensation and the larger the Au 4f shifts.
Bias temperature instability model using dynamic defect potential for predicting CMOS aging
Authors: Fang Runchen , Livingston Ian , Esqueda Ivan Sanchez , Kozicki Michael , Barnaby Hugh
Published: June 2018

This paper describes a new approach for modeling bias-temperature instability (BTI) in nanoscale transistors. The model uses non-iterative surface potential solvers enhanced with dynamic defect potential equations to enable accurate, physics-based circuit level simulations that incorporate BTI effects. Defect maps constructed from experimental data reported on high-k-metal-gate bulk complementary metal-oxide-semiconductor devices are used to parameterize the defect potential equation. By implementing the enhanced surface potential model in Verilog-A, both DC and AC BTI aging effects in combinational circuits are simulated and the results compared conventional threshold voltage shift methods for BTI modeling.
Near field planar microwave probe sensor for nondestructive condition assessment of wood products
Authors: Tiwari Nilesh Kumar , Singh Surya Prakash , Akhtar M. Jaleel
Published: June 2018

In this work, the unified methodology based on the newly designed electrically small planar resonant microwave sensor to detect the subsurface defect in wood products is presented. The proposed planar sensor involves loading of the specially designed coupled microstrip line with a novel small resonating element at its end. The novel design topology of the proposed near field sensor substantially increases the overall resolution and sensitivity of the microwave scanning system due to the strong localization of the electric field in the electrically small sensing region. A detailed electromagnetic and quasi static analysis of the near field scanning mechanism is also described in this work, which helps to understand the physics involved in the proposed scanning mechanism. The prototype of the designed sensor is fabricated on a 0.8 mm Roger 5880 substrate, and accordingly, the scattering parameters of the sensor under both loaded and unloaded conditions are measured. The measured and simulated scattering parameters under the unloaded condition are compared to validate the fabricated sensor, and a closed match between the simulated and measured resonance frequencies is observed. The fabricated sensor is used here for two potential applications, viz., the dielectric sensing of various low permittivity contrast dielectric materials and subsurface imaging of wood products to trace concealed defects and moisture content under the thin paint layer. The proposed resonant sensor can potentially be used to develop the low profile, low cost, non-destructive, and non-invasive quality monitoring system for inspecting various types of wood products without peeling off the upper paint coating.
Semiconducting lithium indium diselenide: Charge-carrier properties and the impacts of high flux thermal neutron irradiation
Authors: Hamm Daniel S. , Rust Mikah , Herrera Elan H. , Matei Liviu , Buliga Vladimir , Groza Michael , Burger Arnold , Stowe Ashley , Preston Jeff , Lukosi Eric D.
Published: June 2018

This paper reports on the charge carrier properties of several lithium indium diselenide (LISe) semiconductors. It was found that the charge collection efficiency of LISe was improved after high flux thermal neutron irradiation including the presence of a typically unobservable alpha peak from hole-only collection. Charge carrier trap energies of the irradiated sample were measured using photo-induced current transient spectroscopy. Compared to previous studies of this material, no significant differences in trap energies were observed. Through trap-filled limited voltage measurements, neutron irradiation was found to increase the density of trap states within the bulk of the semiconductor, which created a polarization effect under alpha exposure but not neutron exposure. Further, the charge collection efficiency of the irradiated sample was higher (14–15 fC) than that of alpha particles (3–5 fC), indicating that an increase in hole signal contribution resulted from the neutron irradiation. Finally, it was observed that significant charge loss takes place near the point of generation, producing a significant scintillation response and artificially inflating the W-value of all semiconducting LISe crystals.
Effective passivation of silicon surfaces by ultrathin atomic-layer deposited niobium oxide
Authors: Macco B. , Bivour M. , Deijkers J. H. , Basuvalingam S. B. , Black L. E. , Melskens J. , van de Loo B. W. H. , Berghuis W. J. H. , Hermle M. , Kessels W. M. M. (Erwin)
Published: June 2018

