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free-energy principle

Sergey Kravtsov, Paul Roebber, Vytaras Brazauskas
The most comprehensive continuous-coverage modern climatic data sets, known as reanalyses, come from combining state-of-the-art numerical weather prediction (NWP) models with diverse available observations. These reanalysis products estimate the path of climate evolution that actually happened, and their use in a probabilistic context-for example, to document trends in extreme events in response to climate change-is, therefore, limited. Free runs of NWP models without data assimilation can in principle be used for the latter purpose, but such simulations are computationally expensive and are prone to systematic biases...
October 17, 2017: Scientific Data
Guoqing Zhao, Myungkwan Song, Hee-Suk Chung, Soo Min Kim, Sang-Geul Lee, Jong-Seong Bae, Tae Sung Bae, Donghwan Kim, Gun-Hwan Lee, Seung Zeon Han, Hae-Seok Lee, Eun-Ae Choi, Jungheum Yun
The development of highly efficient flexible transparent conducting electrodes (FTCEs) supported on polymer substrates is of great importance to the realization of portable and bendable photovoltaic devices. Highly conductive, low-cost Cu has attracted attention as a promising alternative for replacing expensive indium tin oxide (ITO) and Ag. However, highly efficient, Cu-based FTCEs are currently unavailable because of the absence of an efficient means of attaining an atomically thin, completely continuous Cu film that simultaneously exhibits enhanced optical transmittance and electrical conductivity...
October 17, 2017: ACS Applied Materials & Interfaces
Patrick Connolly, Vasi van Deventer
The present paper argues that a systems theory epistemology (and particularly the notion of hierarchical recursive organization) provides the critical theoretical context within which the significance of Friston's (2010a) Free Energy Principle (FEP) for both evolution and psychoanalysis is best understood. Within this perspective, the FEP occupies a particular level of the hierarchical organization of the organism, which is the level of biological self-organization. This form of biological self-organization is in turn understood as foundational and pervasive to the higher levels of organization of the human organism that are of interest to both neuroscience as well as psychoanalysis...
2017: Frontiers in Psychology
Li Gong, Jie-Jie Chen, Yang Mu
Converting CO2 into valuable chemicals and fuels is one of the most practical routes for reducing CO2 emissions while fossil fuels continue to dominate the energy sector. Noble-metal-free NiFe bimetal nanoparticles have shown good catalytic activity in CO2 conversion. Herein we theoretically evaluated the catalytic performance and possible mechanisms of NiFe-based nanoclusters for hydrogenating CO2 to form formic acid and CO through bicarbonate by using a periodic and self-consistent density functional theory (DFT) simulation...
October 16, 2017: Physical Chemistry Chemical Physics: PCCP
Maxwell James Désormeau Ramstead, Paul Benjamin Badcock, Karl John Friston
The free-energy principle (FEP) is a formal model of neuronal processes that is widely recognised in neuroscience as a unifying theory of the brain and biobehaviour. More recently, however, it has been extended beyond the brain to explain the dynamics of living systems, and their unique capacity to avoid decay. The aim of this review is to synthesise these advances with a meta-theoretical ontology of biological systems called variational neuroethology, which integrates the FEP with Tinbergen's four research questions to explain biological systems across spatial and temporal scales...
September 20, 2017: Physics of Life Reviews
Elham Gharibshahi, Elias Saion, Ahmadreza Ashraf, Leila Gharibshahi
Gamma radiolytic synthesis was used to produce size-controlled spherical platinum nanoparticles from an aqueous solution containing platinum tetraammine and polyvinyl pyrrolidone. The structural characterizations were performed using X-ray diffraction, and transmission electron microscopy. The transmission electron microscopy was used to determine the average particle diameter, which decreased from 4.4nm at 80kGy to 2.8nm at 120kGy. The UV-visible absorption spectrum was measured and found that platinum nanoparticles exhibit two steady absorption maxima in UV regions due to plasmonic excitation of conduction electrons, which blue shifted to lower wavelengths with a decrease in particle size...
September 9, 2017: Applied Radiation and Isotopes
Wei Hu, Lin Lin, Ruiqi Zhang, Chao Yang, Jinlong Yang
Two-dimensional phosphorene with desirable optoelectronic properties (ideal band gap, high carrier mobility and strong visible light absorption) is a promising metal-free photocatalyst for water splitting. However, the band edge positions of the valence band maximum (VBM) and conduction band maximum (CBM) of a phosphorene are higher than the redox potentials in photocatalytic water splitting reactions. Thus phosphorene can only be used as the photocathode for hydrogen evolution reaction as a low-efficiency visible-light- driven photocatalyst for hydrogen production in solar water splitting cells...
