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free-energy principle

J Baumann, C Herzog, M Spanier, D Grötzsch, L Lühl, K Witte, A Jonas, S Günther, F Förste, R Hartmann, M Huth, D Kalok, D Steigenhöfer, M Krämer, T Holz, R Dietsch, L Strüder, B Kanngießer, I Mantouvalou
Grazing incidence and grazing emission X-ray fluorescence spectroscopy (GI/GE-XRF) are techniques that enable nondestructive, quantitative analysis of elemental depth profiles with a resolution in the nanometer regime. A laboratory setup for soft X-ray GEXRF measurements is presented. Reasonable measurement times could be achieved by combining a highly brilliant laser produced plasma (LPP) source with a scanning-free GEXRF setup, providing a large solid angle of detection. The detector, a pnCCD, was operated in a single photon counting mode in order to utilize its energy dispersive properties...
January 10, 2017: Analytical Chemistry
S Herminghaus, M G Mazza
The emergence of patterns and phase separation in many-body systems far from thermal equilibrium is discussed using the example of driven granular gases. It is shown that phase separation follows a similar mechanism as in the systems of active Brownian particles. Depending on the quantities chosen for observation, it may or may not be easy to find functionals analogous to the free energy in equilibrium statistical physics. We argue that although such functionals can always be derived from the dynamics, it is of only limited value for predicting relevant aspects of the nonequilibrium steady state of the system...
January 19, 2017: Soft Matter
Jing Yang, Mostafa Youssef, Bilge Yildiz
We present a multi-scale approach to predict equilibrium defect concentrations across oxide/oxide hetero-interfaces. There are three factors that need to be taken into account simultaneously for computing defect redistribution around the hetero-interfaces: the variation of local bonding environment at the interface as epitomized in defect segregation energies, the band offset at the interface, and the equilibration of the chemical potentials of species and electrons via ionic and electronic drift-diffusion fluxes...
January 19, 2017: Physical Chemistry Chemical Physics: PCCP
C Riek, P Sulzer, M Seeger, A S Moskalenko, G Burkard, D V Seletskiy, A Leitenstorfer
Squeezed states of electromagnetic radiation have quantum fluctuations below those of the vacuum field. They offer a unique resource for quantum information systems and precision metrology, including gravitational wave detectors, which require unprecedented sensitivity. Since the first experiments on this non-classical form of light, quantum analysis has been based on homodyning techniques and photon correlation measurements. These methods currently function in the visible to near-infrared and microwave spectral ranges...
January 18, 2017: Nature
Tim Oelze, Bernd Schütte, Maria Müller, Jan P Müller, Marek Wieland, Ulrike Frühling, Markus Drescher, Alaa Al-Shemmary, Torsten Golz, Nikola Stojanovic, Maria Krikunova
Irradiation of nanoscale clusters and large molecules with intense laser pulses transforms them into highly-excited non- equilibrium states. The dynamics of intense laser-cluster interaction is encoded in electron kinetic energy spectra, which contain signatures of direct photoelectron emission as well as emission of thermalized nanoplasma electrons. In this work we report on a so far not observed spectrally narrow bound state signature in the electron kinetic energy spectra from mixed Xe core - Ar shell clusters ionized by intense extreme-ultraviolet (XUV) pulses from a free-electron-laser...
January 18, 2017: Scientific Reports
Ana Rojas, Nika Maisuradze, Khatuna Kachlishvili, Harold A Scheraga, Gia G Maisuradze
Fibrils formed by the β-amyloid (Aβ) peptide play a central role in the development of Alzheimer's disease. In this study, the principles governing their growth and stability are investigated by analyzing canonical and replica-exchange molecular dynamics trajectories of Aβ(9-40) fibrils. In particular, an unstructured monomer was allowed to interact freely with an Aβ fibril template. Trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue and principal components, respectively, were analyzed...