This letter reports on effective surface passivation of n-type crystalline silicon by ultrathin niobium oxide (Nb2O5) films prepared by atomic layer deposition (ALD) and subjected to a forming gas anneal at 300 °C. A champion recombination parameter J0 of 20 fA/cm2 and a surface recombination velocity Seff of 4.8 cm/s have been achieved for ultrathin films of 1 nm. The surface pretreatment was found to have a strong impact on the passivation. Good passivation can be achieved on both HF-treated c-Si surfaces and c-Si surfaces with a wet-chemically grown interfacial silicon oxide layer. On HF-treated surfaces, a minimum film thickness of 3 nm is required to achieve a high level of surface passivation, whereas the use of a wet chemically-grown interfacial oxide enables excellent passivation even for Nb2O5 films of only 1 nm. This discrepancy in passivation between both surface types is attributed to differences in the formation and stoichiometry of interfacial silicon oxide, resulting in different levels of chemical passivation. On both surface types, the high level of passivation of ALD Nb2O5 is aided by field-effect passivation originating from a high fixed negative charge density of 1–2 × 1012 cm−3. Furthermore, it is demonstrated that the passivation level provided by 1 nm of Nb2O5 can be further enhanced through light-soaking. Finally, initial explorations show that a low contact resistivity can be obtained using Nb2O5-based contacts. Together, these properties make ALD Nb2O5 a highly interesting building block for high-efficiency c-Si solar cells.
Comparison of Green’s functions for transition metal atoms using self-energy functional theory and coupled-cluster singles and doubles (CCSD)
Authors: Kosugi Taichi , Nishi Hirofumi , Furukawa Yoritaka , Matsushita Yu-ichiro
Published: June 2018

We demonstrate in the present study that self-consistent calculations based on the self-energy functional theory (SFT) are possible for the electronic structure of realistic systems in the context of quantum chemistry. We describe the procedure of a self-consistent SFT calculation in detail and perform the calculations for isolated 3d transition metal atoms from V to Cu as a preliminary study. We compare the one-particle Green’s functions obtained in this way and those obtained from the coupled-cluster singles and doubles method. Although the SFT calculation starts from the spin-unpolarized Hartree–Fock state for each of the target systems, the self-consistency loop correctly leads to degenerate spin-polarized ground states. We examine the spectral functions in detail to find their commonalities and differences among the atoms by paying attention to the characteristics of the two approaches. It is demonstrated via the two approaches that calculations based on the density functional theory (DFT) can fail in predicting the orbital energy spectra for spherically symmetric systems. It is found that the two methods are quite reliable and useful beyond DFT.
Low contact resistance of NiGe/p-Ge by indium segregation during Ni germanidation
Authors: Li M. , Shin G. , Lee J. , Oh J. , Lee H.-D.
Published: June 2018

Herein, indium-doped p-type source/drain was introduced and the redistribution of indium (In) during the formation of a nickel germanide at the NiGe/Ge interface was characterized. Our results show that In segregates at the NiGe/p-Ge interface during Ni germanidation. The specific contact resistivity, ρc between the NiGe and p-Ge layer, with a substantial low value of 4.04 × 10−8 Ωcm2 was obtained with the activation by rapid thermal annealing (RTA) at 650°C for 10 s. From this result, it can be concluded that Ge p-type metal–oxide–semiconductor field-effect transistors (Ge pMOSFETs) with low parasitic resistance source/drains could be realized by this In segregation.
Propagation of THz pulses in rectangular subwavelength dielectric waveguides
Authors: Lu Yao , Wu Qiang , Zhang Qi , Wang Ride , Zhao Wenjuan , Zhang Deng , Pan Chongpei , Qi Jiwei , Xu Jingjun
Published: June 2018

Rectangular subwavelength waveguides are necessary for the development of micro/nanophotonic devices and on-chip platforms. Using a time-resolved imaging system, we studied the transient properties and the propagation modes of THz pulses in rectangular subwavelength dielectric waveguides. The dynamic process of THz pulses was systematically recorded to a movie. In addition, an anomalous group velocity dispersion was demonstrated in rectangular subwavelength waveguides. By using the effective index method, we theoretically calculated the modes in rectangular subwavelength waveguides, which agree well with the experiments and simulations. This work provides the opportunity to improve the analysis and design of the integrated platforms and photonic devices.
Structural design of giant magnetostrictive actuator
Authors: Gao Xiaohui , Liu Yongguang , Guo Hong , Yang Xiaowei
Published: June 2018

