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free-energy principle

Shao-Kai Sun, He-Fang Wang, Xiu-Ping Yan
Persistent luminescence nanoparticles (PLNPs) are unique optical materials emitting long-lasting luminescence after ceasing excitation. Such a unique optical feature allows luminescence detection without constant external illumination to avoid the interferences of autofluorescence and scattering light from biological fluids and tissues. Besides, near-infrared (NIR) PLNPs have advantages of deep penetration and the reactivation of the persistent luminescence (PL) by red or NIR light. These features make the application of NIR-emitting PLNPs in long-term bioimaging no longer limited by the lifetime of PL...
April 17, 2018: Accounts of Chemical Research
Stephan N Steinmann, Rodrigo Ferreira de Morais, Andreas W Götz, Paul Fleurat-Lessard, Marcella Iannuzzi, Philippe Sautet, Carine Michel
Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water; (ii) a Gaussian term to improve the surface corrugation and (iii) two terms describing the angular dependence of the interaction energy...
April 16, 2018: Journal of Chemical Theory and Computation
Chiara Bulgarelli, Anna Blasi, Simon Arridge, Samuel Powell, Carina de Klerk, Victoria Southgate, Sabrina Brigadoi, William Penny, Sungho Tak, Antonia Hamilton
Tracking the connectivity of the developing brain from infancy through childhood is an area of increasing research interest, and fNIRS provides an ideal method for studying the infant brain as it is compact, safe and robust to motion. However, data analysis methods for fNIRS are still underdeveloped compared to those available for fMRI. Dynamic causal modelling (DCM) is an advanced connectivity technique developed for fMRI data, that aims to estimate the coupling between brain regions and how this might be modulated by changes in experimental conditions...
April 12, 2018: NeuroImage
Joseph Bennett, Diamond Jones, Xu Huang, Robert J Hamers, Sara E Mason
The rapid increase in use of Li-ion batteries in portable electronics has created a pressing need to understand the environmental impact and long-term fate of electonic waste (e-waste) products such as heavy and/or reactive metals. The type of e-waste that we focus on here are the complex metal oxide nanomaterials that compose Li-ion battery cathodes. While in operation the complex metal oxides are in a hermetically sealed container. However, at the end of life, improper disposal can cause structural transformations such as dissolution and metal leaching, resulting in a significant exposure risk to the surrounding environment...
April 13, 2018: Environmental Science & Technology
Md Jobayer Hossain, Alexa Levinson, Donald George, Jose Canas, Seema Kumar, P Babu Balagopal
BACKGROUND: The relationship among inadequate vitamin D status, obesity, and cardiometabolic risk and the potential impact of physical activity-based interventions on vitamin D status are poorly characterized in children. This study aimed to address these issues. METHODS: We studied a total of 21 adolescents (15 obese and 6 normal weight; age: 14-18 years; Tanner stage>IV). Adolescents with obesity (n = 15) underwent a randomized controlled (8 in the intervention group and 7 in the control group) 3-month physical activity-based lifestyle intervention...
March 13, 2018: Metabolic Syndrome and related Disorders
Chaohong Chen, Zhifeng He, Deyao Xie, Liangcheng Zheng, Tianhao Zhao, Xinbo Zhang, Dezhi Cheng
Anaplastic lymphoma kinase (ALK) has been regarded as an essential target for the treatment of non-small cell lung cancer (NSCLC). However, the emergence of G1202R solvent front mutation that confer resistance to the drugs were reported for the first as well as the second generation ALK inhibitors. It was supposed that the G1202R solvent front mutation might hinder the drug binding. In this study, a different fact could be clarified by multiple molecular modeling methodologies through a structural analogue of ceritinib (compound 10, Cpd-10) that is reported to be a potent inhibitor against the G1202R mutation...
