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Search results for: Classical MD
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Classical coloring of graphs.
PublicationRozdział obejmuje klasyczne kolorowanie krawędzi i wierzołków w grafach prostych. Oprócz podstawowych definicji podane zostały najczęściej stosowane metody przybliżone oraz ich właściwości. Dodatkowo rozdział zawiera przegląd znanych benczmarków dla podanych metod w kontekście klasycznego modelu kolorowania.
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Brittle fracture of 100-, 110-, 111-oriented Cu crystals: MD vs. TB/MD approach
PublicationPrzeprowadzono wieloskalowe symulacje nanoindentacji miedzi nieskończenie twardym narzędziem, przy zastosowaniu metody dynamiki molekularnej, z siłami liczonymi na bieżąco w formalizmie ciasnego wiązania (TB). Przedstawiono wyniki dla trzech orientacji krystalicznych podłoża. Badano efekt dołączenia obliczeń TB na siłę normalną odczuwaną przez narzędzie i na przemieszczenia atomów podłoża, przez porównywanie z symulacją czystą...
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Final Farewell to Alberto Zanchetti MD
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Fundamentals of classical and analytical mechanics
PublicationThe book is a monographic description of the present attempt to Newtonian and Lagrangian mechanics. But also, it could be found as a supplementary educational material useful for the graduate courses in mechanics taken by students majoring in mechanical engineering, physics or physical science. In the book you can find a brief introduction to concepts and principles of algebra of vectors; Kinematics of particles, mainly focused...
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Degradation of a nano-cutting tool: an MD simulation
PublicationW pracy przedstawiono wyniki symulacji wielokrotnego oddziaływania realistycznie ukształtowanego ostrza tnącego z modelowym, nieskończenie twardym ziarnem, przy zastosowaniu metody dynamiki molekularnej. Ostrze składało się z kilkuset tysięcy atomów metalu fcc, traktowanego za pomocą potencjału Suttona-Chena, przesuwane było ze stałą prędkością 20 m/s. Obserwowane deformacje plastyczne pojawiające się na skutek kontaktu ostrza...
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Osmotic MD and other membrane distillation variants
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Water demineralisation by NF/MD integrated processes
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Purification of oily wastewater by hybrid UF/MD
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The structure of liquid lead: EXAFS and MD studies
PublicationPraca poświecona jest analizie widm XAFS zmierzonych na krawędzi L3dla ciekłego ołowiu. W analizie strukturalnej EXAFS zastosowano podejście GNXAS. Przetestowano kilka modeli strukturalnych, zarówno numerycznych (MD-DLE, MD-TB), jak i tych otrzymanych doświadczalnie (ND, XRD) i ostatecznie zrekonstruowano pierwszy pik w parowej funkcji rozkładu, g(r). Zweryfikowano wcześniejsze doniesienia o obserwownym za pomocą metody XAFS gwałtownym...
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Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling
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Unifying classical and quantum key distillation
PublicationPrzypuśćmy, że dwie oddalone od siebie osoby, Alicja i Bob, oraz osoba z nimi niewspółpracująca, Ewa, mają dostęp do systemów kwantowych przygotowanych w stanie rho_ABE. Ponadto Alicja i Bob mogą używać lokalnych operacji i uwiarygodnionej komunikacji publicznej. Celem Alicji i Boba jest ustanowienie klucza, który nie będzie znany Ewie. Nasze badania inicjują podejście do wspomnianego zagadnienia oparte na unifikacji dwóch standardowych...
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Complexity of a classical flow restoration problem
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Effect of iron oxides scaling on the MD process performance
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Demineralization of water using a combination of MD and NF(RO)
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Quantum-classical calculations of the nanomechanical properties of metals
PublicationTradycyjnie symulacje komputerowe układów w skali atomowej prowadzone są przy użyciu klasycznej metody dynamiki molekularnej (MD) bądź kwantowych metod ab initio. Główną wadą ujęcia klasycznego jest jego empiryczna natura, a co za tym idzie - niewielka przenośność, jego prostota natomiast pozwala na przeprowadzanie symulacji układów zawierających miliony atomów. W wyniku zastosowania metod kwantowych otrzymuje się bardziej wiarygodne...
