bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Polo-like kinase 1 interaction inhibitors using a novel cell-based assay
Authors: Normandin Karine , Lavallée Jean-François , Futter Marie , Beautrait Alexandre , Duchaine Jean , Guiral Sébastien , Marinier Anne , Archambault Vincent
Published: November 2016

Polo-like kinase 1 (Plk1) plays several roles in cell division and it is a recognized cancer drug target. Plk1 levels are elevated in cancer and several types of cancer cells are hypersensitive to Plk1 inhibition. Small molecule inhibitors of the kinase domain (KD) of Plk1 have been developed. Their selectivity is limited, which likely contributes to their toxicity. Polo-like kinases are characterized by a Polo-Box Domain (PBD), which mediates interactions with phosphorylation substrates or regulators. Inhibition of the PBD could allow better selectivity or result in different effects than inhibition of the KD.In vitroscreens have been used to identify PBD inhibitors with mixed results. We developed the first cell-based assay to screen for PBD inhibitors, using Bioluminescence Resonance Energy Transfer (BRET). We screened through 112 983 compounds and characterized hits in secondary biochemical and biological assays. Subsequent Structure-Activity Relationship (SAR) analysis on our most promising hit revealed that it requires an alkylating function for its activity. In addition, we show that the previously reported PBD inhibitors thymoquinone and Poloxin are also alkylating agents. Our cell-based assay is a promising tool for the identification of new PBD inhibitors with more drug-like profiles using larger and more diverse chemical libraries.
Robust encoding of scene anticipation during human spatial navigation
Authors: Shikauchi Yumi , Ishii Shin
Published: November 2016

In a familiar city, people can recall scene views (e.g., a particular street corner scene) they could encounter again in the future. Complex objects with multiple features are represented by multiple neural units (channels) in the brain, but when anticipating a scene view, the kind of feature that is assigned to a specific channel is unknown. Here, we studied neural encoding of scene view anticipation during spatial navigation, using a novel data-driven analysis to evaluate encoding channels. Our encoding models, based on functional magnetic resonance imaging (fMRI) activity, provided channel error correction via redundant channel assignments that reflected the navigation environment. We also found that our encoding models strongly reflected brain activity in the inferior parietal gyrus and precuneus, and that details of future scenes were locally represented in the superior prefrontal gyrus and temporal pole. Furthermore, a decoder associated with the encoding models accurately predicted future scene views in both passive and active navigation. These results suggest that the human brain uses scene anticipation, mediated especially by parietal and medial prefrontal cortical areas, as a robust and effective navigation processing.
Oligofructose as an adjunct in treatment of diabetes in NOD mice
Authors: Chan Clement , Hyslop Colin M. , Shrivastava Vipul , Ochoa Andrea , Reimer Raylene A. , Huang Carol
Published: November 2016

In type 1 diabetes, restoration of normoglycemia can be achieved if the autoimmune attack on beta cells ceases and insulin requirement is met by the residual beta cells. We hypothesize that an adjunctive therapy that reduces insulin demand by increasing insulin sensitivity will improve the efficacy of an immunotherapy in reversing diabetes. We tested the gut microbiota-modulating prebiotic, oligofructose (OFS), as the adjunctive therapy. We treated non-obese diabetic mice with an immunotherapy, monoclonal anti-CD3 antibody (aCD3), with or without concurrent dietary supplement of OFS. After 8 weeks of OFS supplement, the group that received both aCD3 and OFS (aCD3 + OFS) had a higher diabetes remission rate than the group that received aCD3 alone. The aCD3 + OFS group had higher insulin sensitivity accompanied by reduced lymphocytic infiltrate into the pancreatic islets, higher beta-cell proliferation rate, higher pancreatic insulin content, and secreted more insulin in response to glucose. The addition of OFS also caused a change in gut microbiota, with a higher level of Bifidobacterium and lower Clostridium leptum. Hence, our results suggest that OFS can potentially be an effective therapeutic adjunct in the treatment of type 1 diabetes by improving insulin sensitivity and beta-cell function, leading to improved glycemic control.
Antimicrobial Peptide Potency is Facilitated by Greater Conformational Flexibility when Binding to Gram-negative Bacterial Inner Membranes
Authors: Amos Sarah-Beth T. A. , Vermeer Louic S. , Ferguson Philip M. , Kozlowska Justyna , Davy Matthew , Bui Tam T. , Drake Alex F. , Lorenz Christian D. , Mason A. James
Published: November 2016

