Effectual air quality monitoring network (AQMN) design plays a prominent role in environmental engineering. An optimal AQMN design should consider stations' mutual information and system uncertainties for effectiveness. This study develops a novel optimization model using a non-dominated sorting genetic algorithm II (NSGA-II). The Bayesian maximum entropy (BME) method generates potential stations as the input of a framework based on the transinformation entropy (TE) method to maximize the coverage and minimize the probability of selecting stations. Also, the fuzzy degree of membership and the nonlinear interval number programming (NINP) approaches are used to survey the uncertainty of the joint information. To obtain the best Pareto optimal solution of the AQMN characterization, a robust ranking technique, called Preference Ranking Organization METHod for Enrichment Evaluation (PROMETHEE) approach, is utilized to select the most appropriate AQMN properties. This methodology is applied to Los Angeles, Long Beach, and Anaheim in California, USA. Results suggest using 4, 4, and 5 stations to monitor CO, NO2, and ozone, respectively; however, implementing this recommendation reduces coverage by 3.75, 3.75, and 3 times for CO, NO2, and ozone, respectively. On the positive side, this substantially decreases TE for CO, NO2, and ozone concentrations by 8.25, 5.86, and 4.75 times, respectively.

• Klíčová slova
• Air quality, Bayesian maximum entropy (BME), Fuzzy set theory, Multi-criteria decision-making (MCDM), Nonlinear interval number programming (NINP), Transinformation entropy (TE),
• MeSH
• Bayesova věta MeSH
• entropie MeSH
• monitorování životního prostředí metody   MeSH
• oxid dusičitý analýza   MeSH
• ozon * analýza   MeSH
• teoretické modely MeSH
• znečištění ovzduší * analýza   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• oxid dusičitý MeSH
• ozon * MeSH

In this study, we consider a method for investigating the stochastic response of a nonlinear dynamical system affected by a random seismic process. We present the solution of the probability density of a single/multiple-degree of freedom (SDOF/MDOF) system with several statically stable equilibrium states and with possible jumps of the snap-through type. The system is a Hamiltonian system with weak damping excited by a system of non-stationary Gaussian white noise. The solution based on the Gibbs principle of the maximum entropy of probability could potentially be implemented in various branches of engineering. The search for the extreme of the Gibbs entropy functional is formulated as a constrained optimization problem. The secondary constraints follow from the Fokker-Planck equation (FPE) for the system considered or from the system of ordinary differential equations for the stochastic moments of the response derived from the relevant FPE. In terms of the application type, this strategy is most suitable for SDOF/MDOF systems containing polynomial type nonlinearities. Thus, the solution links up with the customary formulation of the finite elements discretization for strongly nonlinear continuous systems.

• Klíčová slova
• Boltzmann solution, Fokker–Planck equation, Gibbs entropy functional, maximum entropy probability density principle, random earthquake process, stochastically proportional system,
• Publikační typ
• časopisecké články MeSH

Any physical system can be regarded on different levels of description varying by how detailed the description is. We propose a method called Dynamic MaxEnt (DynMaxEnt) that provides a passage from the more detailed evolution equations to equations for the less detailed state variables. The method is based on explicit recognition of the state and conjugate variables, which can relax towards the respective quasi-equilibria in different ways. Detailed state variables are reduced using the usual principle of maximum entropy (MaxEnt), whereas relaxation of conjugate variables guarantees that the reduced equations are closed. Moreover, an infinite chain of consecutive DynMaxEnt approximations can be constructed. The method is demonstrated on a particle with friction, complex fluids (equipped with conformation and Reynolds stress tensors), hyperbolic heat conduction and magnetohydrodynamics.

• Klíčová slova
• MaxEnt, Ohm’s law, complex fluids, dynamic MaxEnt, heat conduction, model reduction, non-equilibrium thermodynamics,
• Publikační typ
• časopisecké články MeSH

The structure of 4-methyl-3-[(tetrahydro-2H-pyran-2-yl)oxy]thiazole-2(3H)-thione (MTTOTHP) was investigated using X-ray diffraction and computational chemistry methods for determining properties of the nitrogen-oxygen bond, which is the least stable entity upon photochemical excitation. Experimentally measured structure factors have been used to determine and characterize charge density via the multipole model (MM) and the maximum entropy method (MEM). Theoretical investigation of the electron density and the electronic structure has been performed in the finite basis set density functional theory (DFT) framework. Quantum Theory of Atoms In Molecules (QTAIM), deformation densities and Laplacians maps have been used to compare theoretical and experimental results. MM experimental results and predictions from theory differ with respect to the sign and/or magnitude of the Laplacian at the N-O bond critical point (BCP), depending on the treatment of n values of the MM radial functions. Such Laplacian differences in the N-O bond case are discussed with respect to a lack of flexibility in the MM radial functions also reported by Rykounov et al. [Acta Cryst. (2011), B67, 425-436]. BCP Hessian eigenvalues show qualitatively matching results between MM and DFT. In addition, the theoretical analysis used domain-averaged fermi holes (DAFH), natural bond orbital (NBO) analysis and localized (LOC) orbitals to characterize the N-O bond as a single σ bond with marginal π character. Hirshfeld atom refinement (HAR) has been employed to compare to the MM refinement results and/or neutron dataset C-H bond lengths and to crystal or single molecule geometry optimizations, including considerations of anisotropy of H atoms. Our findings help to understand properties of molecules like MTTOTHP as progenitors of free oxygen radicals.

