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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublikacjaCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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The finite-difference simulation of x-rays propagation through a system of lenses
PublikacjaThe propagation of X-ray waves through an optical system consisting of 33 aluminum X-ray refractive lenses is considered. For solving the problem, a finite-difference method is suggested and investigated. It is shown that very small steps of the difference grid are necessary for reliable computation of propagation of X-ray waves through the system of lenses. It is shown that the wave phase is a function very quickly increasing...
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Weakly connected Roman domination in graphs
PublikacjaA Roman dominating function on a graph G=(V,E) is defined to be a function f :V → {0,1,2} satisfying the condition that every vertex u for which f(u) = 0 is adjacent to at least one vertex v for which f(v)=2. A dominating set D⊆V is a weakly connected dominating set of G if the graph (V,E∩(D×V)) is connected. We define a weakly connected Roman dominating function on a graph G to be a Roman dominating function such that the set...
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More Just Measure of Fairness for Sharing Network Resources
PublikacjaA more just measure of resource distribution in computer networks is proposed. Classic functions evaluate fairness only “on average”. The proposed new fairness score function ensures that no node is left without resources while on average everything looks good. It is compared with well-known and widely adopted function proposed by Jain, Chiu and Hawe and another one recently proposed fairness function by Chen and Zhang. The function...
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Rating mathematical models for first-pass of tracer in pCT lung studies
PublikacjaThis paper presents a comparison of model based on the Gauss function and the most commonly used Gamma-variate model in perfusion computed tomography (pCT) lung studies. It also verifies whether used model affects value of blood volume parameter. Three mean concentration-time curves were created from actual pCT measurements: arterial input function, blood vessels in lungs and lung parenchyma. On the basis of these mean curves we...
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Clarke duality for Hamiltonian systems with nonstandard growth
PublikacjaWe consider the existence of periodic solutions to Hamiltonian systems with growth conditions involving G-function. We introduce the notion of symplectic G-function and provide relation for the growth of Hamiltonian in terms of certain constant CG associated to symplectic G-function G. We discuss an optimality of this constant for some special cases. We also provide applications to the Φ-laplacian type systems.
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Complex Root Finding Algorithm Based on Delaunay Triangulation
PublikacjaA simple and flexible algorithm for finding zeros of a complex function is presented. An arbitrary-shaped search region can be considered and a very wide class of functions can be analyzed, including those containing singular points or even branch cuts. The proposed technique is based on sampling the function at nodes of a regular or a self-adaptive mesh and on the analysis of the function sign changes. As a result, a set of candidate points...
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Alternative convolution approach to friction in unsteady pipe flow
PublikacjaIn the paper some aspects of the unsteady friction in pipe flow expressed by the convolution are analyzed. This additional term introduced into the motion equation involves the accelerations of fluid occurring in the past and a weighting function. The essence of such approach is to assume the appropriate form of weighting function. However, until now no fully reliable formula for this function has been found. To avoid some inconveniences...
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A high-accuracy complex-phase method of simulating X-ray propagation through a multi-lens system
PublikacjaThe propagation of X-ray waves through an optical system consisting of many X-ray refractive lenses is considered. For solving the problem for an electromagnetic wave, a finite-difference method is applied. The error of simulation is analytically estimated and investigated. It was found that a very detailed difference grid is required for reliable and accurate calculations of the propagation of X-ray waves through a multi-lens...
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A Concept of Thermal Effort for Heat-Induced Metal Plasticity
PublikacjaThis paper proposes a new concept of material effort that considers heat-induced plasticity for heat-resistant steels. These steels indicate a strength differential effect, a stress shearness effect, pressure sensitivity, and other features. Therefore, a three-parameter, temperature-dependent yield function was presented and, next, analytically and geometrically researched. To validate the accuracy of the formulated yield function,...
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Modified Preisach model of hysteresis in multi air gap ferrite core medium frequency transformer
PublikacjaThis article presents the modified Preisach model of hysteresis for a 3-phase medium frequency transformer in a 100 kW dual active bridge converter. The transformer magnetic core is assembled out of ferrite I-cores, which results in multiple parasitic air gaps. For this transformer, the hysteresis loops were measured and parameters of the Preisach model were determined. The Preisach distribution function is approximated with a...
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Testing the impact of simplifications adopted in models describing wave loads on ship
PublikacjaThe wave-ship system in naval architecture is generally assumed to be a linear one. This allows for the computation of a transfer function of ship response to waves including wave loads on ship. The transfer function and the wave spectral density function enable the development of the stochastic process of wave loads on ship, corresponding to the irregular wave generating that loads. If the mathematical models of wave load transfer...