Structural parameters of giant magnetostrictive actuator (GMA) have a greater impact on its output characteristics and how to design them is related to give full play to the material characteristics. On the basis of analyzing working principle of GMA, this paper respectively designs and optimizes the structural parameters of exciting coil, magnetic circuit, preload device and temperature control system. The initial best working conditions are achieved by research on static experiments. The experiment results show that this GMA has better static and dynamic output characteristic, which further improves GMA design theory and expands its applications.
Analysis of electromagnetic scattering characteristics of plasma sheath surrounding a hypersonic aerocraft based on high-order auxiliary differential equation finite-difference time-domain
Authors: Sun Hao-yu , Cui Zhiwei , Wang Jiajie , Han Yiping , Sun Peng , Shi Xiaowei
Published: June 2018

A numerical analysis of electromagnetic (EM) scattering characteristics of a hypersonic aerocraft enveloped by a plasma sheath is presented. The flow field parameters around a hypersonic aerocraft are derived by numerically solving the Navier-Stokes equations. Through multiphysics coupling of flow field and electromagnetic field, distributions of plasma frequency and collision frequency in plasma sheaths are obtained. A high-order auxiliary differential equation finite-difference time-domain algorithm is employed to investigate the EM wave scattering properties of the aerocraft covered by a plasma sheath. The backward radar cross sections (RCSs) of a blunt cone in the hypersonic flows at different velocities and altitudes with frequencies from 0.1 GHz to 18 GHz are studied. Numerical results show that, for the cases of altitude ranging from 50 km to 55 km and velocity ranging from 18 Ma to 20 Ma, the plasma sheath enhances the backscattering of the blunt cone when frequencies are below 1.5 GHz, and it reduces the backward RCSs of the blunt cone as frequency ranges from 1.5 GHz to 13.5 GHz. The plasma sheath has a larger attenuation effect for frequency lying in the range of 2 GHz to 6 GHz, but it has little influence on the backward electromagnetic scattering characteristics when frequencies are above 14 GHz.
Band alignments at Ga2O3 heterojunction interfaces with Si and Ge
Authors: Gibbon J. T. , Jones L. , Roberts J. W. , Althobaiti M. , Chalker P. R. , Mitrovic Ivona Z. , Dhanak V. R.
Published: June 2018

Amorphous Ga2O3 thin films were deposited on p-type (111) and (100) surfaces of silicon and (100) germanium by atomic layer deposition (ALD). X-ray photoelectron spectroscopy (XPS) was used to investigate the band alignments at the interfaces using the Kraut Method. The valence band offsets were determined to be 3.49± 0.08 eV and 3.47± 0.08 eV with Si(111) and Si(100) respectively and 3.51eV± 0.08 eV with Ge(100). Inverse photoemission spectroscopy (IPES) was used to investigate the conduction band of a thick Ga2O3 film and the band gap of the film was determined to be 4.63±0.14 eV. The conduction band offsets were found to be 0.03 eV and 0.05eV with Si(111) and Si(100) respectively, and 0.45eV with Ge(100). The results indicate that the heterojunctions of Ga2O3 with Si(100), Si(111) and Ge(100) are all type I heterojunctions.
Demonstration of long wavelength infrared type-II InAs/InAs1-xSbx superlattices photodiodes on GaSb substrate grown by metalorganic chemical vapor deposition
Authors: Wu D. H. , Dehzangi A. , Zhang Y. Y. , Razeghi M.
Published: June 2018

We report the growth and characterization of long wavelength infrared type-II InAs/InAs1-xSbx superlattice photodiodes with a 50% cut-off wavelength at 8.0 μm on a GaSb substrate grown by metalorganic chemical vapor deposition. At 77 K, the photodiodes exhibited a differential resistance at zero bias (R0A) of 8.0 Ω cm2 and a peak responsivity of 1.26 A/W corresponding to a quantum efficiency of 21%. A specific detectivity of 5.4 × 1010 cm Hz1/2/W was achieved at 7.5 μm.
High pressure magnetic, structural, and electronic transitions in multiferroic Ba3NbFe3Si2O14
Authors: Lyubutin I. S. , Starchikov S. S. , Gavriliuk A. G. , Troyan I. A. , Nikiforova Yu. A. , Ivanova A. G. , Chumakov A. I. , Rüffer R.
Published: June 2018