January 18, 2017: ACS Chemical Neuroscience
Weitao Fu, Lingfeng Chen, Zhe Wang, Yanting Kang, Chao Wu, Qinqin Xia, Zhiguo Liu, Jianmin Zhou, Guang Liang, Yuepiao Cai
The activation and overexpression of fibroblast growth factor receptors (FGFRs) are highly correlated with a variety of cancers. Most small molecule inhibitors of FGFRs selectively target FGFR1-3, but not FGFR4. Hence, designing highly selective inhibitors towards FGFR4 remains a great challenge because FGFR4 and FGFR1 have a high sequence identity. Recently, two small molecule inhibitors of FGFRs, ponatinib and AZD4547, have attracted huge attention. Ponatinib, a type II inhibitor, has high affinity towards FGFR1/4 isoforms, but AZD4547, a type I inhibitor of FGFR1, displays much reduced inhibition toward FGFR4...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
Vivien Ainley, Matthew A J Apps, Aikaterini Fotopoulou, Manos Tsakiris
Individuals differ in their awareness of afferent information from within their bodies, which is typically assessed by a heartbeat perception measure of 'interoceptive accuracy' (IAcc). Neural and behavioural correlates of this trait have been investigated, but a theoretical explanation has yet to be presented. Building on recent models that describe interoception within the free energy/predictive coding framework, this paper applies similar principles to IAcc, proposing that individual differences in IAcc depend on 'precision' in interoceptive systems, i...
November 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Nikolai A Smirnov
The paper presents first-principles FP-LMTO calculations on the relative stability of $fcc$, $bcc$, $hcp$ and $dhcp$ gold under pressure. They were done in Local Density Approximation (LDA), as well as in Generalized Gradient Approximation (GGA) with and without spin-orbit interaction. Phonon spectra for the considered gold structures were obtained from LDA calculations within linear response theory and the contribution of lattice vibrations to the free energy of the system was determined in quasiharmonic approximation...
January 11, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Junhui Law, Ka Wai Kong, Ho-Yin Chan, Winston Sun, Wen Jung Li, Eric Boa Fung Chau, George Kak Man Chan
The development of a novel lead-free microelectromechanical-system (MEMS)-based atomizer using the principle of thermal bubble actuation is presented. It is a low-cost, lead-free design that is environmentally friendly and harmless to humans. It has been tested to be applicable over a wide range of fluid viscosities, ranging from 1 cP (e.g., water) to 200 cP (e.g., oil-like fluid) at room temperature, a range that is difficult to achieve using ordinary atomizers. The results demonstrate that the average power consumption of the atomizer is approximately 1 W with an atomization rate of 0...
January 11, 2017: Scientific Reports
Tuan Anh Pham, Yuan Ping, Giulia Galli
The generation of hydrogen from water and sunlight offers a promising approach for producing scalable and sustainable carbon-free energy. The key of a successful solar-to-fuel technology is the design of efficient, long-lasting and low-cost photoelectrochemical cells, which are responsible for absorbing sunlight and driving water splitting reactions. To this end, a detailed understanding and control of heterogeneous interfaces between photoabsorbers, electrolytes and catalysts present in photoelectrochemical cells is essential...
January 9, 2017: Nature Materials
C Lee, C Cottin-Bizonne, R Fulcrand, L Joly, C Ybert
The classical paradigm for osmotic transport has long related the induced-flow direction to the solute membrane interactions, with the low-to-high concentration flow a direct consequence of the solute rejection from the semipermeable membrane. In principle, the same was thought to occur for the newly demonstrated membrane-free osmotic transport named diffusio-osmosis. Using a recently proposed nanofluidic setup, we revisit this cornerstone of osmotic transport by studying the diffusio-osmotic flows generated at silica surfaces by either poly(ethylene)glycol polymers or ethanol molecules in aqueous solutions...
January 19, 2017: Journal of Physical Chemistry Letters
Chensheng Wu, Jonathan Ko, Christopher C Davis
The plenoptic sensor has been developed to sample complicated beam distortions produced by turbulence in the low atmosphere (deep turbulence or strong turbulence) with high density data samples. In contrast with the conventional Shack-Hartmann wavefront sensor, which utilizes all the pixels under each lenslet of a micro-lens array (MLA) to obtain one data sample indicating sub-aperture phase gradient and photon intensity, the plenoptic sensor uses each illuminated pixel (with significant pixel value) under each MLA lenslet as a data point for local phase gradient and intensity...
December 26, 2016: Optics Express
Ming Yan, Zheng-Qing Huang, Yu Zhang, Chun-Ran Chang
Dissociation of O2 into atomic oxygen is a significant route for O2 activation in metal-catalyzed oxidation reactions. In this study, we systematically investigated the mechanisms of O2 dissociation and the promoting role of water on nine transition metal (Co, Rh, Ir, Ni, Pd, Pt, Cu, Ag, and Au) surfaces. It was found that on clean metal surfaces, the dissociation of O2 was most favorable on Co(0001) and most difficult on Au(111), according to the free energy barriers of Co (0.03 eV) < Rh (0.20 eV) < Ni (0...
