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Chrobak, Artur, Grzegorz Ziółkowski, Dariusz Chrobak i Grażyna Chełkowska. "From Atomic Level to Large-Scale Monte Carlo Magnetic Simulations". Materials 13, nr 17 (21.08.2020): 3696. http://dx.doi.org/10.3390/ma13173696.
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This paper refers to Monte Carlo magnetic simulations for large-scale systems. We propose scaling rules to facilitate analysis of mesoscopic objects using a relatively small amount of system nodes. In our model, each node represents a volume defined by an enlargement factor. As a consequence of this approach, the parameters describing magnetic interactions on the atomic level should also be re-scaled, taking into account the detailed thermodynamic balance as well as energetic equivalence between the real and re-scaled systems. Accuracy and efficiency of the model have been depicted through analysis of the size effects of magnetic moment configuration for various characteristic objects. As shown, the proposed scaling rules, applied to the disorder-based cluster Monte Carlo algorithm, can be considered suitable tools for designing new magnetic materials and a way to include low-level or first principle calculations in finite element Monte Carlo magnetic simulations.
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Bal, Kristof M., i Erik C. Neyts. "Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations". Chemical Science 7, nr 8 (2016): 5280–86. http://dx.doi.org/10.1039/c6sc00498a.
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Bottaro, Sandro, i Kresten Lindorff-Larsen. "Biophysical experiments and biomolecular simulations: A perfect match?" Science 361, nr 6400 (26.07.2018): 355–60. http://dx.doi.org/10.1126/science.aat4010.
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A fundamental challenge in biological research is achieving an atomic-level description and mechanistic understanding of the function of biomolecules. Techniques for biomolecular simulations have undergone substantial developments, and their accuracy and scope have expanded considerably. Progress has been made through an increasingly tight integration of experiments and simulations, with experiments being used to refine simulations and simulations used to interpret experiments. Here we review the underpinnings of this progress, including methods for more efficient conformational sampling, accuracy of the physical models used, and theoretical approaches to integrate experiments and simulations. These developments are enabling detailed studies of complex biomolecular assemblies.
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Mulholland, Adrian J. "Computational enzymology: modelling the mechanisms of biological catalysts". Biochemical Society Transactions 36, nr 1 (22.01.2008): 22–26. http://dx.doi.org/10.1042/bst0360022.
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Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and reliable predictions of mechanisms, revolutionizing enzymology.
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Ding, Jun, Mark Asta i Robert O. Ritchie. "On the question of fractal packing structure in metallic glasses". Proceedings of the National Academy of Sciences 114, nr 32 (25.07.2017): 8458–63. http://dx.doi.org/10.1073/pnas.1705723114.
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This work addresses the long-standing debate over fractal models of packing structure in metallic glasses (MGs). Through detailed fractal and percolation analyses of MG structures, derived from simulations spanning a range of compositions and quenching rates, we conclude that there is no fractal atomic-level structure associated with the packing of all atoms or solute-centered clusters. The results are in contradiction with conclusions derived from previous studies based on analyses of shifts in radial distribution function and structure factor peaks associated with volume changes induced by pressure and compositional variations. The interpretation of such shifts is shown to be challenged by the heterogeneous nature of MG structure and deformation at the atomic scale. Moreover, our analysis in the present work illustrates clearly the percolation theory applied to MGs, for example, the percolation threshold and characteristics of percolation clusters formed by subsets of atoms, which can have important consequences for structure–property relationships in these amorphous materials.
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Comitani, Federico, Claudio Melis i Carla Molteni. "Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations". Biochemical Society Transactions 43, nr 2 (1.04.2015): 151–56. http://dx.doi.org/10.1042/bst20140259.