The magnetic, structural, and electronic properties of multiferroic Ba3NbFe3Si2O14 from the langasite family were investigated by several methods including synchrotron X-ray diffraction (XRD) and synchrotron Mössbauer source (SMS) technique at high hydrostatic pressures (up to 60 GPa) created in diamond anvil cells. A cascade of structural phase transitions at pressures of about 3.5, 17.5, and 41 GPa was revealed by structural XRD, magnetic SMS, and electronic methods, including Raman, Mössbauer, and optical absorption. The transition at 17.5 GPa leads to strong changes in unit cell parameters and a sharp drop in the cell volume by about 7%. This drastically changes the magnetic properties of the crystal, which separates into two magnetic phases. The Néel temperature TN in one of the phases is increased up to 100 K, which is more than three times higher than the TN value of the parent compound (∼27 K). Above 41 GPa, the optical gap decreases to about 0.7 eV, implying a transition from dielectric to a semiconducting state, while the TN value of the magnetic phase decreases from 100 to 58 K. The magnetic transitions are explained by the redistribution of Fe ions between tetrahedral and possibly octahedral (or/and interstitial) sites resulting in enhancement of exchange interactions. The appearance of a low spin state of Fe3+ ions in octahedral sites is also discussed.
Generic parameters of trajectory-extending kinetic Monte Carlo for calculating diffusion coefficients
Authors: Tien Wu-Jhao , Chiu Chi-cheng
Published: June 2018

One of the challenging applications of molecular dynamics (MD) simulations is to determine the dynamic properties such as the diffusion coefficient of the molecule of interest, particularly slow dynamic systems such as hydrogels and polymer melts. Recently, Neyertz et al. proposed a trajectory- extending kinetic Monte Carlo (TEKMC) algorithm combining both MD and kinetic Monte Carlo to probe the penetrant diffusion within the glassy polymer systems (S. Neyertz and D. Brown, Macromolecules 43, 9210, 2010). Yet, the original TEKMC relies on the manual adjustments of the key parameters of the sampling interval τ and the discretizing grid size rgrid, which limits its applicability to systems with unknown kinetic properties. Here, we reviewed the theoretical background of kinetic Monte Carlo to establish the generic criteria for selecting TEKMC parameters. Also, we modified and expanded the TEKMC algorithm for bulk fluid systems. The modified TEKMC algorithm were applied to systems with various kinetic properties, including Lennard Jones liquid, bulk water, Li+ liquid electrolyte, and Li+ polymer electrolyte. The diffusion coefficients obtained from the modified TEKMC and the generic parameter selections were promising and robust compared with the conventional MD results. With the proposed TEKMC approach, one can extend the MD trajectories to unambiguously characterize the diffusion behavior in the long-time diffusive regime.
Stochastic thermodynamics and entropy production of chemical reaction systems
Authors: Tomé Tânia , de Oliveira Mário J.
Published: June 2018

We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end, we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of chemical reaction systems based on a master equation defined on the space of microscopic chemical states and on appropriate definitions of entropy and entropy production. The system is in contact with a heat reservoir and is placed out of equilibrium by the contact with particle reservoirs. In our approach, the fluxes of various types, such as the heat and particle fluxes, play a fundamental role in characterizing the nonequilibrium chemical state. We show that the rate of entropy production in the stationary nonequilibrium state is a bilinear form in the affinities and the fluxes of reaction, which are expressed in terms of rate constants and transition rates, respectively. We also show how the description in terms of microscopic states can be reduced to a description in terms of the numbers of particles of each species, from which follows the chemical master equation. As an example, we calculate the rate of entropy production of the first and second Schlögl reaction models.
Rubber friction: The contribution from the area of real contact
Authors: Tiwari A. , Miyashita N. , Espallargas N. , Persson B. N. J.
Published: June 2018

