Wyniki wyszukiwania dla: amoeba
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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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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublikacjaWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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Chemical composition of shells from red (Strongylocentrotus franciscanum) and green (Strongylocentrotus droeba-chiensis) sea urchin
PublikacjaThe shells from red and green sea urchins accounted for 47.9 and 40.7% of their body weights, respectively. The red and green sea urchin shells contained 91.08 and 90.77% minerals and 4.06 and 4.99% proteins, respectively. The shells did not contain any chitin. Sea urchin shells had a relatively large amount of naphthoquinone pigments, 121 mg per 100 g in red and 163 mg per 100 g in green species. The small quantities of glucosamine...
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Ship weather routing featuring w-MOEA/D and uncertainty handling
PublikacjaThe paper presents a new version of evolutionary multi-objective weather routing (WR) for ships taking into account uncertainties of weather forecasts in route optimization. The method applies authors’ w-MOEA/D algorithm: MOEA/D framework incorporating Decision Maker’s (DM) preferences by means of w-dominance relation. Owing to this, DM preferences are taken into account throughout optimization, allowing the process to focus on...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublikacjaPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Raw data for the paper "Mutually polarizable QM/MM model with in situ optimized localized basis functions"
Dane BadawczeThis dataset contains raw data used to generate plots in the paper Mutually polarizable QM/MM model with in situ optimized localized basis functions. The paper is devoted to a second generation of the TINKTEP model -- an QM/MM approach combining linear-scaling DFT (ONETEP) and a polarizable force field (AMOEBA).
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Estimation of concentration equilibrium constants of reaction between mutagenic HAA and antimutagenic cabbage phytochemicals based on data from Ames test
PublikacjaWykorzystano dane testu Amesa, przy pomocy którego oceniono antymutagenne właściwości fitokompleksu kapusty w stosunku do modelowych kancerogennych heterocyklicznych amin aromatycznych (HAA), do oszacowania stężeniowych stałych reakcji HAA z izotiocyjanianami występującymi w tym warzywie. Wyznaczone stężeniowe stałe reakcji wskazują na dużą stabilność powstałych koniugatów, a zatem sugerują, że kapusta może efektywnie chronić organizm...
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Mechanical Behavior of Plastic Strips-Reinforced Expansive Soils Stabilized with Waste Marble Dust
PublikacjaExpansive soil needs to undergo treatment to be used as safe foundation soil for roads and buildings. From environmental conservation and economical point of view, the usage of agricultural and industrial wastes is the best option. In this study, the effects of utilizing plastic waste and marble waste dust on the engineering properties of expansive soils were examined. Various laboratory tests were carried out on sampled expansive...
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Mechanical Behavior of Plastic Strips-Reinforced Expansive Soils Stabilized with Waste Marble Dust
PublikacjaExpansive soil needs to undergo treatment to be used as safe foundation soil for roads and buildings. From an environmental conservation and economical point of view, the usage of agricultural and industrial wastes is the best option. In this study, the effects of utilizing plastic waste and marble waste dust on the engineering properties of expansive soils were examined. Various laboratory tests were carried out on sampled expansive...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublikacjaIterative 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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EM-Driven Multi-Objective Optimization of Antenna Structures in Multi-Dimensional Design Spaces
PublikacjaFeasible multi-objective optimization of antenna structures is presented. An initial set of Pareto optimal solutions is found using a multi-objective evolutionary algorithm (MOEA) working with a fast surrogate antenna model obtained by kriging interpolation of coarse-discretization EM simulation data. To make the surrogate construction computationally feasible in multi-dimensional design space, the space subset containing non-dominated...
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Rotational Design Space Reduction for Cost-Efficient Multi-Objective Antenna Optimization
PublikacjaCost-efficient multi-objective design of antenna structures is presented. Our approach is based on design space reduction algorithm using auxiliary single-objective optimization runs and coordinate system rotation. The initial set of Pareto-optimal solutions is obtained by optimizing a response surface approximation model established in the reduced space using coarse-discretization EM simulation data. The optimization engine is...
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Fabrication of the cross-linked PVA/TiO2/C nanocomposite membrane for alkaline direct methanol fuel cells
PublikacjaA crosslinked Poly(vinyl alcohol) based composite membrane was developed through a phase inversion process for use in alkaline direct methanol fuel cells (ADMFCs). The titanium dioxide (TiO2) and carbon nanoparticles (NPs) have been incorporated into the PVA polymer matrix to improve the mechanical and thermal properties. The membrane samples were further modified with maleic acid, a carboxylic acid acting as the cross-linker,...
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TOPOLOGICAL CLUES FOR PREDICTING OUTCOMES OF MULTIPLAYER ONLINE BATTLE ARENA GAMES
PublikacjaWith 27 million people playing League of Legends every day, e-sports became more and more important part of our everyday life. Rise of its popularity builds a demand for better understanding e-sports mechanics on a deeper level. In the article, we test a hypothesis that it is possible to predict an outcome of Multiplayer Online Battle Arena game based on topological clues only (such as area of polygon where vertices are players...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublikacjaWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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Fast Multi-Objective Antenna Design Through Variable-Fidelity EM Simulations
PublikacjaA technique for fast multi-objective antenna optimization is introduced. A kriging interpolation surrogate constructed from sampled coarse-mesh EM simulations is utilized by multi-objective evolutionary algorithm (MOEA) to obtain the initial Pareto front approximation. The surrogate is defined in a subset of the original design space, determined by means of independently optimized individual objectives. Response correction techniques...