The interaction of antimicrobial peptides (AMPs) with the inner membrane of Gram-negative bacteria is a key determinant of their abilities to exert diverse bactericidal effects. Here we present a molecular level understanding of the initial target membrane interaction for two cationic α-helical AMPs that share structural similarities but have a ten-fold difference in antibacterial potency towards Gram-negative bacteria. The binding and insertion from solution of pleurocidin or magainin 2 to membranes representing the inner membrane of Gram-negative bacteria, comprising a mixture of 128 anionic and 384 zwitterionic lipids, is monitored over 100 ns in all atom molecular dynamics simulations. The effects of the membrane interaction on both the peptide and lipid constituents are considered and compared with new and published experimental data obtained in the steady state. While both magainin 2 and pleurocidin are capable of disrupting bacterial membranes, the greater potency of pleurocidin is linked to its ability to penetrate within the bacterial cell. We show that pleurocidin displays much greater conformational flexibility when compared with magainin 2, resists self-association at the membrane surface and penetrates further into the hydrophobic core of the lipid bilayer. Conformational flexibility is therefore revealed as a key feature required of apparently α-helical cationic AMPs for enhanced antibacterial potency.
Poly-L-ornithine enhances migration of neural stem/progenitor cells via promoting α-Actinin 4 binding to actin filaments
Authors: Ge Hongfei , Yu Anyong , Chen Jingyu , Yuan Jichao , Yin Yi , Duanmu Wangsheng , Tan Liang , Yang Yang , Lan Chuan , Chen Weixiang , Feng Hua , Hu Rong
Published: November 2016

The recruitment of neural stem/progenitor cells (NSPCs) for brain restoration after injury is a promising regenerative therapeutic strategy. This strategy involves enhancing proliferation, migration and neuronal differentation of NSPCs. To date, the lack of biomaterials, which facilitate these processes to enhance neural regeneration, is an obstacle for the cell replacement therapies. Our previous study has shown that NSPCs grown on poly-L-ornithine (PO) could proliferate more vigorously and differentiate into more neurons than that on Poly-L-Lysine (PLL) and Fibronectin (FN). Here, we demonstrate that PO could promote migration of NSPCs in vitro, and the underlying mechanism is PO activates α-Actinins 4 (ACTN4), which is firstly certified to be expessed in NSPCs, to promote filopodia formation and therefore enhances NSPCs migration. Taken together, PO might serve as a better candidate for transplanted biomaterials in the regenerative therapeutic strategy, compared with PLL and FN.
Structural characterization of EasH (Aspergillus japonicus) – an oxidase involved in cycloclavine biosynthesis
Authors: Jakubczyk Dorota , Caputi Lorenzo , Stevenson Clare E. M. , Lawson David M. , O'Connor Sarah E.
Published: November 2016

Aj_EasH is a non-heme iron- and α-keto-glutarate-dependent oxidase that is responsible for an unusual cyclopropyl ring formation in the biosynthesis of the fungal ergot alkaloid cycloclavine.
Assembly of 1D nanofibers into a 2D bi-layered composite nanofibrous film with different functionalities at the two layers via layer-by-layer electrospinning
Authors: Wang Zijiao , Ma Qianli , Dong Xiangting , Li Dan , Xi Xue , Yu Wensheng , Wang Jinxian , Liu Guixia
Published: November 2016

A unique bi-layered composite nanofibrous film with trifunctionality of electrical conduction, magnetism and photoluminescence has been fabricated via layer-by-layer electrospinning.
Micellization of alkyltrimethylammonium bromide surfactants in choline chloride:glycerol deep eutectic solvent
Authors: Sanchez-Fernandez Adrian , Arnold Thomas , Jackson Andrew J. , Fussell Sian L. , Heenan Richard K. , Campbell Richard A. , Edler Karen J.
Published: November 2016

Cationic surfactant behaviour in choline chloride:glycerol deep eutectic solvent: towards understanding amphiphile self-assembly in the absence of water.
Bulk molybdenum field emitters by inductively coupled plasma etching
Authors: Zhu Ningli , Cole Matthew T. , Milne William I. , Chen Jing
Published: November 2016

Processing conditions are herein explored for the etching of bulk Mo by inductively coupled plasma towards nano tip arrays for field electron emission applications.
An efficient 2D 11B–11B solid-state NMR spectroscopy strategy for monitoring covalent self-assembly of boronic acid-derived compounds: the transformation and unique architecture of bortezomib molecules in the solid state
Authors: Brus J. , Czernek J. , Urbanova M. , Kobera L. , Jegorov A.
Published: November 2016

An efficient 2D 11B–11B ssNMR strategy for exploring the covalent assembly of boronic acid derivatives in the solid state is demonstrated.
Spectral pointillism of enhanced Raman scattering for accessing structural and conformational information on single protein
Authors: Clément Jean-Emmanuel , Leray Aymeric , Bouhelier Alexandre , Finot Eric
Published: November 2016

Temporal fluctuations of surface enhanced Raman spectra stem from single protein subdomains providing access to structural and conformational information on protein.
Photo-catalyzed surface hydrolysis of iridium(iii) ions on semiconductors: a facile method for the preparation of semiconductor/IrOx composite photoanodes toward oxygen evolution reaction
Authors: Wu Qingyong , Xu Di , Xue Ning , Liu Tengyi , Xiang Min , Diao Peng
Published: November 2016

