Wyniki wyszukiwania dla: 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?
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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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
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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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
PublikacjaCoarse-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
PublikacjaCentral 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
PublikacjaCentral-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
PublikacjaThere 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
PublikacjaACCEPTED 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"
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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Insights Into Hydrodynamics of Spinning Fluids Reactor
PublikacjaSpinning 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
Dane BadawczeThis 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
PublikacjaIn 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
PublikacjaAdvanced 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
PublikacjaThe 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
PublikacjaThe 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...