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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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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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On quasi-compact Markov nets
PublikacjaAnalizuje się strukturę ergodyczną netów Markowa. W szczególności podano charakteryzację ściśle ergodycznych minimalnych (L-R) netów markowskich na zwartej przestrzeni fazowej. Uzyskano warunki równoważne quasi-zwartości (L-R) netów Markowa, rozszerzając tzw. ergodyczne twierdzenie Lotz'a.
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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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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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Convex universal fixers
PublikacjaPraca dotyczy dominowania wypukłego w grafach pryzmowych.
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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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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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Bernstein-type theorem for ϕ-Laplacian
PublikacjaIn 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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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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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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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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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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MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
PublikacjaIn 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
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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The Maslov index and the spectral flow—revisited
PublikacjaWe 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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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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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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Low-dimensional bound entanglement with one-way distillable cryptographic key
PublikacjaIn 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
PublikacjaIn 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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Minimum vertex ranking spanning tree problem for chordal and proper interval graphs
PublikacjaW 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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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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Weakly connected domination subdivision numbers
PublikacjaLiczba 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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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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Revisiting Toroidal Dipolar Moment in Planar Metamaterial
PublikacjaThis article revisits the electric, magnetic, and toroidal dipolar moments in the metamaterial structure and presents the flatland design for generating a toroidal dipolar response for the electromagnetic plane wave at normal incidence. Based on the numerical analysis of the surface current, the electric field, the magnetic field, and the quantitative analysis of scattered power supported by the electromagnetic multipole theory,...
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Compact Quasi-Elliptic-Type Inline Waveguide Bandpass Filters With Nonlinear Frequency-Variant Couplings
PublikacjaThis work presents the design techniques to synthesize a class of compact inline quasi-elliptic-type waveguide cavity bandpass filters based on novel nonlinear frequency-variant couplings (NFVCs). These highly dispersive frequency-variant couplings (FVCs) are realized by means of a pair of partial-height posts that are placed at the junctions between every two cavity resonators. Each NFVC produces a transmission pole in between...
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Inverse Nonlinear Eigenvalue Problem Framework for the Synthesis of Coupled-Resonator Filters With Nonresonant Nodes and Arbitrary Frequency-Variant Reactive Couplings
PublikacjaA novel, general circuit-level description of coupledresonator microwave filters is introduced in this article. Unlike well-established coupling-matrix models based on frequency-invariant couplings or linear frequency-variant couplings (LFVCs), a model with arbitrary reactive frequencyvariant coupling (AFVC) networks is proposed. The engineered formulation is more general than prior-art ones—with the only restriction that the coupling...
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Equivariant Conley index in Hilbert spaces and applications to strongly indefinite problems
PublikacjaW pracy zdefiniowano teorię indeksu Conley`a w przestrzeni Hilberta z działaniem zwartej grupy Liego. Została ona wykorzystana do szacowania z dołu ilości rozwiązań periodycznych w teorii nieliniowych autonomicznych układów Hamiltona.
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Numerical conditioning of delta-domain Lyapunov and Riccati equations
PublikacjaW pracy rozważono problem uwarunkowania dyskretno czasowych równań Lapunowa oraz równań Riccatiego - to znaczy problem wrażliwości rozwiązań takich równań na odchyłki ich parametrów od nominalnych wartości. Zdefiniowano odpowiedni "różniczkowy" wskaźnik uwarunkowania oraz podano efektywną metodę szacowania jego wartości. Udowodniono teoretycznie - a także przekonująco zilustrowano na drodze numerycznej - twierdzenie głoszące, iż...
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Scattering in junction by posts consisting of a segment of conducting cy linder.
PublikacjaWykorzystując zmodyfikowaną procedurę iteracyjną i metodę dopasowania rodzajów opracowano teorię rozpraszania fali elektromagnetycznej w złączu falowodowym na obiektach będących wycinkami metalowego cylindra. W wyniku analizy uzyskano wielorodzajową macierz rozproszenia złącza falowodowego zawierającego opisywane elementy. Zarówno zmiana położenia jak i obrót elementu w złączu powoduje zmianę jego parametrów elektrycznych....