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Testing the impact of simplifications adopted in models describing wave loads on ship
PublikacjaThe wave-ship system in naval architecture is generally assumed to be a linear one. This allows for the computation of a transfer function of ship response to waves including wave loads on ship. The transfer function and the wave spectral density function enable the development of the stochastic process of wave loads on ship, corresponding to the irregular wave generating that loads. If the mathematical models of wave load transfer...
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Automated Design of Linear Phase Filters
PublikacjaThis paper presents a fast technique for an automated design of microwave filters with linear phase. The proposed method exploits the cost function defined using the location of complex zeros and poles of the filter’s transfer and reflection function. The effectiveness of the proposed technique is presented with two illustrative examples.
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The influence of pressure drop on the working volume of a hydraulic motor
PublikacjaReliability and maintenance analysis of hydraulic positive machines basicly focused on the processes of their wear and failure. But in order to correctly assess the mechanical and volumetric efficiency of a hydraulic motor, both at the stage of development research or at the stage of control tests during its exploitation, the working volume of this motor must be correctly determined. Therefore this paper proposes a new method of...
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Proposal of New Tracer Concentration Model in Lung PCT Study Comparison with Commonly Used Gamma-variate Model
PublikacjaPerfusion computed tomography (pCT) is one of the methods that enable non-invasive imaging of the hemodynamics of organs and tissues. On the basis of pCT measurements, perfusion parameters such as blood flow (BF), blood volume (BV), mean transit time (MTT) and permeability surface (PS) are calculated and then used for quantitative evaluation of the tissue condition. To calculate perfusion parameters it is necessary to approximate...
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Simplified saturation modelling in three-leg power transformer for the system stability analisys
PublikacjaThe paper presents a simplified method for modelling non-linearity of the magnetic circuit of the power transformer. The saturation effect is implemented by describing the self and mutual inductances as a function of the magnetic flux. The most important element of this function is the saturation coefficient which is calculated based on transient state during the unloaded transformer switch on. The transformer model is described...
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Interpolation properties of domination parameters of a graph
PublikacjaAn integer-valued graph function π is an interpolating function if a set π(T(G))={π(T): T∈TT(G)} consists of consecutive integers, where TT(G) is the set of all spanning trees of a connected graph G. We consider the interpolation properties of domination related parameters.
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Signal Propagation in Electromagnetic Media Modelled by the Two-Sided Fractional Derivative
PublikacjaIn this paper, wave propagation is considered in a medium described by a fractional-order model, which is formulated with the use of the two-sided fractional derivative of Ortigueira and Machado. Although the relation of the derivative to causality is clearly specified in its definition, there is no obvious relation between causality of the derivative and causality of the transfer function induced by this derivative. Hence, causality...
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On root finding algorithms for complex functions with branch cuts
PublikacjaA simple and versatile method is presented, which enhances the complex root finding process by eliminating branch cuts and branch points in the analyzed domain. For any complex function defined by a finite number of Riemann sheets, a pointwise product of all the surfaces can be obtained. Such single-valued function is free of discontinuity caused by branch cuts and branch points. The roots of the new function are the same as the...
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Global Surrogate Modeling by Neural Network-Based Model Uncertainty
PublikacjaThis work proposes a novel adaptive global surrogate modeling algorithm which uses two neural networks, one for prediction and the other for the model uncertainty. Specifically, the algorithm proceeds in cycles and adaptively enhances the neural network-based surrogate model by selecting the next sampling points guided by an auxiliary neural network approximation of the spatial error. The proposed algorithm is tested numerically...
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Zero-range potentials for Dirac particles: Bound-state problems
PublikacjaA model in which a massive Dirac particle in $\mathbb{R}^{3}$ is bound by $N\geqslant1$ spatially distributed zero-range potentials is presented. Interactions between the particle and the potentials are modeled by subjecting a particle's bispinor wave function to certain limiting conditions at the potential centers. Each of these conditions is parametrized by a $2\times2$ Hermitian matrix (or, equivalently, a real scalar and a...
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Representation of magnetic hysteresis in single-phase transformer for circuit simulations
PublikacjaThe paper presents a mathematical model for the hysteresis phenomenon in a multi-winding single-phase core type transformer. In the circuit transformer model, it is assumed that there is a flux common Φ to all windings as nonlinear and hysteretic function of the total currents Θ (Ampere turns) of all windings. To simulate magnetic behaviour of the iron core the feedback scalar Preisach model of hysteresis is developed. The Preisach...
