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Search results for: BACKBONE
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The Backbone Coloring Problem for Bipartite Backbones
PublicationLet G be a simple graph, H be its spanning subgraph and λ≥2 be an integer. By a λ -backbone coloring of G with backbone H we mean any function c that assigns positive integers to vertices of G in such a way that |c(u)−c(v)|≥1 for each edge uv∈E(G) and |c(u)−c(v)|≥λ for each edge uv∈E(H) . The λ -backbone chromatic number BBCλ(G,H) is the smallest integer k such that there exists a λ -backbone coloring c of G with backbone H satisfying...
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Optimal backbone coloring of split graphs with matching backbones
PublicationFor a graph G with a given subgraph H, the backbone coloring is defined as the mapping c: V(G) -> N+ such that |c(u)-c(v)| >= 2 for each edge uv \in E(H) and |c(u)-c(v)| >= 1 for each edge uv \in E(G). The backbone chromatic number BBC(G;H) is the smallest integer k such that there exists a backbone coloring with max c(V(G)) = k. In this paper, we present the algorithm for the backbone coloring of split graphs with matching backbone.
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The computational complexity of the backbone coloring problem for planar graphs with connected backbones
PublicationIn the paper we study the computational complexity of the backbone coloring problem for planar graphs with connected backbones. For every possible value of integer parameters λ≥2 and k≥1 we show that the following problem: Instance: A simple planar graph GG, its connected spanning subgraph (backbone) HH. Question: Is there a λ-backbone coloring c of G with backbone H such that maxc(V(G))≤k? is either NP-complete or polynomially...
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The Backbone Coloring Problem for Small Graphs
PublicationIn this paper we investigate the values of the backbone chromatic number, derived from a mathematical model for the problem of minimization of bandwidth in radio networks, for small connected graphs and connected backbones (up to 7 vertices). We study the relationship of this parameter with the structure of the graph and compare the results with the solutions obtained using the classical graph coloring algorithms (LF, IS), modified...
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The computational complexity of the backbone coloring problem for bounded-degree graphs with connected backbones
PublicationGiven a graph G, a spanning subgraph H of G and an integer λ>=2, a λ-backbone coloring of G with backbone H is a vertex coloring of G using colors 1, 2, ..., in which the color difference between vertices adjacent in H is greater than or equal to lambda. The backbone coloring problem is to find such a coloring with maximum color that does not exceed a given limit k. In this paper, we study the backbone coloring problem for bounded-degree...
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A note on fast approximate backbone coloring of split graphs with star--like backbones
PublicationDla grafu G = (V, E) z wyróżnionym podgrafem H, kolorowanie szkieletowe jest zdefiniowane jako odwzorowanie c spełniające |c(u) - c(v)| > 1 dla każdej krawędzi z E(H) oraz |c(u) - c(v)| > 0 dla każdej krawędzi z E(G). W pracy przedstawiono 1-przybliżony algorytm kolorowania szkieletowego split grafów ze skojarzeniem w szkielecie o złożoności O(|V|) oraz 1-przybliżony algorytm dla split grafów z rozłącznymi gwiazdami w szkielecie.
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Greedy algorithms for backbone graph coloring in KOALA library
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Backbone and Side-Chain Cleavages in Electron Detachment Dissociation (EDD)
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Optimization of condition for demineralization Baltic cod (Gadus morhua) backbone
PublicationKręgosłupy dorsza bałtyckiego (Gadus morhua) są alternatywnym źródłem kolagenu. Aby uzyskać z nich natywny niezanieczyszczony kolagen należy usunąć z nich białka mięśniowe i sole mineralne. Obecność tych związków pogarsza funkcjonalne właściwości preparatu kolagenowego. Dlatego celem pracy było opracowanie optymalnych parametrów demineralizacji kręgosłupów dorsza. Najlepszy efekt demineralizacji, nieomal 100%, przy stratach tylko...
