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Search results for: force fields
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The protein folding problem: global optimization of force fields
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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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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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Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
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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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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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Ensemble fits of restrained peptides’ conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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A subdomain model for armature reaction field and open‐circuit field prediction in consequent pole permanent magnet machines
PublicationIn this paper, the machine quantity, such as electromagnetic torque, self and mutual inductances, and electromotive force, is analytically calculated for non-overlapping winding consequent pole slotted machine for open-circuit field and armature reaction. The sub-domain approach of (2-D) analytical model is developed using Maxwell's equations and divide the problem into slots, slot-openings, airgap and magnets region, the magnet...
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A review on analytical models of brushless permanent magnet machines
PublicationThis study provides an in-depth investigation of the use of analytical and numerical methods in analyzing electrical machines. Although numerical models such as the finite-element method (FEM) can handle complex geometries and saturation effects, they have significant computational burdens, are time-consuming, and are inflexible when it comes to changing machine geometries or input values. Analytical models based on magnetic equivalent...
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Tomasz Maria Boiński dr inż.
PeopleI’m associated with the University since the year 2000 when I started my studies in Computer Science on the Faculty of Electronics, Telecommunications and Informatics. After graduating with honors in 2005, I applied for doctoral studies. During his studies and immediately afterward I was involved in cooperation with Hogart from Warsaw, in the implementation of business solutions in Gdynia company Elektronika SA (Infor FMS SunSystems)...