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Generic emergence of classical features in quantum Darwinism
PublicationQuantum Darwinism posits that only specific information about a quantum system that is redundantly proliferated to many parts of its environment becomes accessible and objective, leading to the emergence of classical reality. However, it is not clear under what conditions this mechanism holds true. Here we prove that the emergence of classical features along the lines of quantum Darwinism is a general feature of any quantum dynamics:...
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NMR and MD Analysis of the Bonding Interaction of Vancomycin with Muramyl Pentapeptide
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FURTHER REMARKS ON THE NEO-CLASSICAL NAVIER-STOKES EQUATIONS
PublicationThe seminal Navier-Stokes equations have been stated yet before creation of principles of thermodynamics and the first and second laws. In the literature there is the common opinion that the Navier-Stokes equations cannot be taken as a thermodynamically correct model of “working fluid” which is able to describe transformation of “ heat” into “work” and vice versa. Therefore, in the paper, a new exposition of thermodynamically...
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On the internal efficiency of a turbine stage: classical and CFD definitions
PublicationAlmost entire fleet of steam turbines in Poland was designed between 1950 – 1980 with the use of the so-called zero dimensional (0D) calculation tools. For several years, design and modernization of the turbines occur in assistance with the state of the art methods that describe working fluid flow field based on 3D models and CFD codes. This cooperation between 0D and 3D codes requires exchange of overall, integral information...
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Quadrotor Flight Controller Design Using Classical Tools
PublicationA principal aspect of quadrocopter in-flight operation is to maintain the required attitude of the craft’s frame, which is done either automatically in the so-called supervised flight mode or manually during man-operated flight mode. This paper deals with the problem of flight controller (logical) structure and algorithm design dedicated for the man-operated flight mode. The role of the controller is to stabilise the rotational...
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Treatment of effluents from the regeneration of ion exchangers using the MD process
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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General paradigm for distilling classical key from quantum states
PublicationIn this paper, we develop a formalism for distilling aclassical key from a quantum state in a systematic way, expandingon our previous work on a secure key from bound entanglement(Horodecki et al., 2005). More detailed proofs, discussion, andexamples are provided of the main results. Namely, we demonstratethat all quantum cryptographic protocols can be recast in away which looks like entanglement theory, with the only changebeing...
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Hybrid quantum-classical approach for atomistic simulation of metallic systems
PublicationThe learn-on-the-fly (LOTF) method [G. Csanyi et al., Phys. Rev. Lett. 93, 175503 (2004)] serves to seamlessly embed quantum-mechanical computations within a molecular-dynamics framework by continual local retuning of the potential's parameters so that it reproduces the quantum-mechanical forces. In its current formulation, it is suitable for systems where the interaction is short-ranged, such as covalently bonded semiconductors....
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On relations between gradient and classical equivariant homotopy groups of spheres
PublicationWe investigate relations between stable equivariant homotopy groups of spheres in classical and gradient categories. To this end, the auxiliary category of orthogonal equivariant maps, a natural enlargement of the category of gradient maps, is used. Our result allows for describing stable equivariant homotopy groups of spheres in the category of orthogonal maps in terms of classical stable equivariant groups of spheres with shifted...
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Statistical properties of a modified standard map in quantum and classical regimes
PublicationWe present a model—a modified standard map. This model has interesting properties that allow quantum–classical correspondences to be studied. For some range of parameters in the classical phase space of this model, there exist large accelerator modes. We can create a family of maps that have large accelerator modes.
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A Comparison between MD and EXAFS extracted Structural Data for TernaryRbBr(1-x)Ix.
PublicationStrukturę trójskładnikowych soli poddano analizie za pomocą metody EXAFS i symulacji M-D. Przedyskutowano przydatność używanego w symulacjach potencjału oddziaływań międzyatomowych.
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Structure recognition in MD-simulated materials: a case study of boroxyl rings in borate glasses
PublicationZanalizowano statystyczne właściwości geometryczne losowo deformowanej jednostki strukturalnej AC_3, gdzie trzy kationyC znajdują się w wierzchołkach trójkąta równobocznego, a anionA - w jego środku. W szczególności opisano rozkłady kątów AAA,ACA i CAA oraz dwóch estymatorów kształtu w funkcji amplitudydeformacji trójkąta. Wyniki analizy stochastycznej zastosowanodo ilościowej oceny stopnia nieuporządkowania w szkle B_2O_3,symulowanym...
