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Search results for: polarizable force fields
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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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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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The protein folding problem: global optimization of force fields
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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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Efficient sampling of high-energy states by machine learning force fields
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Extension of the Force Matching Method to Anisotropic Coarse-Grained Transferable Force Fields: Application to the Unres Model of Proteins
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Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins
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Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
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Ensemble fits of restrained peptides’ conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3
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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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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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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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Central-force decomposition of spline-based modified embedded atom method potential
PublicationCentral-force decompositions are fundamental to the calculation of stress fields in atomic systems by means of Hardy stress. We derive expressions for a central-force decomposition of the spline-based modified embedded atom method (s-MEAM) potential. The expressions are subsequently simplified to a form that can be readily used in molecular-dynamics simulations, enabling the calculation of the spatial distribution of stress in...
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CENTRAL-FORCE DECOMPOSITION OF THE TERSOFF POTENTIAL
PublicationCentral forces play important role in the analysis of results obtained with particle simulation methods, since they allow evaluating stress fields. In this work we derive expressions for a central-force decompositon of the Tersoff potential, which is often used to describe interatomic interactions in covalently bonded materials. We simplify the obtained expressions and discuss their properties.
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Problems in estimation of hand grip force based on EMG signal
PublicationThere has recently been a significant increase in the number of publications on and applications of bioelectric signals for diagnostic purposes. While the use of ECG (electrocardiography) is not surprising, the use of signals from registration of brain activity (EEG) and muscles activity (EMG) still finds new applications in various fields. The authors focus on the use of EMG signals for estimating hand grip force. Currently,...
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Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
PublicationCoarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied. The coarse-grained approaches differ by the scheme of reduction and by the origin...
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Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublicationACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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The influence of external interference on AFM imaging, the use of a protective helmet
Open Research DataThis collection is of purely practical importance, showing how the presence of external disturbances can adversely affect the quality of imaging with an atomic force microscope. For this reason, it is also advisable to provide a link to a workshop-like study [1] as well as a huge number of commercial solutions available after entering the keyword "AFM...
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Insights Into Hydrodynamics of Spinning Fluids Reactor
PublicationSpinning fluids reactor (SFR) is one of the most efficient gas-liquid contacting system with high potential of application in many fields. The unique solution of SFR is the contacting of two spinning fluids which generated centrifugal force. The aim of this study was to investigate the pressure field distribution on the inner surface of reactors dispersing element. Obtained results confirm the high heterogeneity of the field pressure...
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Application of different modes of nanoscale impedance microscopy in materials research
PublicationIn recent years, there is noticeable interest in application of various types of scanning probe microscopy in material science research. One of them is contact atomic force microscopy combined with local impedance measurements, known as nanoscale impedance microscopy. Literature references present its application in investigations of new materials, microelectronics diagnostics, or research of protective coatings performance. In...
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Justyna Szostak dr inż.
PeopleI Gdańsk University of Technology: Chair of the Rector’s Internationalization Committee (October 2020 - Present) Erasmus + Coordinator for students and staff members, Faculty of Applied Physics and Mathematics (Mar 2017 - Present) Dean's Proxy for Internationalization, Faculty of Applied Physics and Mathematics (October 2020 - Present) Coordinator of the International Relations Office of the Faculty of Applied Physics and...
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Application of magnetic nanoparticles for magnetic solid-phase extraction in preparing biological, environmental and food samples
PublicationThe need to obtain meaningful results as the basis for determining the content of trace amounts of analytes has become the driving force behind the development of modern analytical techniques, including sample-preparation techniques, such as solid-phase extraction (SPE). Recently, great interest was aroused in the use of magnetic nanoparticles (MNPs) in SPE. These materials exhibit high selectivity, and, in small amounts, can provide...