October 13, 2017: Journal of the American Chemical Society
Song Ling Wang, Xin Luo, Xiong Zhou, Ye Zhu, Xiao Chi, Wei Chen, Kai Wu, Zheng Liu, Su Ying Quek, Guoqin Xu
The synthesis of free-standing two-dimensional titania (2-D TiO2) with a reduced band gap presents complex chal-lenges to synthetic chemists. Here, we report a free-standing 2-D TiO2 sheet synthesized via a one-step solvothermal methodology, with a measured optical onset at ~ 1.84 eV. Using first principles calculations in combination with experiment, we propose that the as-formed 2-D TiO2 sheets are layers of the lepidocrocite TiO2 structure, but with large non-uniform strains consistent with its crumpled morphology...
October 11, 2017: Journal of the American Chemical Society
Émilie Bordes, Anabela J L Costa, Joanna Szala-Bilnik, Jean-Michel Andanson, José M S S Esperança, Margarida F Costa Gomes, José N Canongia Lopes, Agílio A H Pádua
The aim of this work is to understand the details of the interactions of ionic liquids with carbon nanomaterials (graphene and nanotubes) using polyaromatic compounds as model solutes. We have combined the measurements of thermodynamic quantities of solvation with molecular dynamics simulations to provide a microscopic view. The solubility of five polycyclic aromatic hydrocarbons (naphthalene, anthracene, phenanthrene, pyrene and coronene) was determined in seven ionic liquids ([C4C1im][C(CN)3], [C4C1pyrr][Ntf2], [C10C1im][Ntf2], [C2C1im][C(CN)3], [C2C1im][Ntf2], [C3C1pyrr][N(CN)2] and [C4C1im][N(CN)2]) at 298 K...
October 18, 2017: Physical Chemistry Chemical Physics: PCCP
Lifang Huang, Peijiang Liu, Zhanjiang Yuan, Tianshou Zhou, Jianshe Yu
From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption...
October 3, 2017: Scientific Reports
James K Baird, Joshua R Lang
Liquid mixtures, which have a phase diagram exhibiting a miscibility gap ending in a critical point of solution, have been used as solvents for chemical reactions. The reaction rate in the forward direction has often been observed to slow down as a function of temperature in the critical region. Theories based upon the Gibbs free energy of reaction as the driving force for chemical change have been invoked to explain this behavior. With the assumption that the reaction is proceeding under relaxation conditions, these theories expand the free energy in a Taylor series about the position of equilibrium...
October 13, 2017: Journal of Physical Chemistry. A
Priyanka Seth, Philipp Hansmann, Ambroise van Roekeghem, Loig Vaugier, Silke Biermann
The determination of the effective Coulomb interactions to be used in low-energy Hamiltonians for materials with strong electronic correlations remains one of the bottlenecks for parameter-free electronic structure calculations. We propose and benchmark a scheme for determining the effective local Coulomb interactions for charge-transfer oxides and related compounds. Intershell interactions between electrons in the correlated shell and ligand orbitals are taken into account in an effective manner, leading to a reduction of the effective local interactions on the correlated shell...
August 4, 2017: Physical Review Letters
Dragos Axinte, John Billingham, Aitor Bilbao Guillerna
We demonstrate that, despite differences in their nature, many energy beam controlled-depth machining processes (for example, waterjet, pulsed laser, focused ion beam) can be modeled using the same mathematical framework-a partial differential evolution equation that requires only simple calibrations to capture the physics of each process. The inverse problem can be solved efficiently through the numerical solution of the adjoint problem and leads to beam paths that generate prescribed three-dimensional features with minimal error...
September 2017: Science Advances
Benjamin Gonon, Aurelie Perveaux, Fabien Gatti, David Lauvergnat, Benjamin Lasorne
The primal definition of first-order non-adiabatic couplings among electronic states relies on the knowledge of how electronic wavefunctions vary with nuclear coordinates. However, the non-adiabatic coupling between two electronic states can be obtained in the vicinity of a conical intersection from energies only, as this vector spans the branching plane along which degeneracy is lifted to first order. The gradient difference and derivative coupling are responsible of the two-dimensional cusp of a conical intersection between both potential-energy surfaces and can be identified to the non-trivial eigenvectors of the second derivative of the square energy difference, as first pointed out in Köppel and Schubert [Mol...