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On the role of classical and novel forms of vitamin D in melanoma progression and management
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Purely quantum superadditivity of classical capacities of quantum multiple access channels
PublicationWe are studying classical capacities of quantum memoryless multiaccess channels in geometric terms and we are revealing a break of additivity of the Holevo-like capacity. This effect is a purely quantum mechanical one, since, as we point out, the capacity regions of all classical memoryless multiaccess channels are additive. It is the first such effect revealed in the field of classical information transmission via quantum channels.
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Mixed, quantum-classical description of electron density transfer in the collision process
PublicationIn this work, we investigate an ion-atom model describing the time-dependent evolution of electron density during the collision. For a S3+- H system, numerical simulations are based on classical trajectory calculations, and the electron density behaviour is described with the time-dependent Schrödinger equation. We apply the finite difference method to obtain quantitative insights into the charge transfer dynamics, providing detailed...
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Direct estimation of functional and density operators by local operations and classical communication.
PublicationWykazano, że można dokonywać detekcji splątania w paradygmacie odległych laboratoriów. Pokazano, jak można fizycznie zaimplementować strukturalne przybliżenie fizyczne niefizycznego odwzorowania w tym paradygmacie.
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Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime
PublicationThe four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most...
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Structure of partially reduced xPbO (1-x)SiO2 glasses: combined EXAFS and MD study
PublicationWykorzystując połączenie metody EXAFS (extended X-ray absorption finestructure) i symulacji MD (molecular dynamics) zbadano strukturęczęściowo zredukowanych szkieł ołowiowo-krzemianowych o różnejstechiometrii wyjściowej. W wyniku analizy uzyskano szczegółowyopis struktury lokalnej wokół atomów ołowiu i jej zmiany w funkcjiskładu szkła i poziomu redukcji. Określono również jaką tendencjędo aglomeracji w metaliczne klastry wykazują...
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Rime samples characterization and comparison using classical and fuzzy principal components analysis
PublicationEfektywność dwóch nowych algorytmów w stosunku do klasycznego wariantu techniki PCA porównano analizując dane dotyczące zanieczyszczeń próbek sadzi zebranych na terenie trzech stacji w okresie 2004-2007. Zastosowane algorytmy FPCA-1 i FPCA-o pozwalają na wyodrębnienie większej liczby miejsc zbierania próbek i analitów w stosunku do sytuacji, kiedy stosuje się klasyczny wariant techniki PCA.
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Non-classical operational calculus applied to certain linear discrete time-system
PublicationW pracy zastosowano nieklasyczny rachunek operatorów do wyznaczania odpowiedzi pewnego dyskretnego układu dynamicznego. Pokazano metodę szczególnie przydatną do wyznaczania odpowiedzi pewnych dyskretnych niestacjonarnych układów dynamicznych, przy których zastosowanie przekształcenia Z sprawia duże trudności.
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Distributed correlations and information flows within a hybrid multipartite quantum-classical system
PublicationUnderstanding the non-Markovian mechanisms underlying the revivals of quantum entanglement in the presence of classical environments is central in the theory of quantum information. Tentative interpretations have been given by either the role of the environment as a control device or the concept of hidden entanglement. We address this issue from an information-theoretic point of view. To this aim, we consider a paradigmatic tripartite...
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Assessing the Significance of Displacements Using Local Coefficients of Variance as an Alternative to the Classical Approach
PublicationThe safety of use of civil engineering structures remains an important issue that is approached by various sciences. Due to this fact, geodetic control measurements are conducted with the purpose of identifying threats connected with the potential displacement of structural elements. In this context, the authors discuss issues connected with determining the displacements of controlled points located in the studied object in a three-dimensional...
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A Novel Iterative Decoding for Iterated Codes Using Classical and Convolutional Neural Networks
PublicationForward error correction is crucial for communication, enabling error rate or required SNR reduction. Longer codes improve correction ratio. Iterated codes offer a solution for constructing long codeswith a simple coder and decoder. However, a basic iterative code decoder cannot fully exploit the code’s potential, as some error patterns within its correction capacity remain uncorrected.We propose two neural network-assisted decoders:...
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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The interactions of monomeric acridines and unsymmetrical bisacridines (UAs) with DNA duplexes: an insight provided by NMR and MD studies
PublicationMembers of a novel class of anticancer compounds, exhibiting high antitumor activity, i.e. the unsymmetrical bisacridines (UAs), consist of two heteroaromatic ring systems. One of the ring systems is an imidazoacridinone moiety, with the skeleton identical to the structural base of Symadex. The second one is a 1-nitroacridine moiety, hence it may be regarded as Nitracrine’s structural basis. These monoacridine units are connected...