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The elasto-plastic numerical study of crack initiation in notched PMMA specimens under uniaxial loading conditions – Tension and torsion
PublicationThis paper presents the results of FEM numerical calculations aimed at describing the plastic strain and stress fields under critical loading conditions: tensile force or torsional moment. The calculations were carried out with reference to the results of experimental tensile and torsional tests of flat PMMA specimens weakened with V-notches of different root radii: 0.5, 2 and 10 mm. The procedure for conducting nonlinear numerical...
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A PRELIMINARY STUDY ON THE OPTIMAL CHOICE OF AN IMPLANT AND ITS ORIENTATION IN VENTRAL HERNIA REPAIR
PublicationThis paper addresses the problem of ventral hernia repair. The main goals are to find an optimal surgical mesh for hernia repair and to define its optimal orientation in the abdominal wall to minimise the maximum force at the tissue-implant juncture. The optimal mesh is chosen from a set of orthotropic meshes with different stiffness ratios for typical hernia placement in the abdominal area. The implant is subjected to an anisotropic...
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Mathematical Modeling of Ice Thrusting on the Shore of the Vistula Lagoon (Baltic Sea) and the Proposed Artificial Island
PublicationCoastal lagoons are inland and shallow water bodies, separated from the ocean by a barrier. In cold regions, ice phenomena in shallow water coastal lagoons occur every winter season. Ice is predominantly formed on the surface due to density stratification and surface cooling. The ice dynamics in such areas are dominantly affected by winds. Water dynamics also cause ice movement, but due to the large areal scale of lagoons, the...
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Influence of compaction effectiveness on interlayer bonding of asphalt layers
PublicationThe paper presents the results of research on the interlayer bonding of asphalt layers compacted in the laboratory and in the field. To measure the interlayer bonding at a temperature of 20°C the Leutner test apparatus was used and load was applied at a rate of 50 mm/minute. Three types of interlayer interfaces were tested: no tack coat and tack coats made of two types of the pure bitumen emulsions. Four compaction techniques were...
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AFM-assisted investigation of conformal coatings in electronics
PublicationPurpose – This paper aims to presents a new method of investigation of local properties of conformal coatings utilized in microelectronics. Design/methodology/approach – It is based on atomic force microscopy (AFM) technique supplemented with the ability of local electrical measurements, which apart from topography acquisition allows recording of local impedance spectra, impedance imaging and dc current mapping. Potentialities...
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On the geometrically nonlinear vibration of a piezo-flexomagnetic nanotube
PublicationIn order to describe the behavior of thin elements used in MEMS and NEMS, it is essential to study a nonlinear free vibration of nanotubes under complicated external fields such as magnetic environment. In this regard, the magnetic force applied to the conductive nanotube with piezo-flexomagnetic elastic wall is considered. By the inclusion of Euler-Bernoulli beam and using Hamilton’s principle, the equations governing the system...
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The use of a two-phase Monte Carlo material model to reflect the dispersion of asphalt concrete fracture parameters
PublicationThe work covers comprehensive laboratory tests of semi-circular bending (SCB) of asphalt concrete samples. The results of two test series, including four and 32 SCB specimens, indicate a substantial scatter of force–deflection (F-d) histories. The numerical analysis is aimed to reflect the maximum breaking load and fracture energy of the samples, pointing out their random character. The original simulation-based fictitious Monte...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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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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The thermal effort during marine steam turbine flooding with water
PublicationThe work discussed an extreme case of cooling a steam turbine. The ship's steam turbine was used as an example. In marine transport units with low-speed engines dominate, however, there are also units with steam turbines. An example of analysed marine steam turbine is shown in Fig. 1. When considering the issue of cooling steam turbines, it is necessary to estimate the extreme conditions that may occur during operation of the turbine....
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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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Time-domine Dipole Fields in acoustic and Elektromagnetics
PublicationThe ultrawideband (UWB) radio technique presents a challenge not just for technology. The UWB carrier-free pulses act at a close distance, their electromagnetic fields being very different from classic monochromatic plane wave. The author proposes to adapt a time-domian approach to analysis of broadband spherical fields, both acoustic and electromagnetic, in fundamental cases of quasi-point physical sources.