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On Optimal Backbone Coloring of Split and Threshold Graphs with Pairwise Disjoint Stars
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Isolation and some properties of collagen from the backbone of Baltic cod(Gadus morhua)
PublicationOssein from Baltic cod backbone was obtained after extraction of non-collagenous protein with 0.1 M NaOH solution and demineralization with 1.0 M HCl solution. The extractions were performed at 4 C for24, 48 and 72 h using a solid/solution ratio from 1:4 to 1:8 (w/v). After 48 h of extraction in 0.5 M acetic acid only about 25% of collagen was dissolved. After 48 h of extraction at optimal concentration of pepsin(4 mg/g ossein)...
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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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Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope
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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3-δ oxygen electrodes for solid oxide cells prepared by polymer precursor and nitrates solution infiltration into gadolinium doped ceria backbone
PublicationInfiltration is a method, which can be applied for the electrode preparation. In this paper oxygen electrode is prepared solely by the infiltration of La0.6Sr0.4Co0.2Fe0.8O3‐δ (LSCF) into Ce0.8Gd0.2O2-δ (CGO) backbone. The use a polymer precursor as an infiltrating medium, instead of an aqueous nitrate salts solution is presented. It is shown that the polymer forms the single-phase perovskite at 600 °C, contrary to the nitrates...
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A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Valence and ionic lowest-lying electronic states of small esters studied by high resolution vacuum ultraviolet photoabsorption, photoelectron spectroscopy and ab initio calculations
PublicationEsters are an important class of oxygenated volatile organic compounds used in food flavorings, perfumes and other cosmetic products. They are present in fruits and pheromones and are emitted to the atmosphere naturally. Esters are also formed in the atmosphere as a product of the oxidation of ethers. Some of them form poly-molecule chains and are used in plastics. Phosphoesters form DNA backbone, while nitroesters are known for...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Future research directions in design of reliable communication systems
PublicationIn this position paper on reliable networks, we discuss new trends in the design of reliable communication systems. We focus on a wide range of research directions including protection against software failures as well as failures of communication systems equipment. In particular, we outline future research trends in software failure mitigation, reliability of wireless communications, robust optimization and network design, multilevel...
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Performance of LSP preemption methods in different MPLS networks
PublicationPreemption in Multiprotocol Label Switching (MPLS) is an optional traffic engineering technique used to create a new path of high priority when there is not enough bandwidth available. In such case the path is admitted by removing one or more previously allocated paths of lower priority. As there are usually many possible sets of low priority paths which can be selected, a preemption algorithm is being started to select the best...
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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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INFLUENCE OF A VERTEX REMOVING ON THE CONNECTED DOMINATION NUMBER – APPLICATION TO AD-HOC WIRELESS NETWORKS
PublicationA minimum connected dominating set (MCDS) can be used as virtual backbone in ad-hoc wireless networks for efficient routing and broadcasting tasks. To find the MCDS is an NP- complete problem even in unit disk graphs. Many suboptimal algorithms are reported in the literature to find the MCDS using local information instead to use global network knowledge, achieving an important reduction in complexity. Since a wireless network...
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LaNi1-xCoxO3-δ(x=0.4 to 0.7) cathodes for solid oxide fuel cells by infiltration
PublicationPerformance of LaNi 1-x Co x O 3−δ (LNC) (x=0.4 to 0.7) as a cathode in solid oxide fuel cell (SOFC) is evaluated. Symmetrical cathode/electrolyte/cathode cells for electrochemical testing are prepared by infiltration of yttria stabilized zirconia (YSZ) backbone with LNC solutions. It is showed that the cathode infiltrated with LaNi 0.5 Co 0.5 O 3−δ (LNC155) has the lowest polarization resistance and activation energy, 197 mΩ cm...
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Service-based Resilience for Embedded IoT Networks
PublicationEmbedded IoT networks are the backbone of safety-critical systems like smart factories, autonomous vehicles, and airplanes. Therefore, resilience against failures and attacks should be a prior concern already in their design stage. In this study, we introduce a service-based network model as an MILP optimization problem for the efficient deployment of a service overlay to the embedded network by meeting QoS and resilience requirements....