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Nonadditivity of quantum and classical capacities for entanglement breaking multiple-access channels and the butterfly network
PublicationWe analyze quantum network primitives which are entanglement breaking. We show superadditivity of quantum and classical capacity regions for quantum multiple-access channels and the quantum butterfly network. Since the effects are especially visible at high noise they suggest that quantum information effects may be particularly helpful in the case of the networks with occasional high noise rates. The present effects provide a qualitative...
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Subadditivity of the minimum output entropy and superactivation of the classical capacity of quantum multiple access channels
PublicationWe study subadditivity of the minimum output entropy (Hmin) of quantum multiple access channels (MACs). We provide an example of violation of the additivity theorem for Hmin known in classical information theory. Our result is based on a fundamental property of MACs, i.e., independence of each sender. The channels used in the example can be constructed explicitly. On the basis of subadditivity of Hmin we also provide an example...
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Electronic nose algorithm design using classical system identification for odour intensity detection
PublicationThe two elements considered crucial for constructing an efficient environmental odour intensity monitoring systems are sensors and algorithms typically addressed to as electronic nose sensor (e-nose). Due to operational complexity of biochemical sensors developed in human bodies algorithms based on computational methods of artificial intelligence are typically considered superior to classical model based approaches in development...
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About the Noether’s theorem for fractional Lagrangian systems and a generalization of the classical Jost method of proof
PublicationRecently, the fractional Noether's theorem derived by G. Frederico and D.F.M. Torres in [10] was proved to be wrong by R.A.C. Ferreira and A.B. Malinowska in (see [7]) using a counterexample and doubts are stated about the validity of other Noether's type Theorem, in particular ([9],Theorem 32). However, the counterexample does not explain why and where the proof given in [10] does not work. In this paper, we make a detailed analysis...
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Application of non-classical operational calculus to indicate hazards in numerical solutions of engineering problems
PublicationThe article addresses the application of non- classical operational calculus to approximative solutions of engineering problems. The engineering-sound examples show that a continuous–discrete problem transformation from differential unequivocal problem to a differential wildcard problem, triggering a change in solution quality. A number of approximative methods are capable to alter both quantitative and qualitative...
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Comparison of classical Winter's bracing requirements of compressedtruss chord with stability analysis of 3D truss-model
PublicationMost code requirements concerning bracing are based on principles developed by Winter. The present research is devoted tostudy a lateral buckling of truss with linear elastic side supports. The classical Winter's model of truss chord in the case ofout of the truss plane buckling is compared with nonlinear analysis of 3D truss model. Full bracing condition, that permitsthe truss chord to support load level corresponding to an unbraced...
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Adaptive resolution simulation of liquid para-hydrogen: testing the robustness of the quantum-classical adaptive coupling
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Tribological synergy between classical ZDDP and innovative MoS2 and MoO3 nanotube additives at elevated temperatures
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IDENTIFICATION OF ODOR OF VOLATILE ORGANIC COMPOUNDS USING CLASSICAL SENSORY ANALYSIS AND ELECTRONIC NOSE TECHNIQUE
PublicationThe paper compares two methods of analysis of odour of volatile organic compounds: classical sensory analysis and electronic nose technique. Eight volunteers participated in the classical sensory analysis investigations, which lasted two weeks. An instrumental odour analysis involved a prototype of 6-sensor electronic nose designed by the authors. The research performed with this device provided higher reproducibility and reliability...
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Impact of Tensile and Compressive Stress on Classical and Acoustic Barkhausen Effects in Grain-Oriented Electrical Steel
PublicationIn this paper, we present the results of the investigation of impact of tensile and compressive stress on the classical Barkhausen effect, magnetoacoustic emission (MAE) signal properties, and B(H) hysteresis loops for grain-oriented (GO) electrical steel. Samples have been glued to a nonmagnetic steel bar and stressed within elastic range (±800 μdef) by means of four-point bending method. The samples were cut out in two directions...