Surface hydrolysis of Ir3+ induced by photo-generated holes on n-type semiconductors was developed to prepare semiconductor/IrOx composites for water splitting.
Self-assembling, reactivity and molecular dynamics of fullerenol nanoparticles
Authors: Vraneš Milan , Borišev Ivana , Tot Aleksandar , Armaković Stevan , Armaković Sanja , Jović Danica , Gadžurić Slobodan , Djordjevic Aleksandar
Published: November 2016

Fullerenol nanoparticles show intriguing behaviour concerning their self-assembling at different temperatures and concentrations and as such are promising potential agents for nanodrug delivery.
The structure and volume phase transition behavior of poly(N-vinylcaprolactam)-based hybrid microgels containing carbon nanodots
Authors: Sun Wenhui , Wu Peiyi
Published: November 2016

A schematic illustration of the preparation of P(VCL-co-VIM)/PCND microgels containing different amounts of PCNDs.
Size-controlled growth and antibacterial mechanism for Cu:C nanocomposite thin films
Authors: Javid Amjed , Kumar Manish , Yoon Seokyoung , Lee Jung Heon , Han Jeon Geon
Published: November 2016

Plasma energy induced size reduction of Cu nanoparticles (at fixed volume fraction) in C matrix demonstrated effective antibacterial activity.
Exploration of hydrogen bond networks and potential energy surfaces of methanol clusters using a two-stage clustering algorithm
Authors: Hsu Po-Jen , Ho Kun-Lin , Lin Sheng-Hsien , Kuo Jer-Lai
Published: November 2016

A two-stage algorithm based both on the similarity in shape and hydrogen bond network is developed to explore the potential energy surface of methanol clusters.
A heat capacity model of T3/2 dependence for quantum dots
Authors: Roslee Amirul Edham , Muzakir Saifful Kamaluddin , Ismail Jamil , Yusoff Mashitah M. , Jose Rajan
Published: November 2016

Quantum dots show a T3/2 dependence on heat capacity, while bulk solids show the Debye T3 dependence.
Improving the charge carrier transport of organic solar cells by incorporating a deep energy level molecule
Authors: Liu Chunyu , Li Zhiqi , Zhang Zhihui , Zhang Xinyuan , Shen Liang , Guo Wenbin , Zhang Liu , Long Yongbing , Ruan Shengping
Published: November 2016

A p-type F4-TCNQ molecule was incorporated into the P3HT/ICBA active layer to enhance the device performance of polymer solar cells from 4.50% to 5.83%.
Phase specific dispersion of functional nanoparticles in soft nanocomposites resulting in enhanced electromagnetic screening ability dominated by absorption
Authors: Menon Aishwarya V. , Madras Giridhar , Bose Suryasarathi
Published: November 2016

Phase specific localisation of MWNTs and magnetic FeNi alloy particles resulted in significant electromagnetic (EM) shielding effectiveness in binary co-continuous blends of PVDF and SMA.
An atlas of endohedral Sc2S cluster fullerenes
Authors: Gan Li-Hua , Wu Rui , Tian Jian-Lei , Fowler Patrick W.
Published: November 2016

Low-energy Sc2S@Cnisomers are connected by an intricate web of Stone–Wales isomerization and Endo–Kroto C2insertions, giving clues to their formation.
“Energy Relay Center” for doped mechanoluminescence materials: a case study on Cu-doped and Mn-doped CaZnOS
Authors: Huang Bolong , Peng Dengfeng , Pan Caofeng
Published: November 2016

Schematic for reversible and irreversible mechanical quenching, as well as enhanced luminescence from mechanical loading.
Controllable self-catalytic fabrication of carbon nanomaterials mediated by a nickel metal organic framework
Authors: Zou Fang , Chao Song L. , Wang Yu X. , Wang Yan L. , Guan Qing X. , Li Wei
Published: November 2016

We present a self-catalytic and controllable strategy for the fabrication of different morphologies and species of carbon nanomaterials via a nickel MOF as the precursor.
Hypoaeration of activated sludge to reduce energy requirements at distributed reclaimed water plants: studies at bench and pilot scales
Authors: Ramey Dotti F. , Munakata-Marr Junko , Cath Tzahi Y.
Published: November 2016

Hypoaerobic treatment in an SBR produces effluent quality equal to a standard aeration treatment with 27% less blower energy use.
Semiempirical modeling of electrochemical charge transfer
Authors: Gieseking Rebecca L. , Ratner Mark A. , Schatz George C.
Published: November 2016