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Solid-State Modification of Poly(butylene terephthalate) with a Bio-Based Fatty Acid Dimer Diol Furnishing Copolyesters with Unique Morphologies
PublicationCopolyesters based on poly(butylene terephthalate) (PBT) and a bio-based fatty acid dimer diol (FADD) were prepared by solid-state modification (SSM). The chemical incorporation of the FADD into the backbone of the PBT was proven using various techniques. It was clear that the incorporation rate was diffusion-limited rather than reaction-limited. From quantitative 13C NMR a nonrandom chemical microstructure was obtained at all...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublicationThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublicationThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Wytrzymałość pętli wplatanych na linach podwójnie plecionych
PublicationCechą wyróżniającą statki żaglowe z grona innych obiektów pływających są żagle. To cecha widoczna, za którą kryją się mniej romantyczne elementy, takie jak maszty, liny i osprzęt. Rozpostarcie białych płócien na maszcie i następnie żeglowanie wymaga sprawnego operowania nimi, co wiąże się z doborem odpowiedniego ich zestawu, ułożenia i napięcia. To maszty są kręgosłupem takielunku, a liny jego mięśniami i ścięgnami. Do poprawnego...
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High performance LaNi1-xCoxO3-δ (x = 0.4 to 0.7) infiltrated oxygen electrodes for reversible solid oxide cells
PublicationOxygen electrodes prepared by infiltration of yttria stabilized zirconia backbone with Ce0.8Gd0.2O1.95 barrier layer and LaNi1-xCoxO3-δ (x=0.4 to 0.7) catalyst for application in reversible solid oxide cells have been studied. The effect of temperature and Ni:Co ratio on their phase composition, microstructure and electrochemical properties are discussed. It was shown that oxygen electrodes infiltrated with LaNi0.5Co0.5O3-δ had...
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Preparation and characterisation of solution-cast Nafion membrane
PublicationNafion is a commercial name for a perfluorosulfonic polymer, which has been developed in 1962 by Dupont de Nemours. This polymer consists of a polytetrafluoroethylene backbone and regular spaced long perfluorovinyl ether pendant side chains terminated by a sulfonate ionic group. These sulfonate groups are responsible for cation-exchange properties of Nafion. Thanks to the ion-exchange properties, water permeability, good chemical,...
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Compact global association based adaptive routing framework for personnel behavior understanding
PublicationPersonnel behavior understanding under complex scenarios is a challenging task for computer vision. This paper proposes a novel Compact model, which we refer to as CGARPN that incorporates with Global Association relevance and Adaptive Routing Pose estimation Network. Our framework firstly introduces CGAN backbone to facilitate the feature representation by compressing the kernel parameter space compared with typical algorithms,...
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Why Are Left-Handed G-Quadruplexes Scarce?
PublicationG-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear....
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Towards sugar-derived polyamides as environmentally friendly materials
PublicationAs part of our ongoing study investigating isohexide-based polyamides, we have synthesized isosorbide(bis(propan-1-amine)) (DAPIS) and studied its reactivity in the polymerization towards fully biobased polyamides. Polycondensation of nylon salts with various contributions of DAPIS afforded a family of homo- and copolyamides, which were characterized using complementary spectroscopic techniques. The chemical structure of the materials...
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Unprecedented Adhesive Performance of Propylene-Based Hydroxyl Functionalized Terpolymers
PublicationThe synthesis of hydroxyl functionalized propylene-based terpolymers and their performance as hot melt adhesives were investigated. The products comprise uniformly distributed butyl and 4-hydroxyl-butyl branches along the polypropylene backbone. Despite the low hydroxyl-functionality level of ≤ 0.5 mol%, hydroxyl functionalized terpolymers show formidable adhesion to aluminum and steel providing an adhesive strength exceeding 16...
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BP-EVD: Forward Block-Output Propagation for Efficient Video Denoising
PublicationDenoising videos in real-time is critical in many applications, including robotics and medicine, where varying light conditions, miniaturized sensors, and optics can substantially compromise image quality. This work proposes the first video denoising method based on a deep neural network that achieves state-of-the-art performance on dynamic scenes while running in real-time on VGA video resolution with no frame latency. The backbone...
