Search results for: amoeba
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe 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
PublicationThe 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
PublicationThe 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?
PublicationPreorganization 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"
Open Research DataThis 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
PublicationWykorzystano 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
PublicationExpansive 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
PublicationExpansive 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
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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EM-Driven Multi-Objective Optimization of Antenna Structures in Multi-Dimensional Design Spaces
PublicationFeasible 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
PublicationCost-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
PublicationA 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
PublicationWith 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
PublicationWe 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
PublicationA 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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AMBA - The Association of MBAs Accreditation
ProjectsProject realized in Administration, Faculty of Management and Economics according to MNISW/2018/42/DIR/AZ agreement from 2018-05-21
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Marta Kuc-Czarnecka dr
PeopleMarta Kuc-Czarnecka is the deputy head of the Department of Statistics and Economics at the Faculty of Management and Economics of the Gdańsk University of Technology. She also serves as the Dean's proxy for AMBA accreditation. She is a co-founder of Rethinking Economics Gdańsk and a member of the Foundation Edward Lipiński for the promotion of pluralism in economic sciences. In 2018-2022, she was Eurofound’s quality of life and...
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Low-Cost EM-Simulation-Driven Multi-Objective Optimization of Antennas
PublicationA 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
PublicationA 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...