Nanoelectrochemical experiments using detection based on tip enhanced Raman spectroscopy (TERS) show a broad distribution of single-molecule formal potentials E°′ for large π-conjugated molecules; theoretical studies are needed to understand the origins of this distribution. In this paper, we present a theoretical approach to determine E°′ for electrochemical reactions involving a single molecule interacting with an electrode represented as a metal nanocluster and apply this method to the Ag20–pyridine system. The theory is based on the semiempirical INDO electronic structure approach, together with the COSMO solvation model and an approach for tuning the Fermi energy, in which the silver atomic orbital energies are varied until the ground singlet state of Ag20–pyridine matches the lowest triplet energy, corresponding to electron transfer from the metal cluster to pyridine. Based on this theory, we find that the variation of E°′ with the structure of the Ag20–pyridine system is only weakly correlated with changes in either the ground-state interaction energy or the charge-transfer excited-state energies at zero applied potential, which shows the importance of calculations that include an applied potential in determining the variation of formal potential with geometry. Factors which determine E°′ include wavefunction overlap for geometries when pyridine is close to the surface, and electrostatics when the molecule-cluster separation is large.
A deeper shade of green: inspiring sustainable drug manufacturing
Authors: Roschangar Frank , Colberg Juan , Dunn Peter J. , Gallou Fabrice , Hayler John D. , Koenig Stefan G. , Kopach Michael E. , Leahy David K. , Mergelsberg Ingrid , Tucker John L. , Sheldon Roger A. , Senanayake Chris H.
Published: November 2016

Green and sustainable drug manufacturing goes hand in hand with forward-looking visions seeking to balance the long-term sustainability of business, society, and the environment.
Effect of small molecules on cell reprogramming
Authors: Baranek M. , Belter A. , Naskręt-Barciszewska M. Z. , Stobiecki M. , Markiewicz W. T. , Barciszewski J.
Published: November 2016

Small molecules cause pluripotency induction through epigenetic changes such as DNA methylation, histone modifications, RNA noncoding and chromatin remodeling.
Polyureas derived from CO2 and diamines: highly efficient catalysts for C–H arylation of benzene
Authors: Liu Zhenghui , Yang Zhenzhen , Hao Leiduan , Liu Xinwei , Zhang Hongye , Yu Bo , Liu Zhimin
Published: November 2016

Heterogeneous polyureas were effective for C–H arylation of benzene in the presence of t-BuOK, producing biaryl products in high yields up to 97%.
Natural products as mediators of disease
Authors: Garg Neha , Luzzatto-Knaan Tal , Melnik Alexey V. , Caraballo-Rodríguez Andrés Mauricio , Floros Dimitrios J. , Petras Daniel , Gregor Rachel , Dorrestein Pieter C. , Phelan Vanessa V.
Published: November 2016

The potential effect of microbiome-derived specialized metabolites on human health provides new and exciting avenues for natural product research.
Synthesis and biological evaluation of simplified pironetin analogues with modifications in the side chain and the lactone ring
Authors: Roldán Steven , Cardona Adrià , Conesa Laura , Murga Juan , Falomir Eva , Carda Miguel , Marco J. Alberto
Published: November 2016

The stereoselective syntheses and the biological evaluation of several structurally modified pironetin analogues are discussed. Like the parent compound, some of these analogues have found to be cytotoxic. However, and unlike pironetin, they do not interact with tubulin.
Silver-catalyzed C2-selective direct alkylation of heteroarenes with tertiary cycloalkanols
Authors: Lu Shi-Chao , Li Hong-Shuang , Xu Shu , Duan Gui-Yun
Published: November 2016

A silver-catalyzed regioselective C2-alkylation of heteroarenes with primary radicals produced by tertiary cycloalkanols was developed.
Total synthesis and confirmation of the revised structures of jiangrines A, C and D
Authors: Zhang Zhijiang , Liu Bo
Published: November 2016

The first total synthesis and structural revision of jiangrines A, C and D were achieved in seven steps.
Pd-mediated cross-coupling of C-17 lithiated androst-16-en-3-ol – access to functionalized arylated steroid derivatives
Authors: Koch Vanessa , Bräse Stefan
Published: November 2016

Herein, we report on Pd-mediated cross-coupling of vinyllithium steroids and aryl bromides to introduce various substituted aryls at C-17 of steroidal frameworks based on the structure ofepi-androsterone.
Synthesis and characterization of g-C3N4 nanosheet modified polyamide nanofiltration membranes with good permeation and antifouling properties
Authors: Chen Jianxin , Li Zhiyuan , Wang Chongbin , Wu Hong , Liu Gang
Published: November 2016

Compared with pristine membrane, the properties of water flux and antifouling were improved distinctly.
Fabrication of flame retardant coating on cotton fabric by alternate assembly of exfoliated layered double hydroxides and alginate
Authors: Pan Haifeng , Wang Wei , Shen Qi , Pan Ying , Song Lei , Hu Yuan , Lu Yushi
Published: November 2016

In our current work, a layer-by-layer flame retardant coating, assembled from MgAl layered double hydroxides (MgAl-LDH) and alginate, was firstly fabricated onto the surface of cotton fabric for the purpose of reducing its flammability.
Stress memory materials and their fundamental platform
Authors: Hu Jinlian , Zhu Shanshan , Young Robert J. , Cai Ziqing , Li Liangbin , Han Jianping , Pan Ning
Published: November 2016

Smart materials for stress applications are both sought after in the industry and are also of academic interest.
Solvent-free hierarchization of zeolites by carbochlorination
Authors: Nichterwitz Martin , Grätz Sven , Nickel Winfried , Borchardt Lars
Published: November 2016