There are two contributions to the friction force when a rubber block is sliding on a hard and rough substrate surface, namely, a contribution Fad = τf A from the area of real contact A and a viscoelastic contribution Fvisc from the pulsating forces exerted by the substrate asperities on the rubber block. Here we present experimental results obtained at different sliding speeds and temperatures, and we show that the temperature dependency of the shear stress τf, for temperatures above the rubber glass transition temperature Tg, is weaker than that of the bulk viscoelastic modulus. The physical origin of τf for T > Tg is discussed, and we propose that its temperature dependency is determined by the rubber molecule segment mobility at the sliding interface, which is higher than in the bulk because of increased free-volume effect due to the short-wavelength surface roughness. This is consistent with the often observed reduction in the glass transition temperature in nanometer-thick surface layers of glassy polymers. For temperatures T < Tg, the shear stress τf is nearly velocity independent and of similar magnitude as observed for glassy polymers such as PMMA or polyethylene. In this case, the rubber undergoes plastic deformations in the asperity contact regions and the contact area is determined by the rubber penetration hardness. For this case, we propose that the frictional shear stress is due to slip at the interface between the rubber and a transfer film adsorbed on the concrete surface.
Robust laser-structured asymmetrical PTFE mesh for underwater directional transportation and continuous collection of gas bubbles
Authors: Yin Kai , Yang Shuai , Dong Xinran , Chu Dongkai , Duan Ji-An , He Jun
Published: June 2018

We report a simple, efficient method to fabricate micro/nanoscale hierarchical structures on one side of polytetrafluoroethylene mesh surfaces, using one-step femtosecond laser direct writing technology. The laser-treated surface exhibits superhydrophobicity in air and superaerophilicity in water, resulting in the mesh possessing the hydrophobic/superhydrophobic asymmetrical property. Bubbles can pass through the mesh from the untreated side to the laser-treated side but cannot pass through the mesh in the opposite direction. The asymmetrical mesh can therefore be designed for the directional transportation and continuous collection of gas bubbles in aqueous environments. Furthermore, the asymmetrical mesh shows excellent stability during corrosion and abrasion tests. These findings may provide an efficient route for fabricating a durable asymmetrical mesh for the directional and continuous transport of gas bubbles.
Why copper and zinc are ineffective in reducing soil urease activity in New Zealand dairy-grazed pasture soils
Authors: Adhikari Kamal P. , Saggar Surinder , Hanly James A. , Guinto Danilo F. , Taylor Matthew D.
Published: June 2018

Micronutrients copper (Cu) and zinc (Zn) have the potential to inhibit soil urease activity (UA) and reduce ammonia (NH3) emissions over long duration (8–12 weeks) but have not been tested for reducing NH3 losses from cattle urine deposited in dairy-grazed pasture soils. The objective of this study was to assess the effectiveness and longevity of Cu and Zn in reducing soil UA, for the use of these metals to reduce NH3 emissions from deposited urine by grazing cattle. A series of experiments were conducted to (i) assess the relationship between inherent Cu and Zn status and soil UA of New Zealand dairy-grazed pasture soils, (ii) determine the impact of Cu and Zn addition to pasture soils on soil UA and (iii) investigate how soil organic carbon (C) and other C-related textural and mineralogical properties such as clay content and cation exchange capacity influence the effectiveness of added Cu and Zn in reducing urea hydrolysis. The results showed significant positive correlations of soil total C and total nitrogen (N) with soil UA. However, there were no significant negative correlations of soil UA with inherent Cu and Zn levels. Similarly, addition of Cu and Zn to soil did not significantly reduce soil UA. However, when Cu was added to two different soil supernatants there was a significant reduction in hydrolysis of urea applied at 120 and 600 mg urea-N kg–1 soil. Additions of Zn achieved negligible or small reductions in urea hydrolysis after 120 and 600 mg urea-N kg–1 soil applications to soil supernatants. This result suggests that Cu can inhibit soil UA and urea hydrolysis in soil supernatants with potentially low C, clay and cation exchangeable base contents. However, the interaction of bioavailable Cu with labile soil organic C and clay particles leads to its inactivation, resulting in ineffectiveness in organic C-rich pasture soils. Although most of the added Zn did not complex and remained bioavailable, the observed levels of bioavailable Zn had limited effect on soil UA.
On the role of sidechain size and charge in the aggregation of A
β
42 with familial mutations
Authors: Yang Xiaoting , Meisl Georg , Frohm Birgitta , Thulin Eva , Knowles Tuomas P. J. , Linse Sara
Published: June 2018