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Automatic Regularization by Quantization in Reducible Representations of CCR: Point-Form Quantum Optics with Classical Sources
PublicationElectromagnetic fields are quantized in a manifestly covariant way by means ofa class of reducible "center-of-mass N-representations" of the algebra of canonical commutationrelations (CCR). The four-potential Aa(x) transforms in these representations as aHermitian four-vector field in Minkowski four-position space (without change of gauge), butin momentum space it splits into spin-1 massless photons and two massless scalars. Whatwe...
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Psychometric properties of the Bern illegitimate tasks scale using classical test and item response theories
PublicationCombining a classical test theory and an item response theory (IRT), this study aimed to investigate the psychometric properties of the Bern Illegitimate Tasks Scale (BITS) by measuring two conceptually separate dimensions capturing unnecessary tasks (perceived by employees as pointless) and unreasonable tasks (perceived as unfairly or inappropriately assigned). Data collected among Polish employees in two samples (N= 965 and N=...
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Elastic waves in the railroad track substructures and its surroundings analyzed with non-classical operational methods
PublicationWe analyze the propagation of the waves generated by the rolling stock and the interaction of those waves on the medium and its surroundings. We use non-classical operational methods for monitoring construction of the railway infrastructure and for noise damping.
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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublicationIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
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Schemes of transmission of classical information via quantum channels with many senders: Discrete- and continuous-variable cases
PublicationSuperadditivity effects in the classical capacity of discrete multiaccess channels and continuous variable (CV) Gaussian MACs are analyzed. Several examples of the manifestation of superadditivity in the discrete case are provided, including, in particular, a channel which is fully symmetric with respect to all senders. Furthermore, we consider a class of channels for which input entanglement across more than two copies of the...
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Trends in biomedical analysis of red blood cells – Raman spectroscopy against other spectroscopic, microscopic and classical techniques
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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Energy Efficiency Analysis of Railway Turnout Heating With a Simplified Snow Model Using Classical and Contactless Heating Method
PublicationElectrical heating of railway turnouts is a considerable technical and economic challenge, hence the need to conduct research for optimisation of a railway turnouts heating system. This paper presents results of a numerical analysis and experimental research on heating systems mounted on rail turnouts in line with the classical method and including a heater thermally insulated from the base of a rail. The numerical calculations...
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Investigation of magnetic and magnetomechanical hysteresis properties of Fe Si alloys with classical and mechanical Barkhausen effects and magnetoaco ustic emission.
PublicationW stopach Fe 3,5% Si o strukturze GO oraz NO badano własności histerezowe za pomocą polowego HBE i mechanicznego MEB efektu Barkhausena oraz emisji magnetoakustycznej EMA. Rozkład naprężeń wewnętrznych został wyznaczony wykorzystując zależność natężenia MEB od naprężeń zewnętrznych (próba pierwszego naprężania). Stwierdzenie MEB oraz EMA o znaczącym naprężeniu dowodzi występowania granic typu 90 deg. Są to granice domen typu...
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The Arctic mutation alters helix length and type in the 11–28 β-amyloid peptide monomer—CD, NMR and MD studies in an SDS micelle
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Contribution to the capacity analysis of the classic composite girder of Möller
PublicationThe analysis (brief history, experiments, numerical method) of the classic composite girder of Moller has been presented.
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HYBRID ENERGY SYSTEM FOR A CLASSIC SHIP POWER PLANT
PublicationThe article presents a brief overview of hybrid energy systems used on ships. The area of their application is outlined. The benefits of using such systems are also indicated. Then, the classic ship power plant is defined. The most important part of the article is a proposal how to modify a classic engine room by using a hybrid energy system. The idea is: to accumulate a part of electricity in areas where it is allowed to burn...
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Comparison of classical and modern approach of determination of highly polar compounds by High Performance Liquid Chromatography coupled with Tandem Mass Spectrometry
PublicationAbstract: Sugars and sugar alcohols are known as highly polar compounds. Four analytes were taken into consideration for comparison of classical and modern approach of separation of highly polar substances. Mannitol was chosen as an example of simple sugar alcohol, sucrose and lactulose as examples of disaccharides and structural isomers, raffinose as an example of complex trisaccharide. Raffinose was also used as internal standard...
