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free-energy principle

R R Valiev, V N Cherepanov, G V Baryshnikov, D Sundholm
A method for calculating the rate constants for internal-conversion (k IC ) and intersystem-crossing (k ISC ) processes within the adiabatic and Franck-Condon (FC) approximations is proposed. The applicability of the method is demonstrated by calculation of k IC and k ISC for a set of organic and organometallic compounds with experimentally known spectroscopic properties. The studied molecules were pyrromethene-567 dye, psoralene, hetero[8]circulenes, free-base porphyrin, naphthalene, and larger polyacenes...
February 16, 2018: Physical Chemistry Chemical Physics: PCCP
Naoki Takeuchi, Nobuyuki Yoshikawa
According to Landauer's principle, the minimum heat emission required for computing is linked to logical entropy, or logical reversibility. The validity of Landauer's principle has been investigated for several decades and was finally demonstrated in recent experiments by showing that the minimum heat emission is associated with the reduction in logical entropy during a logically irreversible operation. Although the relationship between minimum heat emission and logical reversibility is being revealed, it is not clear how much free energy is required to be dissipated for a logically irreversible operation...
January 2018: Physical Review. E
Markus Heyl
Quantum theory provides an extensive framework for the description of the equilibrium properties of quantum matter. Yet experiments in quantum simulators have now opened up a route towards generating quantum states beyond this equilibrium paradigm. While these states promise to show properties not constrained by equilibrium principles such as the equal a priori probability of the microcanonical ensemble, identifying general properties of nonequilibrium quantum dynamics remains a major challenge especially in view of the lack of conventional concepts such as free energies...
February 15, 2018: Reports on Progress in Physics
Ewa Lukojko, Ewa Talik, Anna Gagor, Rafal Sitko
A simple method for highly selective determination of trace and ultratrace arsenic ions, i.e. arsenite and arsenate, was developed. The method is based on new miniaturized membranes, 5 mm diameter and 4.4 mg weight, which are prepared by synthesis of amorphous silica coating on cellulose fibers followed by the modification with (3-mercaptopropyl)-trimethoxysilane. The batch adsorption experiments show that membranes have high selectivity toward arsenite in the presence of heavy metals and anions that usually exist in natural water...
May 30, 2018: Analytica Chimica Acta
Yilin Meng, Lalima G Ahuja, Alexandr P Kornev, Susan S Taylor, Benoît Roux
Tyrosine kinases are enzymes playing a critical role in cellular signaling. Molecular dynamics (MD) umbrella sampling potential of mean force (PMF) computations are used to quantify the impact of activating and inactivating mutations of c-Src kinase. The PMF computations predict that a specific double-mutant can stabilize c-Src kinase into an active-like conformation while disabling the binding of ATP in the catalytic active site. The active-like conformational equilibrium of this catalytically-dead kinase is affected by a hydrophobic unit that connects to the hydrophobic spine network via the C-helix...
February 2, 2018: Journal of Molecular Biology
Qingming Deng, Tiantian Wu, Guibin Chen, Heine Anton Hansen, Tejs Vegge
The CO oxidation reaction on single 3d-transition metal catalytic sites in experimentally realized tetracyanoquinodimethane (TM-TCNQ) monolayers (TM = Sc-Zn) is systematically investigated by means of first-principles calculations. Considering the stabilities, adsorption characteristics and thermodynamics of all the ten candidates (Sc-Zn), Sc-TCNQ is found to display the lowest activation energies and yield the highest catalytic activity for room temperature CO oxidation. Exploring the Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms, we find that the rate-limiting step of CO oxidation catalyzed by Sc-TCNQ (CO + O2* → OOCO*) can follow the LH mechanism with free energy barriers as low as 0...
February 2, 2018: Physical Chemistry Chemical Physics: PCCP
Guoxiang Hu, Zili Wu, Sheng Dai, De-En Jiang
Two-dimensional atomically thin hexagonal boron nitride (h-BN) monolayer has attracted considerable research interest. Given the tremendous progress in the synthesis of h-BN monolayers on transition metals and their potential as electrocatalysts, we investigate the electrocatalytic activities of h-BN/Ni, h-BN/Co, and h-BN/Cu interfaces for CO2 reduction by first-principles density functional theory. We find that with the h-BN monolayer on the metal, electrons transfer from the metal to the interface and accumulate under the B atoms...