Significance

The aggregation of the amyloid-

β

(A

β

) peptide into amyloid fibrils is associated with Alzheimer’s disease, and several point mutations leading to early-onset disease have been identified in A

β

. By studying the aggregation of five disease-related mutations in vitro, we rationalize their link to familial Alzheimer’s disease. We have determined the effect of mutations on the individual steps of the overall A

β

42 aggregation reaction and find for four of the mutations a significant increase in the rate of self-replication of fibrils, a process that has been linked to the production of toxic oligomeric species. Furthermore, by investigating the nature of the mutation, we determine the importance of the charge and size of specific residues in the aggregation of the wild-type peptide.
Potential adverse cardiac remodelling in highly trained athletes: still unknown clinical significance
Authors: Gabrielli Luigi , Sitges Marta , Chiong Mario , Jalil Jorge , Ocaranza María , Llevaneras Silvana , Herrera Sebastian , Fernandez Rodrigo , Saavedra Rodrigo , Yañez Fernando , Vergara Luis , Diaz Alexis , Lavandero Sergio , Castro Pablo
Published: June 2018

Moderate endurance exercise has long been considered an essential element to maintain cardiovascular health, and sedentary behaviour in the general population has been related to a significant increase in all‐causes of mortality, cardiovascular disease mortality and cardiovascular disease incidence. However, a growing group of people performs an intense exercise that leads to multiple heart adaptive changes that are collectively called “athlete's heart”. In this review, we discussed the evidence of cardiac remodelling process secondary to repetitive and strenuous exercise in some predisposed athletes that produces intense and probably deleterious changes in cardiac morphology and function with no clear clinical significance in long‐term follow‐up. Moreover, we also discussed the individual biological response to exercise assessed by myocardial damage, inflammation, oxidative stress, fibrosis and ventricular hypertrophy biomarkers showing different intensities with equivalent exertion.
Relationship between accuracy and complexity when learning underarm precision throwing
Authors: Valle Maria Stella , Lombardo Luciano , Cioni Matteo , Casabona Antonino
Published: June 2018

Learning precision ball throwing was mostly studied to explore the early rapid improvement of accuracy, with poor attention on possible adaptive processes occurring later when the rate of improvement is reduced. Here, we tried to demonstrate that the strategy to select angle, speed and height at ball release can be managed during the learning periods following the performance stabilization. To this aim, we used a multivariate linear model with angle, speed and height as predictors of changes in accuracy. Participants performed underarm throws of a tennis ball to hit a target on the floor, 3.42 m away. Two training sessions (S1, S2) and one retention test were executed. Performance accuracy increased over the S1 and stabilized during the S2, with a rate of changes along the throwing axis slower than along the orthogonal axis. However, both the axes contributed to the performance changes over the learning and consolidation time. A stable relationship between the accuracy and the release parameters was observed only during S2, with a good fraction of the performance variance explained by the combination of speed and height. All the variations were maintained during the retention test. Overall, accuracy improvements and reduction in throwing complexity at the ball release followed separate timing over the course of learning and consolidation.
GeneSpy, a user-friendly and flexible genomic context visualizer
Authors: Garcia Pierre Simon , Jauffrit Frédéric , Grangeasse Christophe , Brochier-Armanet Céline
Published: June 2018

The exploration and comparison of genome organization is routinely used in the frame of genomic and phylogenomic analyses. As a consequence, in the past few years, various tools allowing visualizing genomic contexts have been developed. However, their use is often hampered by a lack of flexibility, particularly concerning associated databases input formats and figure customization. Here we present GeneSpy, a graphical user interface that allows the visualization and dynamic exploration of eukaryotic and prokaryotic annotated genomes. GeneSpy relies on user-friendly manageable local databases and allows the easy customization and production of figures in a multitude of formats.

Availability and implementation

GeneSpy is freely available at https://lbbe.univ-lyon1.fr/GeneSpy/ for Linux, Mac OS and Windows under CeCILL license (http://www.cecill.info/licences/). It is written in Python 2.7 and depends on Matplotlib, Tkinter and Sqlite libraries.