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Pentameric ligand-gated ion channels (pLGICs) are important biomolecules that mediate fast synaptic transmission. Their malfunctions are linked to serious neuronal disorders and they are major pharmaceutical targets; in invertebrates, they are involved in insecticide resistance. The complexity of pLGICs and the limited crystallographic information available prevent a detailed understanding of how they function. State-of-the-art computational techniques are therefore crucial to build an accurate picture at the atomic level of the mechanisms which drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand–protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events, with the guidance of mutagenesis electrophysiology experiments, to explore ligand-binding mechanisms, the effects of mutations and the potential role of a proline molecular switch for the gating of the ion channels. Results for the insect RDL receptor, the GABAC receptor, the 5-HT3 receptor and the nicotinic acetylcholine receptor will be reviewed.
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Artyukhov, Vasilii I., Yuanyue Liu i Boris I. Yakobson. "Equilibrium at the edge and atomistic mechanisms of graphene growth". Proceedings of the National Academy of Sciences 109, nr 38 (4.09.2012): 15136–40. http://dx.doi.org/10.1073/pnas.1207519109.
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The morphology of graphene is crucial for its applications, yet an adequate theory of its growth is lacking: It is either simplified to a phenomenological-continuum level or is overly detailed in atomistic simulations, which are often intractable. Here we put forward a comprehensive picture dubbed nanoreactor, which draws from ideas of step-flow crystal growth augmented by detailed first-principles calculations. As the carbon atoms migrate from the feedstock to catalyst to final graphene lattice, they go through a sequence of states whose energy levels can be computed and arranged into a step-by-step map. Analysis begins with the structure and energies of arbitrary edges to yield equilibrium island shapes. Then, it elucidates how the atoms dock at the edges and how they avoid forming defects. The sequence of atomic row assembly determines the kinetic anisotropy of growth, and consequently, graphene island morphology, explaining a number of experimental facts and suggesting how the growth product can further be improved. Finally, this analysis adds a useful perspective on the synthesis of carbon nanotubes and its essential distinction from graphene.
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Herasari, Dian, Rukman Hertadi, Fida M. Warganegara i Akhmaloka Akhmaloka. "Stability and Mobility of Lid Lipmnk in Acetonitrile by Molecular Dynamics Simulations Approach". Biosciences, Biotechnology Research Asia 15, nr 2 (6.06.2018): 295–99. http://dx.doi.org/10.13005/bbra/2632.
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Manuk lipase (lipMNK) from the thermophilic bacterium Geobacillus sp is a double lid lipase containing short and long lid segments. A few studies demonstrated that catalytic action of lipase involved the movement of lid segments from closed to open conformation upon the substrate binding. One factor that affects conformational dynamics of the lid segments is solvent polarity. The presence of acetonitrile in certain concentration has showed to enhance lipase activity. In this study, the effect of acetonitrile to the stability and activity of lipMNK was studied at the atomic level by molecular dynamics (MD) simulation. MD was carried out by NPT ensemble at 358 K for 100 nano seconds in various ratio of acetonitrile:water solvent mixtures. The results showed that the conformation of lipMNK was stable up to 70%. However, the effect of lid movement was significantly observed since the concentration at 20% acetonitrile. Detailed molecular analysis at this acetonitrile concentration revealed that the two lids moved in different modes upon opening and closing movement. In the opening movement, the two lids appeared to move in almost simultaneously, while during the closing movement, it was observed sequentially, started by short segment followed by long segment lid.
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Cayrel, Roger, i Matthias Steffen. "Effects of Photospheric Temperature Inhomogeneities on Lithium abundance Determinations (2D)". Symposium - International Astronomical Union 198 (2000): 437–47. http://dx.doi.org/10.1017/s0074180900167026.
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Based on detailed 2D radiation hydrodynamics (RHD) simulations, we have investigated the effects of photospheric temperature inhomogeneities induced by convection on spectroscopic determinations of the lithium abundance. Computations have been performed both for the solar case and for a metal-poor dwarf. NLTE effects are taken into account, using a five-level atomic model for Li I. Comparisons are presented with traditional 1D models having the same effective temperature and gravity. The net result is that, while LTE results differ dramatically between 1D and 2D models, especially in the metal-poor case, this does not remain true when NLTE effects are included: 1D/2D differences in the inferred NLTE Li abundance are always well below 0.1 dex. The present computations still assume LTE in the continuum. New computations removing this assumption are planned for the near future.
