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Search results for: ITEM RESPONSE THEORY
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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
PublicationIn this paper we present a new environment called MERPSYS that allows simulation of parallel application execution time on cluster-based systems. The environment offers a modeling application using the Java language extended with methods representing message passing type communication routines. It also offers a graphical interface for building a system model that incorporates various hardware components such as CPUs, GPUs, interconnects...
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Equitable coloring of corona multiproducts of graphs
PublicationWe give some results regarding the equitable chromatic number for l-corona product of two graphs: G and H, where G is an equitably 3- or 4-colorable graph and H is an r-partite graph, a cycle or a complete graph. Our proofs lead to polynomial algorithms for equitable coloring of such graph products provided that there is given an equitable coloring of G.
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On incidence coloring of coloring of complete multipartite and semicubic bipartite graphs
PublicationIn the paper, we show that the incidence chromatic number of a complete k-partite graph is at most ∆+2 (i.e., proving the incidence coloring conjecture for these graphs) and it is equal to ∆+1 if and only if the smallest part has only one vertex.
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Amplifying the Randomness of Weak Sources Correlated With Devices
PublicationThe problem of device-independent randomness amplification against no-signaling adversaries has so far been studied under the assumption that the weak source of randomness is uncorrelated with the (quantum) devices used in the amplification procedure. In this paper, we relax this assumption, and reconsider the original protocol of Colbeck and Renner using a Santha-Vazirani (SV) source. To do so, we introduce an SV-like condition...
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Multiple solutions of boundary-value problems for fourth-order differential equations with deviating arguments
PublicationPraca dotyczy równań różniczkowych rzędu czwartego z warunkami brzegowymi i odchylonymi argumentami. Podano wystarczające warunki, dla których problemy dotyczące takich równań mają dodatnie rozwiązania. W pracy rozważa się przypadki kiedy argumenty odchylone są typu opóźnionego lub wyprzedzonego. W celu zapewnienia istnienia przynajmniej trzech dodatnich rozwiązań wykorzystano twierdzenie Avery-Petersona.
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A few steps more towards NPT bound entanglement
PublicationIn this paper, existence of bound entangled states with nonpositive partial transpose (NPT) is considered. As one knows, existence of such states would in particular imply nonadditivity of distillable entanglement. Moreover, it would rule out a simple mathematical description of the set of distillable states. The particular state, known to be 1-copy nondistillable and supposed to be bound entangled, is considered. The problem of...
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Parity vertex colouring of graphs
PublicationA parity path in a vertex colouring of a graph is a path along which each colour is used an even number of times. Let Xp(G) be the least number of colours in a proper vertex colouring of G having no parity path. It is proved that for any graph G we have the following tight bounds X(G) <= Xp(G) <=|V(G)|− a(G)+1, where X(G) and a(G) are the chromatic number and the independence number of G, respectively. The bounds are improved for...
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The complexity of node blocking for dags
PublicationRozważamy następującą grę (pomiędzy dwoma graczami) kombinatoryczną o nazwie ''node blocking''. Dany jest graf skierowany. Każdy wierzchołek może być zajęty przez co najwyżej jeden token. Wyróżniamy dwa kolory tokenów, biały i czarny, każdy gracz może przemieszczać tylko własne tokeny. Gracze wykonują ruchy naprzemiennie. Ruch polega na wyborze dowolnego tokena własnego koloru i przesunięciu go na dowolnego niezajętego przez inny...
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Some variations of perfect graphs
PublicationWe consider (ψk−γk−1)-perfect graphs, i.e., graphs G for which ψk(H) =γk−1(H) for any induced subgraph H of G, where ψk and γk−1 are the k -path vertex cover number and the distance (k−1)-domination number, respectively. We study (ψk−γk−1)-perfect paths, cycles and complete graphs for k≥2. Moreover, we provide a complete characterisation of (ψ2−γ1)-perfect graphs describing the set of its forbidden induced subgraphs and providing...
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On-line P-coloring of graphs
PublicationFor a given induced hereditary property P, a P-coloring of a graph G is an assignment of one color to each vertex such that the subgraphs induced by each of the color classes have property P. We consider the effectiveness of on-line P-coloring algorithms and give the generalizations and extensions of selected results known for on-line proper coloring algorithms. We prove a linear lower bound for the performance guarantee function...