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Re-akredytacja AMBA
ProjektyProjekt realizowany w Administracja Wydziału Zarządzania i Ekonomii zgodnie z porozumieniem MNISW/2018/42/DIR/AZ z dnia 2018-05-21
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Marta Kuc-Czarnecka dr
OsobyMarta Kuc-Czarnecka jest zastępczynią kierownika Katedry Statystyki i Ekonomii na Wydziale Zarządzania i Ekonomii Politechniki Gdańskiej. Pełni również funkcję pełnomocniczki Dziekana ds. akredytacji AMBA. Jest współzałożycielką Rethinking Economics Gdańsk oraz członkinią Fundacji im. Edwarda Lipińskiego na rzecz promocji pluralizmu w naukach ekonomicznych. W latach 2018-2022 była ekspertką Europejskiej Fundacji na Rzecz Poprawy...
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Low-Cost EM-Simulation-Driven Multi-Objective Optimization of Antennas
PublikacjaA surrogate-based method for efficient multi-objective antenna optimization is presented. Our technique exploits response surface approximation (RSA) model constructed from sampled low-fidelity antenna model (here, obtained through coarse-discretization EM simulation). The RSA model enables fast determination of the best available trade-offs between conflicting design goals. A low-cost RSA model construction is possible through...
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Low-Cost Multi-Objective Optimization Yagi-Uda Antenna in Multi-Dimensional Parameter Space
PublikacjaA surrogate-based technique for fast multi-objective optimization of a multi-parameter planar Yagi-Uda antenna structure is presented. The proposed method utilizes response surface approximation (RSA) models constructed using training samples obtained from evaluation of the low-fidelity antenna model. Utilization of the RSA models allowsfor fast determination of the best possible trade-offs between conflicting objectives in multi-objective...
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Computationally Efficient Multi-Objective Optimization of and Experimental Validation of Yagi-Uda Antenna
PublikacjaIn this paper, computationally efficient multi-objective optimization of antenna structures is discussed. As a design case, we consider a multi-parameter planar Yagi-Uda antenna structure, featuring a driven element, three directors, and a feeding structure. Direct optimization of the high-fidelity electromagnetic (EM) antenna model is prohibitive in computational terms. Instead, our design methodology exploits response surface...
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Cost-Efficient Multi-Objective Design of Miniaturized Microwave Circuits Using Machine Learning and Artificial Neural Network
PublikacjaDesigning microwave components involves managing multiple objectives such as center frequencies, impedance matching, and size reduction for miniaturized structures. Traditional multi-objective optimization (MO) approaches heavily rely on computationally expensive population-based methods, especially when exe-cuted with full-wave electromagnetic (EM) analysis to guarantee reliability. This paper introduces a novel and cost-effective...
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Sampling-based novel heterogeneous multi-layer stacking ensemble method for telecom customer churn prediction
PublikacjaIn recent times, customer churn has become one of the most significant issues in business-oriented sectors with telecommunication being no exception. Maintaining current customers is particularly valuable due to the high degree of rivalry among telecommunication companies and the costs of acquiring new ones. The early prediction of churned customers may help telecommunication companies to identify the causes of churn and design...
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Molecular characterization of a cryptic plasmid from the psychrotrophic antarctic bacterium Pseudoalteromonas sp. 643A
PublikacjaW ostatnich latach znacznie wzrosło zainteresowanie organizmami zimnolubnymi, głównie z powodu ich enzymów o biotechnologicznym znaczeniu. Jednak, aby wydajnie produkować takie enzymy w skali przemysłowej użyteczne jest stworzenie rekombinantowych systemów ekspresyjnych, które pozwolą na ich opłacalną produkcję. W osiągnięciu tego celu mogą pomóc odpowiednie wektory, konstruowane na bazie plazmidów pozyskiwanych z bakterii psychrofilnych/psychrotrofowych....
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IP Core of Coprocessor for Multiple-Precision-Arithmetic Computations
PublikacjaIn this paper, we present an IP core of coprocessor supporting computations requiring integer multiple-precision arithmetic (MPA). Whilst standard 32/64-bit arithmetic is sufficient to solve many computing problems, there are still applications that require higher numerical precision. Hence, the purpose of the developed coprocessor is to support and offload central processing unit (CPU) in such computations. The developed digital...
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Intelligent Decision Forest Models for Customer Churn Prediction
PublikacjaCustomer churn is a critical issue impacting enterprises and organizations, particularly in the emerging and highly competitive telecommunications industry. It is important to researchers and industry analysts interested in projecting customer behavior to separate churn from non‐churn consumers. The fundamental incentive is a firm’s intent desire to keep current consumers, along with the exorbitant expense of gaining new ones....
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Beata Krawczyk-Bryłka dr
OsobyPsycholog, doktor nauk humanistycznych w dziedzinie zarządzania, adiunkt w Katedrze przedsiębiorczości. 2018 - 2021: Kierownik projektu NCN: „Efektuacyjny model zespołu przedsiębiorczego. Jak działają przedsiębiorcze zespoły odnoszące sukces" od 2016: Quality Standards Lead filaru People management & personal development na studiach MBA Politechniki Gdańskiej 2008 – 2012: Prodziekan ds kształcenia Wzydziału Zarządzania i Ekonomii...
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Expedited constrained multi-objective aerodynamic shape optimization by means of physics-based surrogates
PublikacjaIn the paper, computationally efficient constrained multi-objective design optimization of transonic airfoil profiles is considered. Our methodology focuses on fixed-lift design aimed at finding the best possible trade-offs between the two objectives: minimization of the drag coefficient and maximization of the pitching moment. The algorithm presented here exploits the surrogate-based optimization principle, variable-fidelity computational...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study
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Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study
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Global variation in postoperative mortality and complications after cancer surgery: a multicentre, prospective cohort study in 82 countries
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Global variation in anastomosis and end colostomy formation following left‐sided colorectal resection
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Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy
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