February 1, 2018: ACS Applied Materials & Interfaces
Cheng Tang, Hao-Fan Wang, Qiang Zhang
Various gas-involving energy electrocatalysis, including oxygen reduction reaction (ORR), oxygen evolution reaction (OER), and hydrogen evolution reaction (HER), has witnessed increasing concerns recently for the sake of clean, renewable, and efficient energy technologies. However, these heterogeneous reactions exhibit sluggish kinetics due to multistep electron transfer and only occur at triple-phase boundary regions. Up to now, tremendous attention has been attracted to develop cost-effective and high-performance electrocatalysts to boost the electrocatalytic activities as promising alternatives to noble metal counterparts...
January 31, 2018: Accounts of Chemical Research
Da Wang, Ning Liu, Zhongnan Guo, Wenjun Wang, Liwei Guo, Wenxia Yuan, Xiaolong Chen
Sufficient spatial separation of photo-generated electrons and holes plays a significant role in affecting the efficiency for solar energy conversion. Non-equivalent facets of a catalyst are known to possess different charge distribution properties. Here, we report that hexagonal 6H-SiC, a metal-free, environmentally friendly, polar semiconductor, exhibits different charge distribution and photocatalytic properties on naturally occurring Si-{0001} and {10-10} facets. Very strong selectivity of metals in situ photodeposition occurs in these two facets, demonstrating that the photo-excited electrons are assembled only on polar Si-{0001} facets while the holes are assembled on non-polar {10-10} facets...
January 31, 2018: Physical Chemistry Chemical Physics: PCCP
Vahid Mahmoodi, Tahereh Rohani Bastami, Ali Ahmadpour
Photocatalytic degradation of toxic organic pollutants in the wastewater using dispersed semiconductor nanophotocatalysts has a number of advantages such as high activity, cost effectiveness, and utilization of free solar energy. However, it is difficult to recover and recycle nanophotocatalysts since the fine dispersed nanoparticles are easily suspended in waters. Furthermore, a large amount of photocatalysts will lead to color contamination. Thus, it is necessary to prepare photocatalysts with easy separation for the reusable application...
January 25, 2018: Environmental Science and Pollution Research International
Aiswarya B Pawar, Durba Sengupta
The association of single transmembrane receptors, such as the ErbB receptors is a key event in initiating cell signaling networks. The interactions between these receptors have been well characterized for both ligand-driven and pre-formed dimers. However, the role of the membrane in modulating association is less well understood and assumes greater importance in light of altered membrane composition in diseased states. Here, we discuss how membrane composition has been observed to induce both structural and dynamic differences in receptor association...
January 19, 2018: Journal of Membrane Biology
Chang Liu, William Fox, Amitava Bhattacharjee, Alexander G R Thomas, Archis S Joglekar
Recent theory has demonstrated a novel physics regime for magnetic reconnection in high-energy-density plasmas where the magnetic field is advected by heat flux via the Nernst effect. Here we elucidate the physics of the electron dissipation layer in this regime. Through fully kinetic simulation and a generalized Ohm's law derived from first principles, we show that momentum transport due to a nonlocal effect, the heat-flux-viscosity, provides the dissipation mechanism for magnetic reconnection. Scaling analysis, and simulations show that the reconnection process comprises a magnetic field compression stage and quasisteady reconnection stage, and the characteristic width of the current sheet in this regime is several electron mean-free paths...
October 2017: Physical Review. E
Rodolfo Paula Leite, Pedro Antonio Santos-Flórez, Maurice de Koning
Using molecular dynamics simulations and nonequilibrium thermodynamic-integration techniques we compute the Helmholtz free energies of the body-centered-cubic (bcc), face-centered-cubic (fcc), hexagonal close-packed, and fluid phases of the Uhlenbeck-Ford model (UFM) and use the results to construct its phase diagram. The pair interaction associated with the UFM is characterized by an ultrasoft, purely repulsive pair potential that diverges logarithmically at the origin. We find that the bcc and fcc are the only thermodynamically stable crystalline phases in the phase diagram...