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Iterative‐recursive estimation of parameters of regression models with resistance to outliers on practical examples
PublicationHere, identification of processes and systems in the sense of the least sum of absolute values is taken into consideration. The respective absolute value estimators are recognised as exceptionally insensitive to large measurement faults or other defects in the processed data, whereas the classical least squares procedure appears to be completely impractical for processing the data contaminated with such parasitic distortions. Since...
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Periodic Solutions of Generalized Lagrangian Systems with Small Perturbations
PublicationIn this paper we study the generalized Lagrangian system with a small perturbation. We assume the main term in the system to have a maximum, but do not suppose any condition for perturbation term. Then we prove the existence of a periodic solution via Ekeland’s principle. Moreover, we prove a convergence theorem for periodic solutions of perturbed systems.
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Distortion in the group of circle homeomorphisms
PublicationLet G be the group PAff+(R/Z) of piecewise affine circle homeomorphisms or the group Diff∞(R/Z) of smooth circle diffeomorphisms. A constructive proof that all irrational rotations are distorted in G is given.
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Efficient parallel implementation of crowd simulation using a hybrid CPU+GPU high performance computing system
PublicationIn the paper we present a modern efficient parallel OpenMP+CUDA implementation of crowd simulation for hybrid CPU+GPU systems and demonstrate its higher performance over CPU-only and GPU-only implementations for several problem sizes including 10 000, 50 000, 100 000, 500 000 and 1 000 000 agents. We show how performance varies for various tile sizes and what CPU–GPU load balancing settings shall be preferred for various domain...
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Graph classes generated by Mycielskians
PublicationIn this paper we use the classical notion of weak Mycielskian M'(G) of a graph G and the following sequence: M'_{0}(G) =G, M'_{1}(G)=M'(G), and M'_{n}(G)=M'(M'_{n−1}(G)), to show that if G is a complete graph oforder p, then the above sequence is a generator of the class of p-colorable graphs. Similarly, using Mycielskian M(G) we show that analogously defined sequence is a generator of the class consisting of graphs for which the...
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A note on polynomial algorithm for cost coloring of bipartite graphs with Δ ≤ 4
PublicationIn the note we consider vertex coloring of a graph in which each color has an associated cost which is incurred each time the color is assigned to a vertex. The cost of coloring is the sum of costs incurred at each vertex. We show that the minimum cost coloring problem for n-vertex bipartite graph of degree ∆≤4 can be solved in O(n^2) time. This extends Jansen’s result [K.Jansen,The optimum cost chromatic partition problem, in:...
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Block graphs with large paired domination multisubdivision number
PublicationThe paired domination multisubdivision number of a nonempty graph G, denoted by msdpr(G), is the smallest positive integer k such that there exists an edge which must be subdivided k times to increase the paired domination number of G. It is known that msdpr(G) ≤ 4 for all graphs G. We characterize block graphs with msdpr(G) = 4.
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On the Characteristic Graph of a Discrete Symmetric Channel
PublicationWe present some characterizations of characteristic graphs of row and/or column symmetric channels. We also give a polynomial-time algorithm that decides whether there exists a discrete symmetric channel whose characteristic graph is equal to a given input graph. In addition, we show several applications of our results.
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Invariant Measures for Uncountable Random Interval Homeomorphisms
PublicationA necessary and sufficient condition for the iterated function system { f (·, ω) | ω ∈ } with probability P to have exactly one invariant measure μ∗ with μ∗((0, 1)) = 1 is given. The main novelty lies in the fact that we only require the transformations f (·, ω) to be increasing homeomorphims, without any smoothness condition, nei- ther we impose conditions on the cardinality of . In particular, positive Lyapunov exponents conditions...
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Domination numbers in graphs with removed edge or set of edges
PublicationW artykule przedstawiony jest wpływ usuwania krawędzi lub zbioru krawędzi na liczby dominowania spójnego i słabo spójnego.
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Predyspozycje zawodowe artysty a cechy przedsiębiorcze
PublicationArtykuł stanowi analizę porównawczą cech osobowości przypisywanych artystom z charakterystyką skutecznego przedsiębiorcy. Podstawą zestawienia jest profil osobowości twórczej, typy osobowości zawodowych oraz profil osobowości przedsiębiorcy. Celem artykułu jest wskazanie zakresu kompetencji, które mogą być niedostępne dla twórców, a które warunkują realizację przedsięwzięć biznesowych. Potwierdzeniem konieczności integracji sylwetki...