• Klíčová slova
• N,O-bond order, O-alkyl thiohydroxamate, charge density, homolytic cleavage, hydroxylamine derivative, maximum entropy method, multipole model, quantum crystallography, quantum information crystallography,
• Publikační typ
• časopisecké články MeSH

Maximum entropy estimation is of broad interest for inferring properties of systems across many disciplines. Using a recently introduced technique for estimating the maximum entropy of a set of random discrete variables when conditioning on bivariate mutual informations and univariate entropies, we show how this can be used to estimate the direct network connectivity between interacting units from observed activity. As a generic example, we consider phase oscillators and show that our approach is typically superior to simply using the mutual information. In addition, we propose a nonparametric formulation of connected informations, used to test the explanatory power of a network description in general. We give an illustrative example showing how this agrees with the existing parametric formulation, and demonstrate its applicability and advantages for resting-state human brain networks, for which we also discuss its direct effective connectivity. Finally, we generalize to continuous random variables and vastly expand the types of information-theoretic quantities one can condition on. This allows us to establish significant advantages of this approach over existing ones. Not only does our method perform favorably in the undersampled regime, where existing methods fail, but it also can be dramatically less computationally expensive as the cardinality of the variables increases.

• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

We tested a Maximum Entropy Method developed for oversampled data (SVD-MEM) on complex analytically simulated exponential decay data consisting of both noisy and noiseless multi-exponential fluorescence decay curves. We observed recovery of simulated parameters for three sets of data: a decay containing three exponential functions in both intensity and anisotropy curves, a set of intensity decays composed of 4, 5 and 6 exponential functions, and a decay characterized by a Gaussian lifetime distribution. The SVD-MEM fitting of the noiseless data returned the simulated parameters with the high accuracy. Noise added to the data affected recovery of the parameters in dependence on a data complexity. At selected realistic noise levels we obtained a good recovery of simulated parameters for all tested data sets. Decay parameters recovered from decays containing discrete lifetime components were almost independent of the value of the entropy scaling parameter γ used in the maximization procedure when it changed across the main peak of its posterior probability. A correct recovery of the Gaussian shaped lifetime distribution required selection of the γ-factor which was by several orders of magnitude larger than its most probable value to avoid a band splitting.

• Publikační typ
• časopisecké články MeSH

The secret to the successful and widespread deployment of solar energy for thermal applications is effective and affordable heat storage. The ability to provide a high energy storage density and the capacity to store heat at a constant temperature corresponding to the phase transition temperature of the heat storage material (phase-change material or PCM) make latent heat storage one of the most alluring methods of heat storage. Today, it can be challenging to obtain all the published data on PCM qualities, including relevant non-thermodynamic properties in addition to thermodynamic ones. The developed new PCM library contains various types of PCMs which possess broad range of operation temperatures. This new library consists of 500 substances along with nine associated properties such as phase change temperature, solidification temperature, maximum operation temperature, density, latent heat and specific heat capacity, thermal conductivity, cycleability and ignition temperature. Furthermore, a new PCM selection method, based on calculating the Rényi entropy for a given set of selection criteria, has been proposed. The newly developed selection method requires no subjective judgements. The idea of the method is inspired by earlier applications of fractal analysis methods in many areas of research.

• Publikační typ
• časopisecké články MeSH

The interaction between fluorescently labeled hyaluronan and cationic surfactants was studied using Fluorescence Correlation Spectroscopy. The hyaluronan was selected at two different molecular weights - specifically, 274 kDa and 710 kDa. Cetyltrimethylammonium bromide and Septonex® were chosen as cationic surfactants to interact with the negatively charged biopolymer. The study focused on changes in the diffusive behavior of a biopolymer that interacts with surfactant molecules in an aqueous environment. Various methods were applied to evaluate the obtained data, these including, among others, the Maximum Entropy Method, which provides the distributional dependences of diffusion coefficients. Without the surfactant, the studied biopolymers showed diffusion behavior comparable to that found in previously published studies. In the presence of surfactants, more intense interaction was observed between Cetyltrimethylammonium bromide and Septonex®. Comparing the molecular weights, the retention of intermolecular aggregates after the precipitation region for the lower weight and the disintegration of these aggregates for the higher weight were observed; moreover, they showed diffusion behavior comparable to the samples without the presence of the surfactant.