Carbochlorination, a solvent-free top-down process, is a novel pathway for the hierarchization of zeolites.
Self-cleaning antireflective coating with a hierarchical texture for light trapping in micromorph solar cells
Authors: Liu Daiming , Wang Qingkang , Shen Wenfei , Wang Danyan
Published: November 2016

Surface texture plays a particularly important role in surface behaviors.
Urea, a true uremic toxin: the empire strikes back
Authors: Lau Wei Ling , Vaziri Nosratola D.
Published: November 2016

Blood levels of urea rise with progressive decline in kidney function. Older studies examining acute urea infusion suggested that urea was well-tolerated at levels 8–10× above normal values. More recent in vitro and in vivo work argue the opposite and demonstrate both direct and indirect toxicities of urea, which probably promote the premature aging phenotype that is pervasive in chronic kidney disease (CKD). Elevated urea at concentrations typically encountered in uremic patients induces disintegration of the gut epithelial barrier, leading to translocation of bacterial toxins into the bloodstream and systemic inflammation. Urea induces apoptosis of vascular smooth muscle cells as well as endothelial dysfunction, thus directly promoting cardiovascular disease. Further, urea stimulates oxidative stress and dysfunction in adipocytes, leading to insulin resistance. Finally, there are widespread indirect effects of elevated urea as a result of the carbamylation reaction, where isocyanic acid (a product of urea catabolism) alters the structure and function of proteins in the body. Carbamylation has been linked with renal fibrosis, atherosclerosis and anaemia. In summary, urea is a re-emerging Dark Force in CKD pathophysiology. Trials examining low protein diet to minimize accumulation of urea and other toxins suggest a clinical benefit in terms of slowing progression of CKD.
Finite‐time robust fault‐tolerant control against actuator faults and saturations
Authors: Jin Xiao‐Zheng , He Yi‐Gang , He You‐Guo
Published: November 2016

The finite‐time robust fault‐tolerant control problem is addressed for a class of perturbed linear systems with actuator faults and input amplitude saturations. A compensation control strategy is proposed to eliminate the effects of actuator faults and non‐linear disturbance‐like inputs within a finite‐time, as well as to ensure the control inputs be limited within a desired constraint. Based on Lyapunov stability theory, it is shown that system states can converge to a small region in the cases of actuator faults and saturations by choosing suitable control parameters. Some relationships among convergence bounds, actuator faults and amplitude limits, as well as the control parameters are studied deeply and illustrated explicitly with formulas. Simulations of a linearised F‐18 longitudinal dynamical control model are given to verify the effectiveness of the proposed method.
Double Crush Syndrome of the Median Nerve: A Literature Review
Authors: Magalhães Marcelo , Correia Alice , da Cruz Emannuelly , Santos Fernanda , Filho José , Lourdes Lorena , Ferreira Luísa , de Quadros Synara
Published: November 2016

Double crush syndrome (DCS) is defined as the compressive involvement of the same peripheral nerve in different segments. When this syndrome affects the median nerve, a proximal compression of a spinal nerve that will constitute this structure (often the spinal nerve at the C6 vertebra) is usually noted at the cervical spine level as a herniated disc and as a distal compression at the level of the carpal tunnel. Epidemiological data on median nerve compromise by DCS are still very scarce in the medical literature. The diagnosis can be inferred by symptoms and signs occurring proximally and distally in the arm, as well as by alterations revealed by upper limb electromyography and neuroimaging studies, such as magnetic resonance imaging (MRI) of the cervical spine. Nowadays, information on which compressed neuroanatomical point should be initially addressed still depends on further studies. Limited data infer that these patients, when submitted to surgical treatment in only one of the median nerve compression points, evolve with worse functional outcomes than the surgically-treated group with carpal tunnel syndrome without DCS.
Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation
Authors: Šarić Anđela , Michaels Thomas C. T. , Zaccone Alessio , Knowles Tuomas P. J. , Frenkel Daan
Published: November 2016

Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that has broad implications in many research areas ranging from medicine to nanotechnology. As such, spontaneous nucleation of protein fibrils has received much attention in recent years with many theoretical and experimental studies focussing on the underlying physical principles. In this paper we make a step forward in this direction and explore the early time behaviour of filamentous protein growth in the context of nucleation theory. We first provide an overview of the thermodynamics and kinetics of spontaneous nucleation of protein filaments in the presence of one relevant degree of freedom, namely the cluster size. In this case, we review how key kinetic observables, such as the reaction order of spontaneous nucleation, are directly related to the physical size of the critical nucleus. We then focus on the increasingly prominent case of filament nucleation that includes a conformational conversion of the nucleating building-block as an additional slow step in the nucleation process. Using computer simulations, we study the concentration dependence of the nucleation rate. We find that, under these circumstances, the reaction order of spontaneous nucleation with respect to the free monomer does no longer relate to the overall physical size of the nucleating aggregate but rather to the portion of the aggregate that actively participates in the conformational conversion. Our results thus provide a novel interpretation of the common kinetic descriptors of protein filament formation, including the reaction order of the nucleation step or the scaling exponent of lag times, and put into perspective current theoretical descriptions of protein aggregation.
Control of oscillations in vibration machines: Start up and passage through resonance
Authors: Fradkov A. , Gorlatov D. , Tomchina O. , Tomchin D.
Published: November 2016