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Conformational solution studies of the SDS micelle-bound 11-28 fragment of two Alzheimer's β-amyloid variants (E22K and A21G) using CD, NMR, and MD techniques
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COMPARISON OF NOISE EMISSION OF HCT AND CLASSIC VEHICLE COMBINATIONS FOR TIMBER TRANSPORTATION IN SWEDEN
PublicationBy means of a special simulation tool, the noise emission of a high-capacity heavy vehicle (11 axles) was compared to that of a classic heavy vehicle (a truck-dolly-semitrailer with 8 axles). The two cases are designated “Extended vehicle” versus “Classic vehicle” in this study, having total lengths of 34 and 25 m, respectively. The Classic vehicle represents the most common articulated heavy vehicle configuration for transport...
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C-1311 (Symadex), a potential anti-cancer drug, intercalates into DNA between A and G moieties. NMR-derived and MD-refined stereostructure of the d(GAGGCCTC) 2 :C-1311 complex
PublicationImidazoacridinone C-1311 (Symadex®) is an antitumor agent which has been recommended for Phase II clinical trials a few years ago. Previously, it was shown experimentally that during the initial stage of its action C-1311 forms stable intercalation complexes with DNA duplexes. Herein, a NMR-derived stereostructure of d(GAGGCCTC)2:C-1311 complex was reported. The ligand was found locating itself between A and G moieties, forming...
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Classic electrocardiogram-based and mobile technology derived approaches to heart rate variability are not equivalent
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Evaluation of applicability of classic methods of a fault loop impedance measurement to circuits with residual current devices
PublicationMeasurement of fault loop impedance in low voltage grids and systems is in most cases performed to verify the effectiveness of protection against electric shock by automatic disconnection of supply. For the sake of measurement accuracy, it is advisable to perform it using large current. Unfortunately, in circuits with residual current devices which are very widely used nowadays, a large measurement current may trigger those devices...
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Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives
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New insights of nanomaterials usage toward superhydrophobic membranes for water desalination via membrane distillation: A review
PublicationMembrane distillation (MD) is a promising technology for seawater desalination due to the ability to process high-salinity waters and the ability to be driven by low-grade or waste heat. However, practical applications of MD membranes are limited by the low vapor flux and fouling problem. Recently, there is a growing interest in developing novel MD membrane materials with enhanced hydrophobicity to improve the efficiency of desalination...
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How to make membrane distillation greener? A review on environmentally friendly and sustainable aspects
PublicationThere is an urgent need for the development of new water resources in order to solve the problem of the world’s growing demand for clean water. Membrane distillation (MD) is a promising alternative to conventional seawater desalination. Although MD itself is often defined as sustainable desalination technology, there are many aspects within the membrane manufacture and process operation that make it far from being green. For instance,...
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Progress in module design for membrane distillation
PublicationThere have been tremendous advances in membrane distillation (MD) since the concept was introduced in 1961: new membrane designs and process configurations have emerged, and its commercial viability has been evaluated in several pilot-scale studies. However, its high energy consumption has hindered its commercialization. One of the most promising ways to overcome this obstacle is to develop more energy-efficient membrane modules....
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The comparison of the removal of copper(II) and zinc(II) ions from aqueous solution using 2,6-diaminopyridine in a polymer inclusion membrane and in a classic solvent extraction
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Membrane distillation assisting food production processes of thermally sensitive food liquid items: a review
PublicationPhysical separation technologies have become important tool for processing in the current food manufacturing industries, especially for the products containing bioactive compounds thanks to their health benefits in costumers. As for the processing of bioactive food ingredients implies the implementation of integrated systems oriented to their separation, fractionation, and recovery. In this field, membrane distillation (MD), which...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Symulacje dynamiczno-molekularne ultraprecyzyjnego skrawania metali.
PublicationW pracy krótko przedstawiono powstałe w latach 1995-2001 algorytmy MD specjalizowane do symulacji przebiegu skrawania w skali nanometrycznej (ARMD iLRMD). W świetle tych algorytmów zaprezentowano opracowany przez autorów nowy algorytm i program do symulacji nanociencia, nano MD, oraz pokazano wybrane wyniki uzyskane za jego pomocą.
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Food Bioactive Ingredients Processing Using Membrane Distillation
PublicationSeparation processes are an important part of today’s food industries, especially in the case of specific bioactive components due to their health benefits. In general, processing of bioactive food ingredients assumes the introduction of integrated system directed to their separation, fractionation, and recovery. Recently, membrane distillation (MD) has been considered as an alternative membrane-based separation and concentration...
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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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Teleportation seen from spacetime: on 2-spinor aspects of quantum information processing
PublicationZastosowanie formalizmu 2-spinowego do kwantowego przetwarzania informacji zilustrowane przykładem teleportacji i relatywistycznej korelacji błędu.