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Structure and Molecular Dynamics in Renewable Polyamides from Dideoxy-Diamino Isohexide
PublicationThe chemical structure, the conformation, andthe flexibility of the polymer chain fragments present in thepolyamides synthesized from 2,5-diamino-2,5-dideoxy-1,4;3,6-dianhydrosorbitol, 1,4-diaminobutane, and either sebacic orbrassylic acid have been studied by liquid-state 2D NMRspectroscopy viz. correlation spectra (COSY) and heteronuclearmultiple-bond correlation spectra (gHMBC), by 13Ccross-polarization/magic-angle spinning...
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Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations
PublicationThis work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from...
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Enhancing Availability for Critical Services
PublicationTraditional approaches to provide classes of resilient service take the physical network availability as an input and then deploy redundancy and restoration techniques at various layers, often without full knowledge of mappings between layers. This makes it hard (and often inefficient) to ensure the high availability required by critical services which are typically a small fraction of the total traffic. Here, the innovative technique...
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Biowaste chicken eggshell powder as a potential cure modifier for epoxy/anhydride systems: competitiveness with terpolymer-modified calcium carbonate at low loading levels
PublicationBiowaste chicken eggshell (ES) powder was applied as a potential cure modifier in epoxy/anhydride systems. Cure behaviour and kinetics of composites filled with very low content (0.1 wt% based on epoxy resin) of ES, calcium carbonate (CaCO3), and terpolymer-modified fillers, mES and mCaCO3, were discussed comparatively. Surface analysis was performed by X-ray photoelectron spectroscopy. Cure kinetics was investigated by differential...
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A new approach to design of weather disruption-tolerant wireless mesh networks
PublicationWireless Mesh Networks, offering transmission rates of 1–10 Gb/s per a millimeter-wave link (utilizing the 71–86 GHz band) seem to be a promising alternative to fiber optic backbone metropolitan area networks because of significantly lower costs of deployment and maintenance. However, despite providing high transmission rates in good weather conditions, high-frequency wireless links are very susceptible to weather disruptions....
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Diaryl Sulfide Derivatives as Potential Iron Corrosion Inhibitors: A Computational Study
PublicationThe present work aimed to assess six diaryl sulfide derivatives as potential corrosion inhibitors. These derivatives were compared with dapsone (4,4′-diaminodiphenyl sulfone), a common leprosy antibiotic that has been shown to resist the corrosion of mild steel in acidic media with a corrosion efficiency exceeding 90%. Since all the studied compounds possess a common molecular backbone (diphenyl sulfide), dapsone was taken as the...
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Categorization of emotions in dog behavior based on the deep neural network
PublicationThe aim of this article is to present a neural system based on stock architecture for recognizing emotional behavior in dogs. Our considerations are inspired by the original work of Franzoni et al. on recognizing dog emotions. An appropriate set of photographic data has been compiled taking into account five classes of emotional behavior in dogs of one breed, including joy, anger, licking, yawning, and sleeping. Focusing on a particular...
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Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublicationInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
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Effect of carbazole and pyrrolidine functionalization of phenanthroline ligand on ground- and excited-state properties of rhenium(I) complexes. Interplay between 3MLCT and 3IL/3ILCT
PublicationNew rhenium(I) tricarbonyl complexes based on the phenanthroline ligand were designed and synthesized to investigate the role of carbazole (cbz) and pyrrolidine (pyrr) substituents in determining thermal, electrochemical and optoelectronic properties. Both pyrr and cbz are electron-releasing substituents, but they differ in the steric hindrance and electron delocalization ability. The impact of pyrr and cbz on ground- and excited-state...
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Investigation into MPI All-Reduce Performance in a Distributed Cluster with Consideration of Imbalanced Process Arrival Patterns
PublicationThe paper presents an evaluation of all-reduce collective MPI algorithms for an environment based on a geographically-distributed compute cluster. The testbed was split into two sites: CI TASK in Gdansk University of Technology and ICM in University of Warsaw, located about 300 km from each other, both connected by a fast optical fiber Ethernet-based 100 Gbps network (900 km part of the PIONIER backbone). Each site hosted a set...