Control of oscillations in mechanical systems in the start-up and passage through resonance modes is studied. In both cases, the control algorithm is based on the speed-gradient method with energy-based goal functions. It is shown that for Hamiltonian 1-degree of freedom (DOF) systems, it is generically possible to move the system from any initial state to any final state by means of a controlling force of arbitrarily small intensity. Controlled passage through resonance is studied for a 5-DOF vibration machine taking friction into account. It is shown by simulation that applying feedback control makes passage through lower resonance feasible with smaller control intensity compared with passage through resonance under constant control torque. The specific feature of this paper is consideration of the case when constant control torques do not allow the rotors even to start rotation. Applying feedback control allows rotors to overcome gravity and to start rotation. Another key novelty of this paper is comparison of the results obtained from the simulation with the experimental results obtained from the two-rotor laboratory mechatronic stand. It appears that most results are qualitatively the same, which confirms the adequacy of the model.
Detailed crystallographic analysis of the ice VI to ice XV hydrogen ordering phase transition
Authors: Salzmann Christoph G. , Slater Ben , Radaelli Paolo G. , Finney John L. , Shephard Jacob J. , Rosillo-Lopez Martin , Hindley James
Published: November 2016

The D2O ice VI to ice XV hydrogen ordering phase transition at ambient pressure is investigated in detail with neutron diffraction. The lattice constants are found to be sensitive indicators for hydrogen ordering. The a and b lattice constants contract whereas a pronounced expansion in c is found upon hydrogen ordering. Overall, the hydrogen ordering transition goes along with a small increase in volume, which explains why the phase transition is more difficult to observe upon cooling under pressure. Slow-cooling ice VI at 1.4 GPa gives essentially fully hydrogen-disordered ice VI. Consistent with earlier studies, the ice XV obtained after slow-cooling at ambient pressure is best described with P-1 space group symmetry. Using a new modelling approach, we achieve the atomistic reconstruction of a supercell structure that is consistent with the average partially ordered structure derived from Rietveld refinements. This shows that C-type networks are most prevalent in ice XV, but other structural motifs outside of the classifications of the fully hydrogen-ordered networks are identified as well. The recently proposed Pmmn structural model for ice XV is found to be incompatible with our diffraction data, and we argue that only structural models that are capable of describing full hydrogen order should be used.
Precision measurement of the rotational energy-level structure of the three-electron molecule He2+
Authors: Semeria Luca , Jansen Paul , Merkt Frédéric
Published: November 2016

The term values of all rotational levels of the 4He2+ X+ 2Σu+ (ν+=0) ground vibronic state with rotational quantum number N+ ≤ 19 have been determined with an accuracy of 8 × 10−4 cm−1 (∼25 MHz) by multichannel-quantum-defect-theory-assisted Rydberg spectroscopy of metastable He2∗. Comparison of these term values with term values recently calculated ab initio by Tung et al. [J. Chem. Phys. 136, 104309 (2012)] reveals discrepancies that rapidly increase with increasing rotational quantum number and reach values of 0.07 cm−1 (∼2.1 GHz) at N+ = 19.
Bohm criterion in dusty plasmas with two species of positive ions and non-thermal electrons
Authors: Fouial N. , Tahraoui A. , Annou R.
Published: November 2016

Bohm criterion is revisited in the framework of a one-dimensional stationary and unmagnetized low-pressure argon and helium plasma mixture containing non-thermal electrons and dust grains model. Dust grains, electron non-thermality, and ions density ratio effects on Bohm velocities along with dust grain charge number |Φd0|, are investigated. It is revealed that Bohm velocities are highly correlated, with their profiles exhibiting a moving peak. Mixing the two gases allowed the appearance of subsonic (argon) as well as supersonic (helium) Bohm velocities. The present model may be generalized to many ion species plasmas.
Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics
Authors: Nandi Prithwish K. , Futera Zdenek , English Niall J.
Published: November 2016

Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ∼220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical transition at a lower temperature (∼200 K) vis-à-vis the zero-field case (∼220 K).
Lagrangian filtered density function for LES-based stochastic modelling of turbulent particle-laden flows
Authors: Innocenti Alessio , Marchioli Cristian , Chibbaro Sergio
Published: November 2016

