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free-energy principle

Miguel A Caro, Olga Lopez-Acevedo, Tomi Laurila
We present a complete methodology to consistently estimate redox potentials strictly from first principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr(+2/+3), V(+2/+3), Ru(NH3)6(+2/+3), Sn(+2/+4), Cu(+1/+2), FcMeOH(0/+1) and Fe(+2/+3) (in aqueous solution) and Fc(0/+1) (in acetonitrile)...
July 17, 2017: Journal of Chemical Theory and Computation
Emiliana Fabbri, Maarten Nachtegaal, Tobias Binninger, Xi Cheng, Bae-Jung Kim, Julien Durst, Francesco Bozza, Thomas Graule, Robin Schäublin, Luke Wiles, Morgan Pertoso, Nemanja Danilovic, Katherine E Ayers, Thomas J Schmidt
The growing need to store increasing amounts of renewable energy has recently triggered substantial R&D efforts towards efficient and stable water electrolysis technologies. The oxygen evolution reaction (OER) occurring at the electrolyser anode is central to the development of a clean, reliable and emission-free hydrogen economy. The development of robust and highly active anode materials for OER is therefore a great challenge and has been the main focus of research. Among potential candidates, perovskites have emerged as promising OER electrocatalysts...
July 17, 2017: Nature Materials
Jason R Dwyer, Maher Harb
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing...
January 1, 2017: Applied Spectroscopy
Daniele De Martino
In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions...
June 2017: Physical Review. E
Suman G Das, Madan Rao, Garud Iyengar
The living cell uses a variety of molecular receptors to read and process chemical signals that vary in space and time. We model the dynamics of such molecular level measurements as Markov processes in steady state, with a coupling between the receptor and the signal. We prove exactly that, when the signal dynamics is not perturbed by the receptors, the free energy consumed by the measurement process is lower bounded by a quantity proportional to the mutual information. Our result is completely independent of the receptor architecture and dependent on signal properties alone, and therefore holds as a general principle for molecular information processing...
June 2017: Physical Review. E
Zeyu Jiang, Zhirong Liu, Yuanchang Li, Wenhui Duan
Using first-principles   GW Bethe-Salpeter equation calculations and the k·p theory, we unambiguously show that for two-dimensional (2D) semiconductors, there exists a robust linear scaling law between the quasiparticle band gap (E_{g}) and the exciton binding energy (E_{b}), namely, E_{b}≈E_{g}/4, regardless of their lattice configuration, bonding characteristic, as well as the topological property. Such a parameter-free universality is never observed in their three-dimensional counterparts. By deriving a simple expression for the 2D polarizability merely with respect to E_{g}, and adopting the screened hydrogen model for E_{b}, the linear scaling law can be deduced analytically...
June 30, 2017: Physical Review Letters
Amir Omidvarnia, Mangor Pedersen, Richard E Rosch, Karl J Friston, Graeme D Jackson
In this opinion paper, we describe a combined view of functional and effective brain connectivity along with the free-energy principle for investigating persistent disruptions in brain networks of patients with focal epilepsy. These changes are likely reflected in effective connectivity along the cortical hierarchy and construct the basis of increased local functional connectivity in focal epilepsy. We propose a testable framework based on dynamic causal modelling and functional connectivity analysis with the capacity of explaining commonly observed connectivity changes during interictal periods...
2017: NeuroImage: Clinical
Heike B Thomas, Matthias Hennemann, Patrick Kibies, Franziska Hoffgaard, Stefan Gussregen, Gerhard Hessler, Stefan M Kast, Timothy Clark
A Neglect of Diatomic Differential Overlap (NDDO) Hamiltonian has been parameterized as an electronic component of a polarizable force field. Coulomb and exchange potentials derived directly from the NDDO Hamiltonian in principle can be used with classical potentials, thus forming the basis for a new generation of efficiently applicable multipolar polarizable force fields. The new hpCADD Hamiltonian uses force-field like atom types and reproduces the electrostatic properties (dipole moment, molecular electrostatic potential) and Koopmans' Theorem ionization potentials closely, as demonstrated for a large training set and an independent test set of small molecules...
July 12, 2017: Journal of Chemical Information and Modeling
Shijie Sheng, Michael Miller, Jianzhong Wu
Solvation plays an important role in diverse chemical processes ranging from reaction kinetics to molecular recognition, solubility, and phase separations. Despite a long-history of theoretical exploration, quantitative prediction of solvation remains a theoretical challenge without relying on the macroscopic properties of the solvent as an input. Here we present a molecular density functional theory that provides a self-consistent description of the solvation structure and thermodynamic properties of small organic molecules in liquid water at different temperatures...
July 11, 2017: Journal of Physical Chemistry. B
Eric Cockayne
We use first-principles density functional theory total energy and linear response phonon calculations to compute the Helmholtz and Gibbs free energy as a function of temperature, pressure, and cell volume in the flexible metal-organic framework material MIL-53(Cr) within the quasiharmonic approximation. GGA and metaGGA calculations were performed, each including empirical van der Waals (vdW) forces under the D2, D3, or D3(BJ) parameterizations. At all temperatures up to 500 K and pressures from -30 MPa to 30 MPa, two minima in the free energy versus volume are found, corresponding to the narrow pore (np) and large pore (lp) structures...