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Pujol-Navarro, Neret, Karina Kubiak-Ossowska, Valerie Ferro i Paul Mulheran. "Simulating Peptide Monolayer Formation: GnRH-I on Silica". International Journal of Molecular Sciences 22, nr 11 (24.05.2021): 5523. http://dx.doi.org/10.3390/ijms22115523.
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Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for both sexes. It was previously shown that inoculation with silica nanoparticles (SiNPs) coated with GnRH-I makes an effective anti-fertility vaccine due to how the peptide adsorbs to the nanoparticle and is presented to the immune system. In this paper, we develop and employ a protocol to simulate the development of a GnRH-I peptide adlayer by allowing peptides to diffuse and adsorb in a staged series of trajectories. The peptides start the simulation in an immobile state in solution above the model silica surface, and are then released sequentially. This facile approach allows the adlayer to develop in a natural manner and appears to be quite versatile. We find that the GnRH-I adlayer tends to be sparse, with electrostatics dominating the interactions. The peptides are collapsed to the surface and are seemingly free to interact with additional solutes, supporting the interpretations of the GNRH-I/SiNP vaccine system.
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Colvin, Michael E., Jennifer C. Sasaki i Ngoc L. Tran. "Chemical Factors in the Action of Phosphoramidic Mustard Alkylating Anticancer Drugs: Roles for Computational Chemistry". Current Pharmaceutical Design 5, nr 8 (sierpień 1999): 645–63. http://dx.doi.org/10.2174/1381612805666230110215849.
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The nitrogen mustard based DNA alkylating agents were the first effective anticancer agents and remain important drugs against many forms of cancer. More than fifty years of research on the nitrogen mustards has yielded a broad range of therapeutically useful compounds and a detailed knowledge of the biochemical mechanism of these drugs. Nevertheless, there is much ongoing research on the phos phosphoramidic and other nitrogen mustards to increase their potency and reduce their toxic and mutagenic side effects. To understand the existing nitrogen mustards, and to design the next generation of these drugs, more knowledge is needed about the effects of chemical modifications on their activation and selectivity. Because of the existing knowledge of these drugs, atomic-level chemical modeling can play an important role in the understanding of the phosphoramidic mustard compounds; however, it has not proved straight forward to directly relate the activity of these mustards with simple chemical properties such as bond lengths or atomic charges. Instead, quantum chemical simulations will be required to simulate the activation and alkylation reactions of these compounds, which will require the newest generation of quantum chemical and solvent modeling methods. Additionally, molecular dynamics simulations of the adducted DNA can provide data on the factors favoring crosslinking and its structural consequences. This review summarizes the extensive literature on the metabolism, activation, and action of the phosphoramidic mustards, with an emphasis on the roles that chemical modeling has and will play in the development of this important class of drugs.
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Taddei, Mario, Marco Garavelli, Saeed Amirjalayer, Irene Conti i Artur Nenov. "Modus Operandi of a Pedalo-Type Molecular Switch: Insight from Dynamics and Theoretical Spectroscopy". Molecules 28, nr 2 (13.01.2023): 816. http://dx.doi.org/10.3390/molecules28020816.
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Molecular switches which can be triggered by light to interconvert between two or more well-defined conformation differing in their chemical or physical properties are fundamental for the development of materials with on-demand functionalities. Recently, a novel molecular switch based on a the azodicarboxamide core has been reported. It exhibits a volume-conserving conformational change upon excitation, making it a promising candidate for embedding in confined environments. In order to rationally implement and efficiently utilize the azodicarboxamide molecular switch, detailed insight into the coordinates governing the excited-state dynamics is needed. Here, we report a detailed comparative picture of the molecular motion at the atomic level in the presence and absence of explicit solvent. Our hybrid quantum mechanics/molecular mechanics (QM/MM) excited state simulations reveal that, although the energy landscape is slightly modulated by the solvation, the light-induced motion is dominated by a bending-assisted pedalo-type motion independent of the solvation. To support the predicted mechanism, we simulate time-resolved IR spectroscopy from first principles, thereby resolving fingerprints of the light-induced switching process. Our calculated time-resolved data are in good agreement with previously reported measured spectra.