The Eulerian-Lagrangian approach based on Large-Eddy Simulation (LES) is one of the most promising and viable numerical tools to study particle-laden turbulent flows, when the computational cost of Direct Numerical Simulation (DNS) becomes too expensive. The applicability of this approach is however limited if the effects of the Sub-Grid Scales (SGSs) of the flow on particle dynamics are neglected. In this paper, we propose to take these effects into account by means of a Lagrangian stochastic SGS model for the equations of particle motion. The model extends to particle-laden flows the velocity-filtered density function method originally developed for reactive flows. The underlying filtered density function is simulated through a Lagrangian Monte Carlo procedure that solves a set of Stochastic Differential Equations (SDEs) along individual particle trajectories. The resulting model is tested for the reference case of turbulent channel flow, using a hybrid algorithm in which the fluid velocity field is provided by LES and then used to advance the SDEs in time. The model consistency is assessed in the limit of particles with zero inertia, when “duplicate fields” are available from both the Eulerian LES and the Lagrangian tracking. Tests with inertial particles were performed to examine the capability of the model to capture the particle preferential concentration and near-wall segregation. Upon comparison with DNS-based statistics, our results show improved accuracy and considerably reduced errors with respect to the case in which no SGS model is used in the equations of particle motion.
Short- and long-range corrected hybrid density functionals with the D3 dispersion corrections
Authors: Wang Chih-Wei , Hui Kerwin , Chai Jeng-Da
Published: November 2016

We propose a short- and long-range corrected (SLC) hybrid scheme employing 100% Hartree-Fock exchange at both zero and infinite interelectronic distances, wherein three SLC hybrid density functionals with the D3 dispersion corrections (SLC-LDA-D3, SLC-PBE-D3, and SLC-B97-D3) are developed. SLC-PBE-D3 and SLC-B97-D3 are shown to be accurate for a very diverse range of applications, such as core ionization and excitation energies, thermochemistry, kinetics, noncovalent interactions, dissociation of symmetric radical cations, vertical ionization potentials, vertical electron affinities, fundamental gaps, and valence, Rydberg, and long-range charge-transfer excitation energies. Relative to ωB97X-D, SLC-B97-D3 provides significant improvement for core ionization and excitation energies and noticeable improvement for the self-interaction, asymptote, energy-gap, and charge-transfer problems, while performing similarly for thermochemistry, kinetics, and noncovalent interactions.
Can dispersion corrections annihilate the dispersion-driven nano-aggregation of non-polar groups? An ab initio molecular dynamics study of ionic liquid systems
Authors: Firaha Dzmitry S. , Thomas Martin , Hollóczki Oldamur , Korth Martin , Kirchner Barbara
Published: November 2016

In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.
Identifying barriers to charge-carriers in the bulk and surface regions of Cu2ZnSnS4 nanocrystal films by x-ray absorption fine structures (XAFSs)
Authors: Turnbull Matthew J. , Vaccarello Daniel , Yiu Yun Mui , Sham Tsun-Kong , Ding Zhifeng
Published: November 2016

Solar cell performance is most affected by the quality of the light absorber layer. For thin-film devices, this becomes a two-fold problem of maintaining a low-cost design with well-ordered nanocrystal (NC) structure. The use of Cu2ZnSnS4 (CZTS) NCs as the light absorber films forms an ideal low-cost design, but the quaternary structure makes it difficult to maintain a well-ordered layer without the use of high-temperature treatments. There is little understanding of how CZTS NC structures affect the photoconversion efficiency, the charge-carriers, and therefore the performance of the device manufactured from it. To examine these relationships, the measured photoresponse from the photo-generation of charge-carrier electron-hole pairs was compared against the crystal structure, as short-range and long-range crystal orders for the films. The photoresponse simplifies the electronic properties into three basic steps that can be associated with changes in energy levels within the band structure. These changes result in the formation of barriers to charge-carrier flow. The extent of these barriers was determined using synchrotron-based X-ray absorbance fine structure to probe the individual metal centers in the film, and comparing these to molecular simulations of the ideal extended x-ray absorbance fine structure scattering. This allowed for the quantification of bond lengths, and thus an interpretation of the distortions in the crystal lattice. The various characteristics of the photoresponse were then correlated to the crystallographic order and used to gain physical insight into barriers to charge-carriers in the bulk and surface regions of CZTS films.
Molecular dynamics study of nano-porous materials—Enhancement of mobility of Li ions in lithium disilicate
Authors: Habasaki Junko
Published: November 2016

In several nano-porous materials and their composites, enhancement of ionic conductivity has been reported and several mechanisms having different origins have been proposed so far. In the present work, ionic motion of Li ions in porous lithium disilicates is examined by molecular dynamics simulation in the constant volume conditions and the enhancement of the dynamics is predicted. Structures and dynamics of ions in a nano-porous system were characterized and visualized to clarify the mechanism of the enhancement. The diffusion coefficient of Li ions has shown the maximum in the medium density (and porosity) region, and near the maximum, shortening of the nearly constant loss region in the mean squared displacement of ions as well as changes of the structures of the coordination polyhedra, LiOx is found. It suggests that the loosening of the cage, which increases the jump rate of ions, is an origin of the enhancement. When larger (but still in a nano-scale) voids are formed with a further decrease of density, more tight cages are reconstructed and the diffusion coefficient decreases again. These behaviors are closely related to the residual stress in the system. It is noteworthy that the explanation is not based on the percolation of the path only or formation of boundaries, although the former also affects the dynamics.
Tunneling modulation of a quantum-well transistor laser
Authors: Feng M. , Qiu J. , Wang C. Y. , Holonyak N.
Published: November 2016