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Some remarks about numerical conditioning of discrete time Riccati eqations.
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Finite-difference analysis of a loaded hemispherical resonator
PublikacjaPrzedstawiono analizę osiowo symetrycznej struktury otwartego rezonatora he-misferycznego zawierającego warstwowe ośrodki dielektryczne. W analizie wy-korzystano metodę różnic skończonych w dziedzinie częstotliwości (FDFD). Wcelu osiągnięcia wysokiej dokładności obliczeń zastosowano zaawansowane me-tody modelowania warunków brzegowych i granicznych.
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A general approach to continuous time Gm-C filters.
PublikacjaW pracy zaproponowano ogólną strukturę filtrów Gm-C z odpowiednim opisem macierzowym. W odniesieniu do tej struktury podano formuły analizy wrażliwościowej dla dowolnego filtru Gm-C czasu ciągłego. Analiza oparta na opisie macierzowym była wykorzystana również do porównania właściwości filtrów Gm-Ctrybu napięciowego i prądowego. Zdefiniowano dwie kanoniczne transformacje dla klasy filtrów zmiennych stanu.
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Dimensional Synthesis of Coupled-Resonator Pseudoelliptic Microwave Bandpass Filters with Constant and Dispersive Couplings
PublikacjaIn this paper, we propose a novel technique for the dimensional synthesis of coupled-resonator pseudoelliptic microwave filters with constant and dispersive couplings. The proposed technique is based on numerical simulations of small structures, involving up to two adjacent resonators, and it accounts for a loading effect from other resonators by replacing them with terminations coupled through appropriately scaled inverters. The...
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Fixed orbit index for equivariant maps
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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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Low-Cost Method for Internal Surface Roughness Reduction of Additively Manufactured All-Metal Waveguide Components
PublikacjaIn this study, a novel low-cost polishing method for internal surface roughness reduction of additively manufactured components, developed for waveguide (WG) circuits operating in the millimeter frequency range is proposed. WG components fabricated using powder bed fusion (PBF) generally feature roughness of ten to fifty microns, which influences the increase of roughness-related conductor power losses having a major effect on...
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Comments on ''An innovative fast powerful method for tackling electromagnetic eigenvalue problems for multistrip transmission lines''
PublikacjaPraca stanowi komentarz do publikacji Casanuevy i Garcii dotyczącej techniki szybkiego obliczania charakterystyk dyspersyjnych falowodów z niejednorodnym wypełnieniem. Zwrócono uwagę na niepotrzebną komplikację zagadnienia poprzez zastosowanie techniki rozkładu na wartości szczególne.
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Coupled - mode design of ferrite loaded coupled microstrip lines section
PublikacjaMetodę rodzajów sprzężonych zastosowano do analizy i projektowania sekcji ferrytowych mikropaskowych linii sprzężonych magnesowanych podłużnie (FCL). W wyniku analizy określono macierz rozproszenia sekcji oraz warunki umożliwiające jej zastosowanie do realizacji cyrkulatora projetowanego jako połączenie badanej sekcji FCL z mikropaskowym rozgałęzieniem typu T. W oparciu o opracowane oprogramowanie przeprowadzono modelowanie parametrów...
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A new class of eigenfunction expansion methods for fast frequency-domain analysis of waveguides
PublikacjaZaprezentowano nową technikę szybkiego obliczania charakterystyk dyspersyjnych falowodów z niejednorodnym wypełnieniem. Metoda ta oblicza przybliżone wartości stałej propagacji dla wymaganej częstotliwości, bazując na bardziej dokładnych wyliczeniach rozkładu pola i stałej propagacji dla kilku wybranych punktów częstotliwości.
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Frequency-Variant Double-Zero Single-Pole Reactive Coupling Networks for Coupled-Resonator Microwave Bandpass Filters
PublikacjaIn this work, a family of frequency-variant reactive coupling (FVRC) networks is introduced and discussed as new building blocks for the synthesis of coupled-resonator bandpass filters with real or complex transmission zeros (TZs). The FVRC is a type of nonideal frequency-dependent inverter that has nonzero elements on the diagonal of the impedance matrix, along with a nonlinear frequency-variation profile of its transimpedance...