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The role of low-energy electrons in the charging process of LISA test masses
PublicationThe estimate of the total electron yield is fundamental for our understanding of the test-mass charging associated with cosmic rays in the Laser Interferometer Space Antenna (LISA) Pathfinder mission and in the forthcoming gravitational wave observatory LISA. To unveil the role of low energy electrons in this process owing to galactic and solar energetic particle events, in this work we study the interaction of keV and sub-keV...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity 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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"Car-Parrinello molecular dynamics" jako kluczowe narzędzie informatyczne w badaniach syntezy cienkich warstw diamentowych metodą PA CVD
PublicationPraca omawia zastosowanie metody Car-Parrinello MD w symulacji procesu wzrostu cienkich warstw diamentowych w metodzie PAC VD.
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Improvements to the two-phase sandwich method for calculating the melting points of pure metals
PublicationThe thermophysical properties of metal alloys are often investigated via molecular dynamics (MD) simulations.An exact and reliable estimation of the thermophysical parameters from the MD data requires a properly and carefullyelaborated methodology. In this paper, an improved two-phase sandwich method for the determination of the metal meltingtemperature is proposed, based on the solid-liquid equilibrium theory. The new method was...
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublicationHuman immunodeficiency virus type 1 protease (HIV-1 PR) is a viral-encoded enzyme that forms a homodimer. HIV-1 PR is essential for replication and assembly of the virus and inactivation of HIV-1 PR enzyme causes production of immature, noninfectious viral particles and thus HIV-1 PR is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Efficient Recovery of Noble Metal Ions (Pd2+, Ag+, Pt2+, and Au3+) from Aqueous Solutions Using N,N'-Bis(salicylidene)ethylenediamine (Salen) as an Extractant (Classic Solvent Extraction) and Carrier (Polymer Membranes)
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Sensorless Rotor Position Estimation of Doubly-Fed Induction Generator Based on Backstepping Technique
PublicationThis paper proposes a speed observer algorithm for the sensorless control of a doubly-fed induction generator based on classical adaptive backstepping technique. The sensorless control is shown using classic stator field oriented control which is used to active and reactive power control. Performance of the proposed algorithm of a speed observer is validated by simulation and experimental results obtained using a small-rating generator...
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublicationPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Bounds on the cover time of parallel rotor walks
PublicationThe rotor-router mechanism was introduced as a deterministic alternative to the random walk in undirected graphs. In this model, a set of k identical walkers is deployed in parallel, starting from a chosen subset of nodes, and moving around the graph in synchronous steps. During the process, each node successively propagates walkers visiting it along its outgoing arcs in round-robin fashion, according to a fixed ordering. We consider...
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Bounds on the Cover Time of Parallel Rotor Walks
PublicationThe rotor-router mechanism was introduced as a deterministic alternative to the random walk in undirected graphs. In this model, a set of k identical walkers is deployed in parallel, starting from a chosen subset of nodes, and moving around the graph in synchronous steps. During the process, each node maintains a cyclic ordering of its outgoing arcs, and successively propagates walkers which visit it along its outgoing arcs in...
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Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
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Characterization of PVDF/Graphene Nanocomposite Membranes for Water Desalination with Enhanced Antifungal Activity
PublicationSeawater desalination is a worldwide concern for the sustainable production of drinking water. In this regard, membrane distillation (MD) has shown the potential for effective brine treatment. However, the lack of appropriate MD membranes limits its industrial expansion since they experience fouling and wetting issues. Therefore, hydrophobic membranes are promising candidates to successfully deal with such phenomena that are typical...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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2,6-Bis((benzoyl-R)amino)pyridine (R = H, 4-Me, and 4-NMe2) Derivatives for the Removal of Cu(II), Ni(II), Co(II), and Zn(II) Ions from Aqueous Solutions in Classic Solvent Extraction and a Membrane Extraction
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Objectivity in a Noisy Photonic Environment through Quantum State Information Broadcasting
PublicationRecently, the emergence of classical objectivity as a property of a quantum state has been explicitly derived for a small object embedded in a photonic environment in terms of a spectrum broadcast form—a specific classically correlated state, redundantly encoding information about the preferred states of the object in the environment. However, the environment was in a pure state and the fundamental problem was how generic and robust...
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....