September 2017: Physical Review. E
Michael Kirchhoff, Thomas Parr, Ensor Palacios, Karl Friston, Julian Kiverstein
This work addresses the autonomous organization of biological systems. It does so by considering the boundaries of biological systems, from individual cells to Home sapiens, in terms of the presence of Markov blankets under the active inference scheme-a corollary of the free energy principle. A Markov blanket defines the boundaries of a system in a statistical sense. Here we consider how a collective of Markov blankets can self-assemble into a global system that itself has a Markov blanket; thereby providing an illustration of how autonomous systems can be understood as having layers of nested and self-sustaining boundaries...
January 2018: Journal of the Royal Society, Interface
Jian Zhou, Qiang Sun, Puru Jena
The valley-polarized quantum anomalous Hall effect (VP-QAHE), which combines valleytronics and topology in one material, is of significant fundamental and practical importance in condensed-matter physics and materials science. In previous model studies, VP-QAHE occurs under strong Rashba spin-orbit coupling (SOC), which is an extrinsic effect. Here, using a low energy k·p model, we propose a different mechanism of VP-QAHE by introducing an intrinsic staggered magnetic exchange field and develop a general picture of valley dependent band inversion in honeycomb lattice...
July 28, 2017: Physical Review Letters
Andrew P Owens, Karl J Friston, David A Low, Christopher J Mathias, Hugo D Critchley
Predictive coding models, such as the 'free-energy principle' (FEP), have recently been discussed in relation to how interoceptive (afferent visceral feedback) signals update predictions about the state of the body, thereby driving autonomic mediation of homeostasis. This study appealed to 'interoceptive inference', under the FEP, to seek new insights into autonomic (dys)function and brain-body integration by examining the relationship between cardiac interoception and autonomic cardiac control in healthy controls and patients with forms of orthostatic intolerance (OI); to (i) seek empirical support for interoceptive inference and (ii) delineate if this relationship was sensitive to increased interoceptive prediction error in OI patients during head-up tilt (HUT)/symptom provocation...
January 9, 2018: Autonomic Neuroscience: Basic & Clinical
Jaydeep Sinha, Stephen B Duffull, Hesham S Al-Sallami
Fat-free mass (FFM) represents the lean component of the body devoid of fat. It has been shown to be a useful predictor of drug dose requirements, particularly in obesity where the excess fat mass does not contribute to drug clearance. However, measuring FFM involves complex and/or expensive experimental methodologies that preclude their use in routine clinical practice. Thus, models to predict FFM from readily measurable variables, such as body weight and height, have been developed and are used in both population pharmacokinetic modelling and clinical practice...
January 12, 2018: Clinical Pharmacokinetics
Wonseok Hwang, Changbong Hyeon
An efficient molecular motor would deliver cargos to the target site at a high speed and in a punctual manner while consuming a minimal amount of energy. According to a recently formulated thermodynamic principle, referred to as the thermodynamic uncertainty relation, the travel distance of a motor and its variance are, however, constrained by the free energy being consumed. Here we use the principle underlying the uncertainty relation to quantify the transport efficiency of molecular motors for varying ATP concentration ([ATP]) and applied load (f)...
January 12, 2018: Journal of Physical Chemistry Letters
Ioana C Gârlea, Bela M Mulder
We design a novel microscopic mean-field theory of inhomogeneous nematic liquid crystals formulated entirely in terms of the tensor order parameter field. It combines the virtues of the Landau-de Gennes approach in allowing both the direction and magnitude of the local order to vary, with a self-consistent treatment of the local free-energy valid beyond the small order parameter limit. As a proof of principle, we apply this theory to the well-studied problem of a colloid dispersed in a nematic liquid crystal by including a tunable wall coupling term...
December 28, 2017: Journal of Chemical Physics
Hao Yan, Karthik Narasimha, Jonathan Denlinger, Fei Hua Li, Sung-Kwan Mo, J Nathan Hohman, Jeremy E P Dahl, Robert M K Carlson, Boryslav A Tkachenko, Andrey A Fokin, Peter R Schreiner, Zahid Hussain, Zhi-Xun Shen, Nicholas A Melosh
The monochromatic photoemission from diamondoid monolayers provides a new strategy to create electron sources with low energy dispersion, and enables compact electron guns with high brightness and low beam emittance for aberration-free imaging, lithography and accelerators. However, these potential applications are hindered by degradation of diamondoid monolayers under photon irradiation and electron bombardment. Here we report a graphene-protected diamondoid monolayer photocathode with four-fold enhancement of stability compared to the bare diamondoid counterpart...
December 29, 2017: Nano Letters
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