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Idea zastosowania sztucznej inteligencji w prognozowaniu wpływu drgań komunikacyjnych na odpowiedź dynamiczną budynków mieszkalnych
PublicationW poniższym artykule autorzy analizują wpływ drgań komunikacyjnych na budynki mieszkalne oraz metodykę pomiarową według PN-85 B-02170 [1]. Problemem badawczym jest opracowanie prostej metody prognozowania wpływu drgań na budynki mieszkalne w taki sposób, aby nie było konieczne przeprowadzanie pracochłonnych i kosztownych pomiarów polowych. W tym celu wykonano analizę przy użyciu algorytmów opartych na sztucznej inteligencji oraz...
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Pupil size reflects successful encoding and recall of memory in humans
PublicationPupil responses are known to indicate brain processes involved in perception, attention and decision-making. They can provide an accessible biomarker of human memory performance and cognitive states in general. Here we investigated changes in the pupil size during encoding and recall of word lists. Consistent patterns in the pupil response were found across and within distinct phases of the free recall task. The pupil was most...
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Multi-Fidelity Local Surrogate Model for Computationally Efficient Microwave Component Design Optimization
PublicationIn order to minimize the number of evaluations of high-fidelity (“fine”) model in the optimization process, to increase the optimization speed, and to improve optimal solution accuracy, a robust and computational-efficient multi-fidelity local surrogate-model optimization method is proposed. Based on the principle of response surface approximation, the proposed method exploits the multi-fidelity coarse models and polynomial interpolation...
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Determination of toxic gases based on the responses of a single electrocatalytic sensor and pattern recognition techniques
PublicationA response from an electrocatalytic gas sensor contains fingerprint information about the type of gas and its concentration. As a result, a single gas sensor can be used for the determination of different gases. However, information about the type of gas and its concentration is hidden in the unique shape of the current–voltage response and it is quite difficult to explore. One of the ways to get precise information about the measured...
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Polymeric Bearings – A New Base Isolation System to Reduce Structural Damage during Earthquakes
PublicationBase isolators, like lead rubber bearings, high damping rubber bearings or friction pendulum systems are extensively used in practice in many seismically active regions to protect structures against earthquake forces. The present paper reports the results obtained from the experimental study aimed to determine the effectiveness of the Polymeric Bearings in suppressing structural vibrations during dynamic excitations and therefore...
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Traffic Model of IMS/NGN Architecture with Transport Stratum Based on MPLS Technology
PublicationGrowing expectations for a fast access to information create strong demands for a universal telecommunication network architecture, which provides various services with strictly determined quality. Currently it is assumed that these requirements will be satisfied by Next Generation Network (NGN), which consists of two stratums and includes IP Multimedia Subsystem (IMS) elements. To guarantee Quality of Service (QoS) all NGN stratums...
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Synthesis of thiol derivatives of azobenzocrown ethers. The preliminary studies on recognition of alkali metal ions by gold nanoparticles functionalized with azobenzocrown and lipoic acid
PublicationThe article presents the synthesis of novel 13- and 16-membered azobenzocrown derivatives with peripheral thiol moieties and preliminary studies assessing their possible application in plasmonic sensors based on gold nanoparticles. The effect of the length of the chain connecting the macrocycle with the thiol group and the effect of the presence of the additional functional compound,...
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Photoinactivation of Staphylococcus aureus using protoporphyrin IX: the role of haem-regulated transporter HrtA
PublicationLight- and photosensitiser-based antimicrobial photodynamic therapy is a very promising approach to the control of microbial infections. How the phenotypic features of a microorganism affect its response to photosensitiser-based photokilling represents an area of substantial research interest. To understand the mechanisms governing the phenomenon of a strain-dependent response to photodynamic inactivation (PDI), we analysed the...
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Reduction of vibrations of steel structure models with Polymeric Bearings - experimental study
PublicationEarthquake-induced ground motions are the most severe and unpredictable threats to the structures all around the world. Therefore, designing earthquake protective systems has become an extremely challenging problem in civil engineering. Base isolation is one of the most popular and widely adopted methods of protecting structures against earthquake forces. The present paper reports the results obtained from the shaking table experimental...
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Pounding between Inelastic Three-Storey Buildings under Seismic Excitations
PublicationStructural interactions between adjacent, insufficiently separated buildings have been repeatedly observed during damaging ground motions. This phenomenon, known as the structural pounding, may result in substantial damage or even total collapse of structures. The aim of the present paper is to show the results of the nonlinear numerical analysis focused on pounding between inelastic three-storey buildings under seismic excitations....