January 18, 2017: Physical Chemistry Chemical Physics: PCCP
Yiliang Liu, Yawen Hua, Anying Yan, Shuang Wu, Fanjie Kong
One-dimensional (1D) gold nanostructures have been extensively studied due to their potential applications in nanoelectronic devices. Using first-principles calculations, composites consisting of a well-defined linear Au n (n = 2-4) chain encapsulated in a (9,0) single-walled carbon nanotube (SWCNT) were studied. The translational energy barrier of a single Au atom in a (9,0) SWCNT was found to be 0.03 eV. This low barrier guaranteed the formation of Au n @ (9,0) SWCNT (n = 1-4) composites. Bond lengths, differential charge densities, and electronic band structures of the composites were studied...
January 2017: Journal of Molecular Modeling
Christopher Ian Cave-Ayland, Chris-Kriton Skylaris, Jonathan W Essex
Hybrid free energy methods allow estimation of free energy differences at the quantum mechanics (QM) level with high efficiency by performing sampling at the classical mechanics (MM) level. Various approaches to allow the calculation of QM corrections to classical free energies have been proposed. The single step free energy perturbation approach starts with a classically generated ensemble, a subset of structures of which are post-processed to obtain QM energies for use with the Zwanzig equation. This gives an estimate of the free energy difference associated with the change from an MM to a QM Hamiltonian...
December 28, 2016: Journal of Chemical Theory and Computation
Michael S Titus, Robert K Rhein, Peter B Wells, Philip C Dodge, Gopal Babu Viswanathan, Michael J Mills, Anton Van der Ven, Tresa M Pollock
It has long been known that solute segregation at crystalline defects can have profound effects on material properties. Nevertheless, quantifying the extent of solute segregation at nanoscale defects has proven challenging due to experimental limitations. A combined experimental and first-principles approach has been used to study solute segregation at extended intermetallic phases ranging from 4 to 35 atomic layers in thickness. Chemical mapping by both atom probe tomography and high-resolution scanning transmission electron microscopy demonstrates a markedly different composition for the 4-atomic-layer-thick phase, where segregation has occurred, compared to the approximately 35-atomic-layer-thick bulk phase of the same crystal structure...
December 2016: Science Advances
Simone Latini, Kirsten Trøstrup Winther, Thomas Olsen, Kristian S Thygesen
Van der Waals heterostructures (vdWH) provide an ideal playground for exploring light-matter interactions at the atomic scale. In particular, structures with a type-II band alignment can yield detailed insight into free carrier-to-photon conversion pro- cesses, which are central to e.g. solar cells and light emitting diodes. An important first step in describing such processes is to obtain the energies of the interlayer exciton states existing at the interface. Here we present a general first-principles method to compute the electronic quasi-particle (QP) band structure and excitonic binding en- ergies of incommensurate vdWHs...
December 27, 2016: Nano Letters
Parvathi Krishnakumar, Dilip Kumar Maity
A systematic theoretical study has been carried out on the effect of sequential addition of water molecules to neutral and mono positively charged acetic acid molecules by applying first principle based electronic structure theory. Geometry, dipole moment, and polarizability of hydrated clusters of neutral and mono positively charged acetic acid of the type CH3COOH·nH2O (n = 1-8) and [CH3COOH·nH2O](+) (n = 1, 2) are calculated at the ωB97X-D/aug-cc-pVDZ level of theory. Free energies of formation of the hydrated acid clusters, at different temperatures and pressures are determined...
January 19, 2017: Journal of Physical Chemistry. A
Teruo Hirakawa, Yuta Uramoto, Daisuke Mimura, Atsuya Takeda, Susumu Yanagisawa, Takashi Ikeda, Kouji Inagaki, Yoshitada Morikawa
We investigated the oxidative addition of PhX (X = Cl, Br) to a single Pd(0) atom or a PdX(-) complex in water using first-principles molecular dynamics simulations, with solvent H2O molecules explicitly included in the calculation models, to clarify the origin of the extremely high reactivity of a ligand-free Pd catalyst in an aqueous solution for the Suzuki-Miyaura reaction. The free-energy profiles are estimated using blue moon ensemble sampling to include the entropy effect in chemical reactions in a water solvent...
January 4, 2017: Journal of Physical Chemistry. B
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