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New potential functions for greedy independence and coloring
PublikacjaA potential function $f_G$ of a finite, simple and undirected graph $G=(V,E)$ is an arbitrary function $f_G : V(G) \rightarrow \mathbb{N}_0$ that assigns a nonnegative integer to every vertex of a graph $G$. In this paper we define the iterative process of computing the step potential function $q_G$ such that $q_G(v)\leq d_G(v)$ for all $v\in V(G)$. We use this function in the development of new Caro-Wei-type and Brooks-type...
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Substrate-integrated waveguide (SIW) filter design using space mapping
PublikacjaIn this paper, we present a fast technique for an automated design of microwave filters in substrate integrated wave (SIW) technology. The proposed methodology combines the space mapping technique with a cost function defined using the location of complex zeros and poles of filter’s transfer and reflection function and uses a rectangular waveguide as a surrogate model. The effectiveness of the proposed technique is presented with...
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Secure Italian domination in graphs
PublikacjaAn Italian dominating function (IDF) on a graph G is a function f:V(G)→{0,1,2} such that for every vertex v with f(v)=0, the total weight of f assigned to the neighbours of v is at least two, i.e., ∑u∈NG(v)f(u)≥2. For any function f:V(G)→{0,1,2} and any pair of adjacent vertices with f(v)=0 and u with f(u)>0, the function fu→v is defined by fu→v(v)=1, fu→v(u)=f(u)−1 and fu→v(x)=f(x) whenever x∈V(G)∖{u,v}. A secure Italian dominating...
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Multimodal Genetic Algorithm with Phase Analysis to Solve Complex Equations of Electromagnetic Analysis
PublikacjaIn this contribution, a new genetic-algorithm-based method of finding roots and poles of a complex function of a complex variable is presented. The algorithm employs the phase analysis of the function to explore the complex plane with the use of the genetic algorithm. Hence, the candidate regions of root and pole occurrences are selected and verified with the use of discrete Cauchy's argument principle. The algorithm is evaluated...
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Modeling variable curvature on the turnout diverging track length
PublikacjaThe paper presents three variants of variable curvature application on the entire length of the turnout diverging track. One linear and two nonlinear curvature cases: described the function of C1 and C0 class were considered. It turned out that both linear curve and the function of C1 class requires a significant (even twice) length of diverging track extending with respect to the base turnout. The curvature described by the function...
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Measures of region failure survivability for wireless mesh networks
PublikacjaWireless mesh networks (WMNs) are considered as a promising alternative to wired local, or metropolitan area networks. However, owing to their exposure to various disruptive events, including natural disasters, or human threats, many WMN network elements located close to the failure epicentre are frequently in danger of a simultaneous failure, referred to as a region failure. Therefore, network survivability, being the ability...
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Termination functions for evolutionary path planning algorithm
PublikacjaIn this paper a study of termination functions (stop criterion) for evolutionary path planning algorithm is presented. Tested algorithm is used to determine close to optimal ship paths in collision avoidance situation. For this purpose a path planning problem is defined. A specific structure of the individual path and fitness function is presented. For the simulation purposes a close to real tested environment is created. Five...
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Investigation of Liquid–Gas Flow in a Horizontal Pipeline Using Gamma-Ray Technique and Modified Cross-Correlation
PublikacjaThis article presents the application of the radioisotope absorption method in the study of two-phase water–air flow in a horizontal pipe. The measurement principle and the test stand are briefly described. The main part of the article presents the signal analysis methods applied to data obtained from scintillation detectors. Because these signals are mostly stochastic waveforms, they were analyzed statistically using the cross-correlation...
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Representation of magnetic hysteresis in a circuit model of a single-phase transformer
PublikacjaThe paper presents a mathematical model for the hysteresis phenomenon in a multi-winding single-phase core type transformer. The set of loop differential equations was developed for K-th winding transformer model where the flux linkages of each winding includes a flux common Φ to all windings as function of magneto motive force Θ of all windings. The first purpose of this paper is to determine a hysteresis nonlinearity involved...
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On Surface Kinetic Constitutive Relations
PublikacjaIn the framework of the strain gradient surface elasticity we discuss a consistent form of surface kinetic energy. This kinetic constitutive equation completes the statement of initial–boundary value problems. The proposed surface kinetic energy density is the most general function consistent with the constitutive relations in bulk. As the surface strain energy depends on the surface deformation gradient and its gradient, the kinetic...