March 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Boyeong Kang, Woojin Yang, Sebok Lee, Sudipto Mukherjee, Jonathan Forstater, Hanna Kim, Byoungsook Goh, Tae-Young Kim, Vincent A Voelz, Yoonsoo Pang, Jiwon Seo
The energy flow during natural photosynthesis is controlled by maintaining the spatial arrangement of pigments, employing helices as scaffolds. In this study, we have developed porphyrin-peptoid (pigment-helix) conjugates (PPCs) that can modulate the donor-acceptor energy transfer efficiency with exceptional precision by controlling the relative distance and orientation of the two pigments. Five donor-acceptor molecular dyads were constructed using zinc porphyrin and free base porphyrin (Zn(i + 2)-Zn(i + 6)), and highly efficient energy transfer was demonstrated with estimated efficiencies ranging from 92% to 96% measured by static fluorescence emission in CH2Cl2 and from 96...
July 6, 2017: Scientific Reports
Wei Zhao, Lei Xing, Qiude Zhang, Qingguo Xie, Tianye Niu
An x-ray energy spectrum plays an essential role in computed tomography (CT) imaging and related tasks. Because of the high photon flux of clinical CT scanners, most of the spectrum estimation methods are indirect and usually suffer from various limitations. In this study, we aim to provide a segmentation-free, indirect transmission measurement-based energy spectrum estimation method using dual-energy material decomposition. The general principle of this method is to minimize the quadratic error between the polychromatic forward projection and the raw projection to calibrate a set of unknown weights, which are used to express the unknown spectrum together with a set of model spectra...
April 2017: Journal of Medical Imaging
Siheon Ryee, Myung Joon Han
A systematic first-principles study has been performed to understand the magnetism of thin film SrRuO3 which lots of research efforts have been devoted to but no clear consensus has been reached about its ground state properties. The relative t 2g level difference, lattice distortion as well as the layer thickness play together in determining the spin order. In particular, it is important to understand the difference between two standard approximations, namely LDA and GGA, in describing this metallic magnetism...
July 5, 2017: Scientific Reports
Xiandong Liu, Xiancai Lu, Yingchun Zhang, Chi Zhang, Rucheng Wang
We report a first principles molecular dynamics (FPMD) study of carboxylate complexation on clay surfaces. By taking acetate as a model carboxylate, we investigate its inner-sphere complexes adsorbed on clay edges (including (010) and (110) surfaces) and in interlayer space. Simulations show that acetate forms stable monodentate complexes on edge surfaces and a bidentate complex with Ca(2+) in the interlayer region. The free energy calculations indicate that the complexation on edge surfaces is slightly more stable than in interlayer space...
July 5, 2017: Physical Chemistry Chemical Physics: PCCP
William Cannon, Scott Baker
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants...
July 4, 2017: Physical Biology
Anthonie W J Muller
As cancer usually follows reproduction, it is generally assumed that cancer does not select. Graham has however argued that juvenile cancer, which precedes reproduction, could during evolution have implemented a "cancer selection" that resulted in novel traits that suppress this juvenile cancer; an example is protection against UV sunlight-induced cancer, required for the emergence of terrestrial animals from the sea. We modify the cancer selection mechanism to the posited "cancer adaptation" mechanism, in which juvenile mortality is enhanced through the diminished care received by juveniles from their (grand) parents when these suffer from cancer in old age...
July 2017: Medical Hypotheses
Jongmin Kim, Chang-Hyung Choi, Su-Jin Yeom, Naye Eom, Kyoung-Ku Kang, Chang-Soo Lee
This study demonstrates the possibility of controlling the directed self-assembly of microsized Janus cylinders by changing the solvent polarity of the assembly media. Experimental results are analyzed and theoretical calculations of the free energy of adhesion (ΔG(ad)) are performed to elucidate the underlying basic principles and investigate the effects of the solvent on the self-assembled structures. This approach will pave a predictive route for controlling the structures of assembly depending on the solvent polarity...
July 3, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Yoshitaka Saga, Keiya Hirota, Hitoshi Asakawa, Kazufumi Takao, Takeshi Fukuma
Light-harvesting complex 2 (LH2) is an integral membrane protein in purple photosynthetic bacteria. This protein possesses two types of bacteriochlorophyll (BChl) a, termed B800 and B850, which exhibit lowest-energy absorption bands (Qy bands) around 800 and 850 nm. These BChl a pigments in the LH2 protein play crucial roles not only in photosynthetic functions but also in folding and maintaining its protein structure. We report herein the reversible structural changes in the LH2 protein derived from a purple photosynthetic bacterium, Rhodoblastus acidophilus, induced by the removal of B800 BChl a (denoted as B800-free LH2) and the reconstitution of exogenous BChl a...
June 28, 2017: Biochemistry
Christoph Hage, Francesco Falvo, Mathias Schäfer, Andrea Sinz
The chemical cross-linking/mass spectrometry (MS) approach is gaining increasing importance as an alternative method for studying protein conformation and for deciphering protein interaction networks. This study is part of our ongoing efforts to develop innovative cross-linking principles for a facile and efficient assignment of cross-linked products. We evaluate two homobifunctional, amine-reactive, and MS-cleavable cross-linkers regarding their potential for automated analysis of cross-linked products. We introduce the bromine phenylurea (BrPU) linker that possesses a unique structure yielding a distinctive fragmentation pattern on collisional activation...
June 26, 2017: Journal of the American Society for Mass Spectrometry
Jonathan M Skelton, Lee A Burton, Fumiyasu Oba, Aron Walsh
The tin sulfides represent a materials platform for earth-abundant semiconductor technologies. We present a first-principles study of the five known and proposed phases of SnS together with SnS2 and Sn2S3. Lattice-dynamics techniques are used to evaluate the dynamical stability and temperature-dependent thermodynamic free energy, and we also consider the effect of dispersion forces on the energetics. The recently identified π-cubic phase of SnS is found to be metastable with respect to the well-known orthorhombic Pnma/Cmcm equilibrium...
March 30, 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
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