April 12, 2018: Journal of Physical Chemistry. B
Shuying Nong, Wujie Dong, Junwen Yin, Bowei Dong, Yue Lu, Xiaotao Yuan, Xin Wang, Kejun Bu, Mingyang Chen, Shangda Jiang, Li-Min Liu, Manling Sui, Fuqiang Huang
TiO2 mesoporous crystal has been prepared by one-step corroding process via an oriented attachment (OA) mechanism with SrTiO3 as precursor. High resolution transmission electron microscopy (HRTEM) and nitrogen adsorption-desorption isotherms confirm its mesoporous crystal structure. Well-dispersed ruthenium (Ru) in the mesoporous nanocrystal TiO2 can be attained by the same process using Ru-doped precursor SrTi1-x Rux O3 . Ru is doped into lattice of TiO2 , which is identified by HRTEM and super energy dispersive spectrometer (super-EDS) elemental mapping...
April 12, 2018: Journal of the American Chemical Society
Axel Constant, Maxwell J D Ramstead, Samuel P L Veissière, John O Campbell, Karl J Friston
In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference...
April 2018: Journal of the Royal Society, Interface
Petch Khunpetch, Xingkun Man, Toshihiro Kawakatsu, Masao Doi
We study the translocation process of a vesicle through a hole in a solid membrane separating two chambers by using the Onsager principle. By considering the stretching energy of the vesicle and the driving force due to pressure difference, we derive a free energy that shows clearly a decrease in the energy barrier as the pressure difference between two sides of the membrane increases. The difference between the reaction path obtained from the string method and the actual kinetic paths obtained from the Onsager principle is discussed when the friction parameter changes...
April 7, 2018: Journal of Chemical Physics
Jochen Kieninger, Andreas Weltin, Hubert Flamm, Gerald A Urban
Microsensor systems for cell metabolism are essential tools for investigation and standardization in cell culture. Electrochemical and optical read-out schemes dominate, which enable the marker-free, continuous, online recording of transient effects and deliver information beyond microscopy and end-point tests. There has been much progress in microfluidics and microsensors, but the translation of both into standard cell culture procedures is still limited. Within this critical review, we discuss different cell culture formats ranging from standard culture vessels to dedicated microfluidic platforms...
April 5, 2018: Lab on a Chip
Soo Kim, Vinay I Hegde, Zhenpeng Yao, Zhi Lu, Maximilian Amsler, Jiangang He, Shiqiang Hao, Jason R Croy, Eungje Lee, Michael M Thackeray, Chris Wolverton
Embedding a lithiated cobalt oxide spinel (Li2Co2O4; or LiCoO2) component or a nickel-substituted LiCo1-xNixO2 analogue in structurally-integrated cathodes such as xLi2MnO3∙(1-x)LiM'O2 (M' = Ni/Co/Mn) has been recently proposed as an approach to advance the performance of lithium-ion batteries (LIBs). Here, we first revisit the phase stability and electrochemical performance of LiCoO2 synthesized at different temperatures using density functional theory (DFT) calculations. Consistent with previous studies, we find that the occurrence of low- and high-temperature structures (i...
April 4, 2018: ACS Applied Materials & Interfaces
Si Zhou, Xiaowei Yang, Wei Pei, Nanshu Liu, Jijun Zhao
MXenes with versatile chemistry and superior electrical conductivity are prevalent candidate materials for energy storage and catalysts. Inspired by recent experiments of hybridizing MXenes with carbon materials, here we theoretically design a series of heterostructures of N-doped graphene supported by MXene monolayers as bifunctional electrocatalysts for the oxygen reduction reaction (ORR) and hydrogen evolution reaction (HER). Our first-principles calculations show that the graphitic sheet on V2C and Mo2C MXenes are highly active with an ORR overpotential down to 0...
April 4, 2018: Nanoscale
Zengsong Zhang, Guangtao Yu, Hui Li, Jingwei Liu, Xuri Huang, Wei Chen
On the basis of the first-principles DFT computations, we have systematically investigated the structures and hydrogen evolution reaction (HER) catalytic activities for pristine and Ni-doped Cu3P systems. It was revealed that the (11[combining macron]0) surface could be the one with the most exposure for the Cu3P structure. The calculated free energy values of H* (ΔGH*) are in the range from 0.012 to 0.320 eV, reflecting the HER activity on the (11[combining macron]0) surface, which is consistent with the experimentally reported results...
April 3, 2018: Physical Chemistry Chemical Physics: PCCP
Ewa Anna Oprzeska-Zingrebe, Jens Smiatek
Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes...