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Wykładnicze równanie Arrheniusa jako funkcja dojrzałości twardniejącego betonu
PublikacjaPoprawne określenie funkcji dojrzałości dla mieszanki betonowej warunkuje powodzenie szacowania wytrzymałości na ściskanie na bazie pomiarów temperatury in situ. W artykule omówiono zastosowanie równania Arrheniusa do opisu funkcji dojrzewania twardniejącego betonu. Szczególną uwagę zwrócono na zależności szybkości zachodzenia reakcji w odmiennych warunkach temperaturowych. Przedstawiono wyniki własnych badań na kostkach zaprawy...
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Density smoothness estimation problem using a wavelet approach
PublikacjaIn this paper we consider a smoothness parameter estimation problem for a density function. The smoothness parameter of a function is defined in terms of Besov spaces. This paper is an extension of recent results (K. Dziedziul, M. Kucharska, B. Wolnik, Estimation of the smoothness parameter ). The construction of the estimator is based on wavelets coefficients. Although we believe that the effective estimation of the smoothness...
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Adaptive CAD-Model Construction Schemes
PublikacjaTwo advanced surrogate model construction techniques are discussed in this paper. The models employ radial basis function (RBF)interpolation scheme or artificial neural networks (ANN) with a new training algorithm. Adaptive sampling technique is applied withrespect to all variables. Histograms showing the quality of the models are presented. While the quality of RBF models is satisfactory, theperformance of the ANN models obtained...
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Technical Limitations in Merging Secular and Sacred Functions in Monumental Churches
PublikacjaThe abandonment of churches and their adaptation for secular purposes is a current subject in Europe and worldwide. Most cases involve objects that were desacralized and then rebuilt as a whole object for alternative functions. Thus far, the merging of secular and sacred functions in one monumental Catholic church has not raised any issues. The paper describes the case of St. Catherine’s Church in Gdansk, Poland, where sacred function...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublikacjaEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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Multi-Option Model of Railway Traffic Organization Including the Energy Recuperation
PublikacjaThe article presents the issue of organization of railway traffic within the station, taking into account energy recuperation. We identified a number of factors which affect the energy efficiency of recuperation, including the issue of transfer of energy technology between a few vehicles. We presented some aspects of the decision problem of graphic train timetable construction with regard to recuperation. As an indicator of quality...
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Firing map for periodically and almost-periodically driven integrate-and-fire models: a dynamical systems approach
PublikacjaWe consider the Leaky Integrate-and-Fire and Perfect Integrator models of neuron’s dynamics with the input function being periodic and almost-periodic (in the sense of Stepanov). In particular we analyze properties and dynamics of the so-called firing map, which iterations give timings of consecutive spikes of a neuron. In case of a periodic input function we provide a detailed description of the sequence of interspike-intervals,...
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Zero-Pole Space Mapping for CAD of Filters
PublikacjaIn this paper, we propose a new space-mapping technique tailored to the CAD of microwave filters. The goal of space mapping is to achieve a satisfactory design with the minimal number of fine model evaluations. In our approach, the filter is represented by a rational function. To quickly align the coarse and fine models, and to speed up the direct optimization of the coarse model, we propose matching the zeros and poles of a rational...
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Możliwość oszacowania niezawodności silników o zapłonie samoczynnym z zastosowaniem teorii procesów semi-Markowa oraz podejmowania decyzji eksploatacyjnych z uwzględnieniem wiarygodności diagnozy o stanie technicznym tego rodzaju silników spalinowych = Possibility of estimating the reliability of diesel engines by applying the theory of semi-Markov processes and making operational decisions by considering reliability of diagnosis on technical state of this sort of combustion engines/
PublikacjaThe paper presents semi-Markov models of technical state transitions for diesel engines, useful for determining reliability of the engines. A possibility of application of a three-state model with a simplified matrix function, or even a two-state model, to determine reliability of the engines, has been described herein on examples of known from literature semi-Markov models, for the case when appropriate diagnosing systems (SDG)...
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Testing Stability of Digital Filters Using Multimodal Particle Swarm Optimization with Phase Analysis
PublikacjaIn this paper, a novel meta-heuristic method for evaluation of digital filter stability is presented. The proposed method is very general because it allows one to evaluate stability of systems whose characteristic equations are not based on polynomials. The method combines an efficient evolutionary algorithm represented by the particle swarm optimization and the phase analysis of a complex function in the characteristic equation....
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Influence of water and mineral oil on the leaks in satellite motor commutation unit clearances
PublikacjaThe article describes the flow rates of mineral oil and water flowing, as working media, through the commutation unit of a hydraulic satellite motor. It is demonstrated that geometrical dimensions of commutation unit clearances change as a function of the machine shaft rotation angle. Methods for measuring the rate of this flow and the pressure in the working chamber are presented. The results of pressure measurements in the working...