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The Hopf theorem for gradient local vector fields on manifolds
PublicationWe prove the Hopf theorem for gradient local vector fields on manifolds, i.e., we show that there is a natural bijection between the set of gradient otopy classes of gradient local vector fields and the integers if the manifold is connected Riemannian without boundary.
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Connected components of the space of proper gradient vector fields
PublicationWe show that there exist two proper gradient vector fields on Rn which are homotopic in the category of proper maps but not homotopic in the category of proper gradient maps.
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Air Force Magazine
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Detection and time/frequency analysis of electric fields in the ground
PublicationThis paper sets out to detect and characterize electric fields in the ground (such as stray current fields) using a tandem time/frequency method of signal analysis. Results were obtained from investigations performed in the presence of a generated electric field with controlled variable characteristics, and in the presence of an electric field generated by a tramline. The analysis of measurement registers was performed using Short‐Time...
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The homotopy type of the space of gradient vector fields on the two-dimensional disc
PublicationWe prove that the inclusion of the space of gradient vector fields into the space of all vector fields on D^2 non-vanishing in S^1 is a homotopy equivalence
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Verification of the method of reconstructing convective velocity fields on the basis of temperature fields in vertical, differential and equally heated, open and closed channels
PublicationThis paper describes a method of reconstructing velocity fields, i.e. a numerical reconstruction procedure (NRP) that involves the numerical processing of experimentally measured temperature distributions in free convection heat transfer. The NRP consists in solving only the continuity and Navier–Stokes equations with an additional source term. This term is proportional to a known temperature (e.g. from a thermal imaging camera)...
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Scholarly communication activities in the fields of chemistry and economics. A Polish perspective
PublicationThis study examines the scholarly communication activities in two scientific fields, chemistry and economics, in a Polish context. The dissertation aims at investigating what characterises the publishing choices of researchers and what supplementary forms for the dissemination of research output are used by scholars. In addition, the paper is looking into what are the views and awareness of open access and institutional repositories...
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FINITE FIELDS AND THEIR APPLICATIONS
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Zero phase shift digital filtering for assessment of exposure to non-sinusoidal magnetic fields
PublicationAccuracy of assessment of human body exposure to magnetic fields is affected by several uncertainty sources. One of them is estimation of the total exposure to non-sinusoidal fields. Standard methods can be implemented using analogue or digital filters that introduce a phase shift that affect the result of total exposure level estimation. The paper presents a new method that allows performing more precise assessment of exposure...
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Perceptual and Motor Effects of Muscle Co-activation in a Force Production Task
PublicationWe tested several predictions of the theory of motor control with spatial referent coordinates related to effects of muscle coactivation on force production and perception. In particular, we predicted that subjects would produce unintentional force increase by finger flexors and be unaware of this force increase. Healthy subjects performed steady force production task in isometric conditions with visual feedback on the force level....
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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Simplified AutoDock force field for hydrated binding sites
Publicationhas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...
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Homoclinics for singular strong force Lagrangian systems
PublicationWe study the existence of homoclinic solutions for a class of generalized Lagrangian systems in the plane, with a C1-smooth potential with a single well of infinite depth at a point ξ and a unique strict global maximum 0 at the origin.Under a strong force condition around the singular point ξ, via minimization of an action integral, we will prove the existence of at least two geometrically distinct homoclinic solutions.
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Generation of random fields to reflect material and geometric imperfections of plates and shells
PublicationThe paper covers two patterns of random field generation: conditional acceptance – rejection method and Karhunen – Loève expansion. The generation of two-dimensional random fields is essential in plates and shells analysis, allowing for a relevant limit and critical state assessment of geometrically and ma-terially imperfect structures. The features of both generation methods dedicate them to selected problems.