Different than the Bardeen and Brattain transistor (1947) with the current gain depending on the ratio of the base carrier spontaneous recombination lifetime to the emitter-collector transit time, the Feng and Holonyak transistor laser current gain depends upon the base electron-hole (e-h) stimulated recombination, the base dielectric relaxation transport, and the collector stimulated tunneling. For the n-p-n transistor laser tunneling operation, the electron–hole pairs are generated at the collector junction under the influence of intra-cavity photon-assisted tunneling, with electrons drifting to the collector and holes drifting to the base. The excess charge in the base lowers the emitter junction energy barrier, allowing emitter electron injection into the base and satisfying charge neutrality via base dielectric relaxation transport (∼femtoseconds). The excess electrons near the collector junction undergo stimulated recombination at the base quantum-well or transport to the collector, thus supporting tunneling current amplification and optical modulation of the transistor laser.
Spatio-temporal optimization of a laser produced Al-plasma: Generation of highly ionized species
Authors: Smijesh N. , H. Rao Kavya , Klemke N. , Philip R. , Litvinyuk I. V. , Sang R. T.
Published: November 2016

Laser produced plasmas are transient in nature, and their properties, which depend on the laser parameters as well as the material properties and the irradiation conditions, can be tailored for different applications. Highly ionized Al plasmas generated using 7 ns and negatively chirped 60 ps pulses are optimized for the purpose of generating Al IV and Al III, respectively. The plasma is optimized spatio-temporally for Al IV or Al III with irradiation energy as the control parameter using time-resolved optical emission spectroscopy. Plasmas attuned for higher charged states could be utilized as a good alternative source for the generation of high order harmonics.
Polymer extension under flow: Some statistical properties of the work distribution function
Authors: Ghosal Aishani , Cherayil Binny J.
Published: November 2016

In an extension of earlier studies from this group on the application of the Jarzynski equality to the determination of the elastic properties of a finitely extensible Rouse model of polymers under flow [A. Ghosal and B. J. Cherayil, J. Chem. Phys. 144, 214902 (2016)], we derive several new theoretical results in this paper on the nature of the distribution function P(w) that governs the long-time limit t>>1 of the fluctuations in the work w performed by the polymer during flow-induced stretching. In particular, we show that an expression for the average of the nth power of the work, ⟨wn(t)⟩, can be obtained in closed form in this limit, making it possible to exactly calculate three important statistical measures of P(w): the mean μ, the skewness γ1, and the kurtosis γ2 (apart from the variance σ2). We find, for instance, that to leading order in t, the mean grows linearly with t at a constant value of the dimensionless flow rate Wi and that the slope of the μ−t curve increases with increasing Wi. These observations are in complete qualitative agreement with data from Brownian dynamics simulations of flow-driven double-stranded DNA by Latinwo and Schroeder [Macromolecules 46, 8345 (2013)]. We also find that the skewness γ1 exhibits an interesting inversion of sign as a function of Wi, starting off at positive values at low Wi and changing to negative values at larger Wi. The inversion takes place in the vicinity of what we interpret as a coil-stretch transition. Again, the finding exactly reproduces behavior seen in other numerical and experimental work by the above group Latinwo et al. [J. Chem. Phys. 141, 174903 (2014)]. Additionally, at essentially the same value of Wi at which this sign inversion takes place, we observe that the kurtosis reaches a minimum, close to 1, providing further evidence of the existence of a coil-stretch transition at this location. Our calculations reproduce another numerical finding: a power law dependence on Wi of the rate of work production that is characterized by two distinct regimes, one lying below the putative coil-stretch transition, where the exponent assumes one value, and the other above, where it assumes a second.
Simultaneous simulation of microhollow cathode discharge and its sustained discharge with split third electrodes
Authors: Das Ratan Kumar , Shin Jichul
Published: November 2016

Simultaneous simulation of microhollow cathode discharge (MHCD) and its sustained discharge in argon is attempted with a two dimensional, self-consistent, continuum fluid model. Bell-shape enlarged volume discharge is simulated with a single third electrode, and further expansion in the discharge volume of the sustained discharge is demonstrated with split third electrodes. In the sustained discharge region, monomer metastable is a dominant species and the number density of dimer ions is higher than that of monomer ions. The expansion in the sustained discharge does not alter the characteristics of the MHCD observed with a single electrode. But electrons and metastables in the sustained discharge region are expanded when the third electrodes are turned on. The simulated distribution of metastable species shows a rake-like structure that is also observed in experiments. As the pressure increases, a ratio of dimer-to-monomer metastable number density increases.