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Search results for: NONLOCAL THEORY OF ERINGEN
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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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Minimum vertex ranking spanning tree problem for chordal and proper interval graphs
PublicationW pracy rozważamy problem szukania, dla danego grafu prostego, drzewa spinającego, którego uporządkowana liczba chromatyczna jest minimalna. K.~Miyata i inni dowiedli w [Np-hardness proof and an approximation algorithm for the minimum vertex ranking spanning tree problem,Discrete Appl. Math. 154 (2006) 2402-2410], że odpowiedni problem decyzyjny jest NP-trudny już w przypadku pytania o istnienie uporządkowanego 4-pokolorowania....
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Squashed entanglement for multipartite states and entanglement measures based on the mixed convex roof
PublicationNew measures of multipartite entanglement are constructedbased on two definitions of multipartite information anddifferent methods of optimizing over extensions of the states. Oneis a generalization of the squashed entanglement where one takesthe mutual information of parties conditioned on the state's extensionand takes the infimum over such extensions. Additivity ofthe multipartite squashed entanglement is proved for both versionsof...
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Four-point boundary-value problems for differential-algebraic systems
PublicationBadane 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
PublicationIn 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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Boundary value problems for ordinary differential equations with deviated arguments
PublicationDyskutowane 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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Trees with equal restrained domination and total restrained domination numbers
PublicationW publikacji scharakteryzowano wszystkie drzewa, w których liczby dominowania powściągniętego oraz podwójnie totalnego są sobie równe.
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Cooperative mobile guards in grids
PublicationPraca 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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Weakly connected domination subdivision numbers
PublicationLiczba podziału krawędzi dla dominowania słabo spójnego to najmniejsza liczba krawędzi jaką należy podzielić, aby wzrosła liczba dominowania słabo wypukłego. W pracy przedstawione są własności liczby podziału krawędzi dla dominowania słabo spójnego dla różnych grafów.
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Some remarks on the Euler ring U(G)
PublicationNiech 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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Low-dimensional bound entanglement with one-way distillable cryptographic key
PublicationIn this paper, we provide a class of bound entangled states that have positive distillable secure key rate. The smallest state of this kind is 4 circle times 4, which shows that peculiar security contained in bound entangled states does not need high-dimensional systems. We show that for these states a positive key rate can be obtained by one-way Devetak-Winter (DW) protocol. Subsequently, the volume of bound entangled key-distillable...
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Quantum key distribution based on private states: Unconditional security over untrusted channels with zero quantum capacity
PublicationIn this paper, we prove unconditional security for a quantum key distribution (QKD) protocol based on distilling pbits (twisted ebits) from an arbitrary untrusted state that is claimed to contain distillable key. Our main result is that we can verify security using only public communication-via parameter estimation of the given untrusted state. The technique applies even to bound-entangled states, thus extending QKD to the regime...
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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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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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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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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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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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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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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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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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Theoretical Assessment of Excited State Gradients and Resonance Raman Intensities for the Azobenzene Molecule
PublicationThe 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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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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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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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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Bernstein-type theorem for ϕ-Laplacian
PublicationIn this paper we obtain a solution to the second-order boundary value problem of the form \frac{d}{dt}\varPhi'(\dot{u})=f(t,u,\dot{u}), t\in [0,1], u\colon \mathbb {R}\to \mathbb {R} with Sturm–Liouville boundary conditions, where \varPhi\colon \mathbb {R}\to \mathbb {R} is a strictly convex, differentiable function and f\colon[0,1]\times \mathbb {R}\times \mathbb {R}\to \mathbb {R} is continuous and satisfies a suitable growth...
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T-colorings, divisibility and circular chromatic number
PublicationLet 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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Periodic Points for Sphere Maps Preserving MonopoleFoliations
PublicationLet 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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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublicationThe 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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The Maslov index and the spectral flow—revisited
PublicationWe give an elementary proof of a celebrated theorem of Cappell, Lee and Miller which relates the Maslov index of a pair of paths of Lagrangian subspaces to the spectral flow of an associated path of self-adjoint first-order operators. We particularly pay attention to the continuity of the latter path of operators, where we consider the gap-metric on the set of all closed operators on a Hilbert space. Finally, we obtain from Cappell,...
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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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Interval incidence coloring of subcubic graphs
PublicationIn 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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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublicationWe 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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Domination subdivision and domination multisubdivision numbers of graphs
PublicationThe 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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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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TOTAL DOMINATION MULTISUBDIVISION NUMBER OF A GRAPH
PublicationThe 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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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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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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Reply to Maarit Johnson's Letter to the Editor
PublicationWe wrote in response to the Letter to the Editor from Maarit Johnson regarding our article “Exploring the factor structure and the validity of the abbreviated Basic and Earning self-esteem Scales” (Dåderman & Basinska, 2013). We discussed two main issues: (a) the theory underlying the development of the longer (i.e., original) versions of the Basic and Earning SES, as well as the role of earning SE; and (b) the selection of items...
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On the Bending of Multilayered Plates Considering Surface Viscoelasticity
PublicationWe discuss the bending resistance of multilayered plates taking into account surface/interfacial viscoelasticity. Within the linear surface viscoelasticity we introduce the surface/interfacial stresses linearly dependent on the history of surface strains. In order to underline the surface viscoelasticity contribution to the bending response we restrict ourselves to the elastic behaviour in the bulk. Using the correspondence principle...
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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...