September 21, 2017: Journal of Chemical Physics
Rosely Almeida, Amitava Banerjee, Sudip Chakraborty, Jailton Almeida, Rajeev Ahuja
First principles electronic structure calculations based on density functional theory (DFT) framework are performed to investigate hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) on two-dimensional Al2C monolayer. The monolayer is functionalized with several dopants and four prominent doping elements are nitrogen (N), phosphorous (P), boron (B) and sulphur (S). After determining the individual adsorption energy of hydrogen and oxygen on different functionalized Al2C monolayer, the adsorption free energies are predicted subsequently for each of the functionalized cases in order to predict which case of functionalization serves better for HER or OER...
September 19, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Laurentiu Spiridon, David D L Minh
Compared to fully flexible molecular dynamics, simulations of constrained systems can use larger time steps and focus kinetic energy on soft degrees of freedom. Achieving ergodic sampling from the Boltzmann distribution, however, has proven challenging. Using recent generalizations of the equipartition principle and Fixman potential, here we implement Hamiltonian Monte Carlo based on constrained molecular dynamics as a Gibbs sampling move. By mixing Hamiltonian Monte Carlo based on fully flexible and torsional dynamics, we are able to reproduce free energy landscapes of simple model systems and enhance sampling of macrocycles...
October 10, 2017: Journal of Chemical Theory and Computation
Donghui Wei, Xiaoqin Huang, Yan Qiao, Jingjing Rao, Lu Wang, Fei Liao, Chang-Guo Zhan
First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy calculations have been performed to uncover how uricase catalyzes metabolic reactions of uric acid (UA), demonstrating that the entire reaction process of UA in uricase consists of two stages-oxidation followed by hydration. The oxidation consists of four steps: (1) chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, which is different from the previously proposed electron-transfer mechanism that involves a dianion intermediate (UA(2-)) during the catalytic reaction process; (2) proton transfer to the O2(-) anion (radical); (3) diradical recombination to form a peroxo intermediate; (4) dissociation of H2O2 to generate the dehydrourate...
July 7, 2017: ACS Catalysis
Hai Zhang, Yahong Zhao, Zhengxiang Xia, Hongli Du, Yue Gao, Dan Xue, Zhenyu Zhu, Yifeng Chai
ETHNOPHARMACOLOGICAL RELEVANCE: Myocardial ischemia-reperfusion (I/R) injury is a serious injury that is resulted from the recovery of blood supply after myocardial ischemia. Yangxinshi tablet is a compound Chinese herbal preparation and often used to alleviate the myocardial ischemia in clinical, but its protective mechanism of anti-myocardial ischemia reperfusion injury remains unclear. The objective of this study was to evaluate the anti-I/R injury effect of Yangxinshi tablet on a myocardial I/R rat model and to identify serum biomarker metabolites associated with I/R based on ultra-high performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF/MS) metabolomic method, and explore the metabolic mechanism of anti-I/R injury of Yangxinshi tablet...
September 7, 2017: Journal of Ethnopharmacology
Peng Zhang, Jonathon L Yuly, Carolyn E Lubner, David W Mulder, Paul W King, John W Peters, David N Beratan
How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently...
September 6, 2017: Accounts of Chemical Research
Qingbo Wang, Chaoping Liang, Yongping Zheng, Nickolas Ashburn, Young Jun Oh, Fantai Kong, Chenxi Zhang, Yifan Nie, Jian Sun, Kaihua He, Yu Ye, Rong Chen, Bin Shan, Kyeongjae Cho
Transition metal (TM) modification is a common strategy for converting an earth-abundant mineral into a cost-effective catalyst for industrial applications. Among a variety of minerals, Al2SiO5, which has three phases, andalusite, sillimanite and kyanite, is emerging as a promising candidate for new catalyst development. In this paper, we use Mn to demonstrate the rationale of 3d TM doping at the Al sites in each of these three phases through first-principles calculations and the cluster expansion method. The results of cluster expansion show that Mn has a strong site preference for the six-coordinated Al octahedral chains in the andalusite and sillimanite phases, while distributing randomly in the kyanite phase...
September 20, 2017: Physical Chemistry Chemical Physics: PCCP
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