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Tuning the photocatalytic performance through magnetization in Co-Zn ferrite nanoparticles
PublicationIn this work, the link between the photocatalytic performance of Co-Zn ferrite nanoparticles and the net magnetic moment is analyzed. CoxZn1-xFe2O4 nanoparticles (0 ≤ x ≤ 1) were synthesized by co-precipitation method and different physicochemical techniques were employed to characterize the samples (X-ray diffraction, Transmission Electron Microscopy (TEM), BET surface area, Diffuse Reflectance Spectroscopy (DRS), Photoluminescence spectroscopy,...
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Analysis of ultimate compressive strength of cracked plates with the use of DOE techniques
PublicationThe objective of this work is to investigate the structural compressive response of plates with locked cracks accounting for all relevant factors and correlation between them. The nonlinear FE model considering both geometric and material nonlinearities is employed herein, and the FE model of the structural response of intact plates is validated with the available experimental data. In the common studies, based on One Factor at...
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Fluctuation-enhanced and conductometric gas sensing with nanocrystalline NiO thin films: A comparison
PublicationNanocrystalline thin films of NiO were prepared by advanced reactive gas deposition, and their responses to formaldehyde, ethanol and methane gases were studied via fluctuation-enhanced and conductometric methods Thin films with thicknesses in the 200–1700-nm range were investigated in as-deposited form and after annealing at 400 and 500 °C. Morphological and structural analyses showed porous deposits with NiO nanocrystals having...
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Waves Along Fractal Coastlines: From Fractal Arithmetic to Wave Equations
PublicationBeginning with addition and multiplication intrinsic to a Koch-type curve, we formulate and solve wave equation describing wave propagation along a fractal coastline. As opposed to examples known from the literature, we do not replace the fractal by the continuum in which it is embedded. This seems to be the first example of a truly intrinsic description of wave propagation along a fractal curve. The theory is relativistically...
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A study on transverse shear correction for laminated sandwich panels
PublicationThe paper presents a study on an application of the First Order Shear Deformation Theory in a linear static analysis of elastic sandwich panels. A special attention has been given to the issue of the transverse shear correction. Two benchmark examples of sandwich plate problems with known reference solutions have been selected for a comparative analysis performed with own Finite Element codes. Interesting results allowed for drawing...
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Effects of consecutive apneas on pial artery pulsation and subarachnoid width in healthy subjects
PublicationHypercapnia is known to dilate the pial artery, disrupt cerebral autoregulation and increase pial artery pulsation. The cerebral blood flow velocity (CBFV) response to hypercapnia is biphasic. Below the threshold for the increase of blood pressure (BP) with carbon dioxide partial pressure (pCO2), the CBFV measurement reflects vascular reactivity to pCO2 alone at a constant BP. Above this threshold, the CBFV measurement provides...
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Fast and reliable knowledge-based design closure of antennas by means of iterative prediction-correction scheme
PublicationA novel framework for expedited antenna optimization with an iterative prediction-correction scheme is proposed. The methodology is comprehensively validated using three real-world antenna structures: narrow-band, dual-band and wideband, optimized under various design scenarios. The keystone of the proposed approach is to reuse designs pre-optimized for various sets of performance specifications and to encode them into metamodels...
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Identification of defected sensors in an array of amperometric gas sensors
PublicationPurpose Amperometric gas sensors are commonly used in air quality monitoring in long-term measurements. Baseline shift of sensor responses and power failure may occur over time, which is an obstacle for reliable operation of the entire system. The purpose of this study is to check the possibility of using PCA method to detect defected samples, identify faulty sensor and correct the responses of the sensor identified as faulty. Design/methodology/approach In...
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Self-adjusting sub-sample delay estimator based on fractional delaying Hilbert transform filter
PublicationZaprezentowano nowe rozwiązanie samo-nastrajalnego estymatora opóźnienia sygnału sinusoidalnego, działającego w czasie dyskretnym. Zastosowano filtr Hilberta o skończonej odpowiedzi ipulsowej (FIR od ang. finite impulse response) zagregowany z filtrem ułamkowo-opóźniającym. Zilustrowano performancję estymatora, również w obecności szumu. Przeanalizowano jego złożoność numeryczną.