April 2, 2018: Biophysical Reviews
Rita Prosmiti, Daniel J Arismendi-Arrieta, Alvaro Valdés de Luxán
CO2 clathrate hydrates have been proposed as potential molecular materials in tackling important environmental problems related with greenhouse gases capture and storage. Despite the increasing interest in such hydrates and their technological applications, a molecular-level understanding of their formation and properties is still far from complete. Modeling interactions is a challenging and computational demanding task, essential to reliably determine molecular properties. First-principles calculations for the CO2 guest in all sI, sII, and sH clathrate cages were performed, and the nature of the guest-host interactions, dominated by both hydrogen-bond and van der Waals forces, was systematically investigated...
March 30, 2018: Chemistry: a European Journal
Matteo Aldeghi, Joseph P Bluck, Philip C Biggin
Many thermodynamic quantities can be extracted from computer simulations that generate an ensemble of microstates according to the principles of statistical mechanics. Among these quantities is the free energy of binding of a small molecule to a macromolecule, such as a protein. Here, we present an introductory overview of a protocol that allows for the estimation of ligand binding free energies via molecular dynamics simulations. While we focus on the binding of organic molecules to proteins, the approach is in principle transferable to any pair of molecules...
2018: Methods in Molecular Biology
Austin P Ladshaw, Alexander S Ivanov, Sadananda Das, Vyacheslav S Bryantsev, Costas Tsouris, Sotira Yiacoumi
Nuclear power is a relatively carbon free energy source that has the capacity to be utilized today in an effort to stem the tides of global warming. The growing demand for nuclear energy, however, could put significant strain on our uranium ore resources and the mining activities utilized to extract that ore can leave behind long-term environmental damage. A potential solution to enhance supply of uranium fuel is to recover uranium from seawater using amidoximated adsorbent fibers. This technology has been studied for decades, but is currently plagued by the material's relatively poor selectivity of uranium over its main competitor vanadium...
March 27, 2018: ACS Applied Materials & Interfaces
Nathan C Frey, Bryan W Byles, Hemant Kumar, Dequan Er, Ekaterina Pomerantseva, Vivek B Shenoy
Crystal water has been shown to stabilize next-generation energy storage electrodes with structural tunnels to accommodate cation intercalation, but the stabilization mechanism is poorly understood. In this study, we present a simple physical model to explain the energetics of interactions between the electrode crystal lattice, structural water, and electrochemically cycled ions. Our model is applied to understand the effects of crystal water on sodium ion intercalation in a tunnel manganese oxide structure, and we predict that precisely controlling the crystal water concentration can optimize the ion intercalation voltage and capacity and promote stable cycling...
March 23, 2018: Physical Chemistry Chemical Physics: PCCP
Shuai Zhang, Burkhard Militzer, Lorin X Benedict, François Soubiran, Philip A Sterne, Kevin P Driver
Carbon-hydrogen plasmas and hydrocarbon materials are of broad interest to laser shock experimentalists, high energy density physicists, and astrophysicists. Accurate equations of state (EOSs) of hydrocarbons are valuable for various studies from inertial confinement fusion to planetary science. By combining path integral Monte Carlo (PIMC) results at high temperatures and density functional theory molecular dynamics results at lower temperatures, we compute the EOSs for hydrocarbons from simulations performed at 1473 separate (ρ, T)-points distributed over a range of compositions...
March 14, 2018: Journal of Chemical Physics
Tsukuru Ohwaki, Taisuke Ozaki, Yukihiro Okuno, Tamio Ikeshoji, Hideto Imai, Minoru Otani
We report the result of a large-scale first-principles molecular dynamics simulation under different electric biases performed to understand the charge transfer process coupling with lithium deposition and desolvation processes. We applied the effective screening medium (ESM) method to control the bias across the electrode/solution interface, and simulated a series of Li de-solvation and Li-deposition reactions occurring under the bias. Solvated Li+ in the bulk propylene carbonate migrates to the Si electrode surface and gradually de-solvates through the transition state...
March 14, 2018: Physical Chemistry Chemical Physics: PCCP
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