Supplementary information

Supplementary data are available at Bioinformatics online.
Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile
Authors: Guan Yuanfang , Li Tingyang , Zhang Hongjiu , Zhu Fan , Omenn Gilbert S
Published: June 2018

Motivation

Finding driver genes that are responsible for the aberrant proliferation rate of cancer cells is informative for both cancer research and the development of targeted drugs. The established experimental and computational methods are labor-intensive. To make algorithms feasible in real clinical settings, methods that can predict driver genes using less experimental data are urgently needed.

Results

We designed an effective feature selection method and used Support Vector Machines (SVM) to predict the essentiality of the potential driver genes in cancer cell lines with only 10 genes as features. The accuracy of our predictions was the highest in the Broad-DREAM Gene Essentiality Prediction Challenge. We also found a set of genes whose essentiality could be predicted much more accurately than others, which we called Accurately Predicted (AP) genes. Our method can serve as a new way of assessing the essentiality of genes in cancer cells.

Availability and implementation

The raw data that support the findings of this study are available at Synapse. https://www.synapse.org/#! Synapse: syn2384331/wiki/62825. Source code is available at GitHub. https://github.com/GuanLab/DREAM-Gene-Essentiality-Challenge.

Supplementary information

Supplementary data are available at Bioinformatics online.
13Check_RNA: a tool to evaluate 13C chemical shift assignments of RNA
Authors: Icazatti A A , Martin O A , Villegas M , Szleifer I , Vila J A
Published: June 2018

Motivation

Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for evaluating the referencing of RNA 13 C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors.

Results

Based on an existent method we have implemented an open source python module to correct 13 C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one.

Availability and implementation

This software is available on GitHub at https://github.com/BIOS-IMASL/13Check_RNA under a MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies
Authors: Sanyal Nilotpal , Lo Min-Tzu , Kauppi Karolina , Djurovic Srdjan , Andreassen Ole A , Johnson Valen E , Chen Chi-Hua
Published: June 2018

Motivation

Multiple marker analysis of the genome-wide association study (GWAS) data has gained ample attention in recent years. However, because of the ultra high-dimensionality of GWAS data, such analysis is challenging. Frequently used penalized regression methods often lead to large number of false positives, whereas Bayesian methods are computationally very expensive. Motivated to ameliorate these issues simultaneously, we consider the novel approach of using non-local priors in an iterative variable selection framework.

Results

We develop a variable selection method, named, iterative non-local prior based selection for GWAS, or GWASinlps, that combines, in an iterative variable selection framework, the computational efficiency of the screen-and-select approach based on some association learning and the parsimonious uncertainty quantification provided by the use of non-local priors. The hallmark of our method is the introduction of ‘structured screen-and-select’ strategy, that considers hierarchical screening, which is not only based on response-predictor associations, but also based on response-response associations and concatenates variable selection within that hierarchy. Extensive simulation studies with single nucleotide polymorphisms having realistic linkage disequilibrium structures demonstrate the advantages of our computationally efficient method compared to several frequentist and Bayesian variable selection methods, in terms of true positive rate, false discovery rate, mean squared error and effect size estimation error. Further, we provide empirical power analysis useful for study design. Finally, a real GWAS data application was considered with human height as phenotype.

Availability and implementation

An R-package for implementing the GWASinlps method is available at https://cran.r-project.org/web/packages/GWASinlps/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts
Authors: Laajala Teemu D , Murtojärvi Mika , Virkki Arho , Aittokallio Tero
Published: June 2018

Motivation

Prognostic models are widely used in clinical decision-making, such as risk stratification and tailoring treatment strategies, with the aim to improve patient outcomes while reducing overall healthcare costs. While prognostic models have been adopted into clinical use, benchmarking their performance has been difficult due to lack of open clinical datasets. The recent DREAM 9.5 Prostate Cancer Challenge carried out an extensive benchmarking of prognostic models for metastatic Castration-Resistant Prostate Cancer (mCRPC), based on multiple cohorts of open clinical trial data.

Results

We make available an open-source implementation of the top-performing model, ePCR, along with an extended toolbox for its further re-use and development, and demonstrate how to best apply the implemented model to real-world data cohorts of advanced prostate cancer patients.

Availability and implementation

The open-source R-package ePCR and its reference documentation are available at the Central R Archive Network (CRAN): https://CRAN.R-project.org/package=ePCR. R-vignette provides step-by-step examples for the ePCR usage.

Supplementary information

Supplementary data are available at Bioinformatics online.