• Klíčová slova
• Cetyltrimethylammonium bromide, Fluorescence correlation spectroscopy, Hyaluronan, Maximum entropy method, Septonex®,
• MeSH
• biopolymery MeSH
• cetrimonium MeSH
• fluorescenční spektrometrie MeSH
• kvartérní amoniové sloučeniny * MeSH
• kyselina hyaluronová * chemie   MeSH
• povrchově aktivní látky * chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biopolymery MeSH
• cetrimonium MeSH
• kvartérní amoniové sloučeniny * MeSH
• kyselina hyaluronová * MeSH
• povrchově aktivní látky * MeSH
• Septonex MeSH Prohlížeč

Hydrogen-Deuterium exchange mass spectrometry's (HDX-MS) utility in identifying and characterizing protein-small molecule interaction sites has been established. The regions that are seen to be protected from exchange upon ligand binding indicate regions that may be interacting with the ligand, giving a qualitative understanding of the ligand binding pocket. However, quantitatively deriving an accurate high-resolution structure of the protein-ligand complex from the HDX-MS data remains a challenge, often limiting its use in applications such as small molecule drug design. Recent efforts have focused on the development of methods to quantitatively model Hydrogen-Deuterium exchange (HDX) data from computationally modeled structures to garner atomic level insights from peptide-level resolution HDX-MS. One such method, HDX ensemble reweighting (HDXer), employs maximum entropy reweighting of simulated HDX data to experimental HDX-MS to model structural ensembles. In this study, we implement and validate a workflow which quantitatively leverages HDX-MS data to accurately model protein-small molecule ligand interactions. To that end, we employ a strategy combining computational protein-ligand docking, molecular dynamics simulations, HDXer, and dimensional reduction and clustering approaches to extract high-resolution drug binding poses that most accurately conform with HDX-MS data. We apply this workflow to model the interaction of ERK2 and FosA with small molecule compounds and inhibitors they are known to bind. In five out of six of the protein-ligand pairs tested, the HDX derived protein-ligand complexes result in a ligand root-mean-square deviation (RMSD) within 2.5 Å of the known crystal structure ligand.

• Klíčová slova
• Computational Docking, ERK2, FosAKP, HDX-MS, HDXer, Hydrogen−Deuterium Exchange, Maximum Entropy Reweighting, Molecular Dynamics Simulations, Protein−Ligand Modeling, Protein−Small Molecule Interactions, Structure Based Drug Design,
• MeSH
• konformace proteinů MeSH
• ligandy MeSH
• proteiny chemie   metabolismus   MeSH
• simulace molekulární dynamiky * MeSH
• simulace molekulového dockingu MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vodík/deuteriová výměna a hmotnostní spektrometrie * metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• ligandy MeSH
• proteiny MeSH

Time-resolved femtosecond-stimulated Raman spectroscopy (FSRS) provides valuable information on the structural dynamics of biomolecules. However, FSRS has been applied mainly up to the nanoseconds regime and above 700 cm-1, which covers only part of the spectrum of biologically relevant time scales and Raman shifts. Here we report on a broadband (~200-2200 cm-1) dual transient visible absorption (visTA)/FSRS set-up that can accommodate time delays from a few femtoseconds to several hundreds of microseconds after illumination with an actinic pump. The extended time scale and wavenumber range allowed us to monitor the complete excited-state dynamics of the biological chromophore flavin mononucleotide (FMN), both free in solution and embedded in two variants of the bacterial light-oxygen-voltage (LOV) photoreceptor EL222. The observed lifetimes and intermediate states (singlet, triplet, and adduct) are in agreement with previous time-resolved infrared spectroscopy experiments. Importantly, we found evidence for additional dynamical events, particularly upon analysis of the low-frequency Raman region below 1000 cm-1. We show that fs-to-sub-ms visTA/FSRS with a broad wavenumber range is a useful tool to characterize short-lived conformationally excited states in flavoproteins and potentially other light-responsive proteins.

• Klíčová slova
• femtosecond-stimulated Raman spectroscopy (FSRS), flavins, kinetic isotope effect (KIE), lifetime distribution analysis (LDA), light-oxygen-voltage (LOV) photosensors, maximum entropy method, photobiology, photochemistry, protein structural dynamics, time-resolved vibrational spectroscopy, transient visible absorption (visTA) spectroscopy,
• MeSH
• Ramanova spektroskopie * metody   MeSH
• spektrofotometrie infračervená MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH