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Wyniki wyszukiwania dla: TITSCHMARSCH’S THEOREM
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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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Cooperative mobile guards in grids
PublikacjaPraca dotyczy problemu strzeżenia dwuwymiarowych krat ortogonalnych, przy założeniu, że obszar widoczności strażnika obejmuje jedną ulicę oraz wszystkie ulice ją przecinające. Rozważano wariant straży słabo współpracujących, w którym dodatkowo każdy strażnik musi widzieć przynajmniej jednego innego strażnika. Podano dowód NP-trudności problemu optymalizacyjnego w przypadku ogólnym, algorytm dokładny o złożoności O(n log n) dla...
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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TOTAL DOMINATION MULTISUBDIVISION NUMBER OF A GRAPH
PublikacjaThe domination multisubdivision number of a nonempty graph G was defined in [3] as the minimum positive integer k such that there exists an edge which must be subdivided k times to increase the domination number of G. Similarly we define the total domination multisubdivision number msd_t (G) of a graph G and we show that for any connected graph G of order at least two, msd_t (G) ≤ 3. We show that for trees the total domination...
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An Assessment of RASSCF and TDDFT Energies and Gradients on an Organic Donor−Acceptor Dye Assisted by Resonance Raman Spectroscopy
PublikacjaThe excitation energies and gradients in the ground and the first excited state of a novel donor−(π- bridge)−acceptor 4-methoxy-1,3-thiazole-based chromophore were investigated by means of MS-RASPT2/RASSCF and TDDFT in solution. Within both methods, the excitation energies strongly depend on the employed equilibrium structures, whose differences can be rationalized in terms of bond length alternation indexes. It is shown that functionals with...
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Optimal backbone coloring of split graphs with matching backbones
PublikacjaFor a graph G with a given subgraph H, the backbone coloring is defined as the mapping c: V(G) -> N+ such that |c(u)-c(v)| >= 2 for each edge uv \in E(H) and |c(u)-c(v)| >= 1 for each edge uv \in E(G). The backbone chromatic number BBC(G;H) is the smallest integer k such that there exists a backbone coloring with max c(V(G)) = k. In this paper, we present the algorithm for the backbone coloring of split graphs with matching backbone.
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Total outer-connected domination in trees
PublikacjaW pracy przedstawiono dolne ograniczenie na liczbę dominowania totalnego zewnętrznie spójnego w grafach oraz scharakteryzowano wszystkie drzewa osiągające to ograniczenie.
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Nordhaus-Gaddum results for the weakly convex domination number of a graph
PublikacjaArtykuł dotyczy ograniczenia z góry i z dołu (ze względu na ilość wierzchołków) sumy i iloczynu liczb dominowania wypukłego grafu i jego dopełnienia.
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A few steps more towards NPT bound entanglement
PublikacjaIn 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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The complexity of node blocking for dags
PublikacjaRozważamy 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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Positive solutions of one-dimensional p-Laplacian boundary value problems for fourth-order differential equations with deviating arguments
PublikacjaPraca dotyczy istnienia dodatnich rozwiązań dla równań różniczkowych rzędu czwartego z warunkami brzegowymi z odchylonymi argumentami. Stosując twierdzenie o punkcie stałym dla stożków podano warunki dostateczne na istnienia takich rozwiązań.
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Graphs with equal domination and 2-distance domination numbers
PublikacjaW publikacji scharakteryzowane są wszystkie te drzewa i grafy jednocykliczne, w których liczba dominowania oraz liczba 2-dominowania na odległość są sobie równe.
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Non-quadratic quality criteria in parameter estimation of continuous-time models
PublikacjaW pracy wykorzystuje się procedury estymacji parametrycznej do identyfikacji modeli z czasem ciągłym. Rozważane algorytmy minimalizują wskaźnik jakości w postaci sumy lub całki wartości bezwzględnej błędu predykcji. Zastosowanie techniki zmiennych instrumentalnych umożliwia ponadto znaczące polepszenie dokładności ocen parametrów, a wprowadzony do w procedur estymacji mechanizm ważenia błędów predykcji pozwala identyfikować modele...
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Four-point boundary-value problems for differential-algebraic systems
PublikacjaBadane są czteropunktowe problemy brzegowe dla układów równań różniczkowo-algebraicznych. Stosując metodę iteracji monotonicznych, podano warunki dostateczne na istnienie rozwiązań (jednego lub ekstremalnych) takich problemów. Podano przykład ilustrujacy otrzymane wyniki teoretyczne.
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Relations between the domination parameters and the chromatic index of a graph
PublikacjaIn this paper we show bounds for the sum and the product of the domination parameters and the chromatic index of a graph. We alsopresent some families of graphs for which these bounds are achieved.
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Efficient list cost coloring of vertices and/or edges of bounded cyclicity graphs
PublikacjaW artykule rozważamy listowo-kosztowe kolorowanie wierzchołków i krawędzi grafu w modelu wierzchołkowym, krawędziowym, totalnym i pseudototalnym. Stosujemy programowanie dynamiczne w celu otrzymania algorytmów wielomianowych dla drzew. Następnie uogólniamy to podejście na dowolne grafy z ograniczonymi liczbami cyklomatycznymi i na ich multikolorowania.
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Multiple solutions of boundary-value problems for fourth-order differential equations with deviating arguments
PublikacjaPraca 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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Iterative‐recursive estimation of parameters of regression models with resistance to outliers on practical examples
PublikacjaHere, 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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Distortion in the group of circle homeomorphisms
PublikacjaLet 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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A note on polynomial algorithm for cost coloring of bipartite graphs with Δ ≤ 4
PublikacjaIn 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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Graph classes generated by Mycielskians
PublikacjaIn 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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Domination numbers in graphs with removed edge or set of edges
PublikacjaW artykule przedstawiony jest wpływ usuwania krawędzi lub zbioru krawędzi na liczby dominowania spójnego i słabo spójnego.
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Trees with equal restrained domination and total restrained domination numbers
PublikacjaW publikacji scharakteryzowano wszystkie drzewa, w których liczby dominowania powściągniętego oraz podwójnie totalnego są sobie równe.
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Boundary value problems for ordinary differential equations with deviated arguments
PublikacjaDyskutowane są równania różniczkowe z dwupunktowym nieliniowym warunkiem brzegowym z argumentami typu odchylonego. Podano warunki dostateczne które gwarantują iż problem wyjściowy ma kwazi-rozwiązania. Podano też warunki przy których problem ten ma rozwiązanie. Wyniki uzyskano stosując metodę iteracji monotonicznych.Badano też pewne nierówności różniczkowe z odchylonymi argumentami.
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Some remarks on the Euler ring U(G)
PublikacjaNiech G będzie zwartą grupą Liego i niech U(G) oznacza pierściń Eulera G skonstruoawany przez tom Diecka w [5,6]. Główny wynikpracy (Twierdzenie 4.1) opisuje homomorfizm pierścienia U(SO(3)) w pierścień U(SO(2))indukowany przez włożenie grupy SO(2) w grupę SO(3).
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Efficient parallel implementation of crowd simulation using a hybrid CPU+GPU high performance computing system
PublikacjaIn 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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On the Characteristic Graph of a Discrete Symmetric Channel
PublikacjaWe 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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Block graphs with large paired domination multisubdivision number
PublikacjaThe 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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Parity vertex colouring of graphs
PublikacjaA 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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Domination subdivision and domination multisubdivision numbers of graphs
PublikacjaThe domination subdivision number sd(G) of a graph G is the minimum number of edges that must be subdivided (where an edge can be subdivided at most once) in order to increase the domination number of G. It has been shown [10] that sd(T)<=3 for any tree T. We prove that the decision problem of the domination subdivision number is NP-complete even for bipartite graphs. For this reason we define the domination multisubdivision number...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublikacjaDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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T-colorings, divisibility and circular chromatic number
PublikacjaLet T be a T-set, i.e., a finite set of nonnegative integers satisfying 0 ∈ T, and G be a graph. In the paper we study relations between the T-edge spans espT (G) and espd⊙T (G), where d is a positive integer and d ⊙ T = {0 ≤ t ≤ d (max T + 1): d |t ⇒ t/d ∈ T} . We show that espd⊙T (G) = d espT (G) − r, where r, 0 ≤ r ≤ d − 1, is an integer that depends on T and G. Next we focus on the case T = {0} and show that espd⊙{0} (G) =...
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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublikacjaWe describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublikacjaThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Periodic Points for Sphere Maps Preserving MonopoleFoliations
PublikacjaLet S^2 be a two-dimensional sphere. We consider two types of its foliations with one singularity and maps f:S^2→S^2 preserving these foliations, more and less regular. We prove that in both cases f has at least |deg(f)| fixed points, where deg(f) is a topological degree of f. In particular, the lower growth rate of the number of fixed points of the iterations of f is at least log|deg(f)|. This confirms the Shub’s conjecture in...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublikacjaBrominated 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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On incidence coloring of coloring of complete multipartite and semicubic bipartite graphs
PublikacjaIn 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
PublikacjaThe 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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Total domination in versus paired-domination in regular graphs
PublikacjaA subset S of vertices of a graph G is a dominating set of G if every vertex not in S has a neighbor in S, while S is a total dominating set of G if every vertex has a neighbor in S. If S is a dominating set with the additional property that the subgraph induced by S contains a perfect matching, then S is a paired-dominating set. The domination number, denoted γ(G), is the minimum cardinality of a dominating set of G, while the...
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Interval incidence coloring of subcubic graphs
PublikacjaIn this paper we study the problem of interval incidence coloring of subcubic graphs. In [14] the authors proved that the interval incidence 4-coloring problem is polynomially solvable and the interval incidence 5-coloring problem is N P-complete, and they asked if χii(G) ≤ 2∆(G) holds for an arbitrary graph G. In this paper, we prove that an interval incidence 6-coloring always exists for any subcubic graph G with ∆(G) = 3.
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Theoretical Assessment of Excited State Gradients and Resonance Raman Intensities for the Azobenzene Molecule
PublikacjaThe ground state geometries and vibrational frequencies as well as the excitation energies and excited state gradients of the S 1(nπ*) and S 2(ππ * ) states of trans - and cis -azobenzene are investigated by several DFT methods, namely B3LYP, PBE, M06-2X, CAM-B3LYP, and ω B97X. Excited state properties and in particular gradients are also assessed using the wave function based methods EOM-CCSD and RASPT2/RASSCF. Comparison with...
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublikacjaThe 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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Equitable coloring of corona multiproducts of graphs
PublikacjaWe 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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Types of Markov Fields and Tilings
PublikacjaThe method of types is one of the most popular techniques in information theory and combinatorics. However, thus far the method has been mostly applied to one-dimensional Markov processes, and it has not been thoroughly studied for general Markov fields. Markov fields over a finite alphabet of size m ≥ 2 can be viewed as models for multi-dimensional systems with local interactions. The locality of these interactions is represented...
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Some variations of perfect graphs
PublikacjaWe 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
PublikacjaFor 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...