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Nolden, Markus, Agnes Scaramus, Rahim Nabbi, Frank Charlier i Klaus Fischer-Appelt. "Radiological characterization of a German pressurized water reactor based on a highly resolved method for activity analysis and dose rate calculation". Safety of Nuclear Waste Disposal 1 (10.11.2021): 25–26. http://dx.doi.org/10.5194/sand-1-25-2021.
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Abstract. The amendment to the atomic act in 2011 results to phase out nuclear energy in Germany until the end of 2022. Subsequently, the licensee of the nuclear power plant is responsible for decommissioning and dismantling. During operation, activation of structures near the core of the reactor occur which govern the amount of radioactive waste, the dose rate distribution and dismantling strategies. Thus, a detailed radiological characterization of in-core and out-core structures is required to optimize decommissioning processes regarding the quantification and minimization of radioactive waste, radiation protection and reducing radiation exposure. These objectives are achieved using an innovative and efficient method developed and applied at the Chair of Repository Safety (Lehrstuhl für Endlagersicherheit, ELS) RWTH Aachen University. Within the framework of the joint project „Development of a methodology for activity analysis and dose rate estimation“, funded by the Federal ministry of Education and Research, approaches the objective to develop a standardized and highly resolved method to calculate time-dependent activity of components and structures near the reactor core based on operating history of the nuclear power plant and neutron fluence distribution. The approach requires the development of a detailed model for Monte-Carlo simulations which provides the basis to neutron fluence, neutron spectra and radiation transport simulations. To calculate the nuclide specific 3-Dimensional (3D) activity distribution of the entire facility, a facility-dependent activation cross section library is produced which focuses on recent nuclear databases (ENDF/B-VIII.0). A highly resolved and space-dependent 3D activity distribution of the entire facility is obtained using a modular program package, developed at ELS, including the activation code ORIGEN2. The results are produced in the form of detailed 3D activity maps. The source terms are generated on the basis of the space-dependent 3D activity distribution using an additional module of the program package. The combination of recent nuclear databases focusing on ENDF/B-VII.1 and complemented by JEFF-3.3 ensures a comprehensive characterisation of source terms. Subsequently, source terms are prepared for 3D radiation transport simulation using the Monte-Carlo method and the computer code MCNP. The simulations are conducted separately for each individual component obtaining the partial contribution of all in-core and out-core structures as well as the dose rate distribution of the entire facility. Similar to the activity calculation, the simulation results are used to generate 3D gamma flux and dose rate maps using the graphic module of the whole program system. On the basis of the radiological characterisation and in view of a high-level radiation protection these maps allow the optimum planning and realisation of the decommissioning and dismantling process of the nuclear power plant.
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Sejdiu, Besian I., i D. Peter Tieleman. "ProLint: a web-based framework for the automated data analysis and visualization of lipid–protein interactions". Nucleic Acids Research 49, W1 (26.05.2021): W544—W550. http://dx.doi.org/10.1093/nar/gkab409.
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Abstract The functional activity of membrane proteins is carried out in a complex lipid environment. Increasingly, it is becoming clear that lipids are an important player in regulating or generally modulating their activity. A routinely used method to gain insight into this interplay between lipids and proteins are Molecular Dynamics (MD) simulations, since they allow us to study interactions at atomic or near-atomic detail as a function of time. A major bottleneck, however, is analyzing and visualizing lipid–protein interactions, which, in practice, is a time-demanding task. Here, we present ProLint (www.prolint.ca), a webserver that completely automates analysis of MD generated files and visualization of lipid–protein interactions. Analysis is modular allowing users to select their preferred method, and visualization is entirely interactive through custom built applications that enable a detailed qualitative and quantitative exploration of lipid–protein interactions. ProLint also includes a database of published MD results that have been processed through the ProLint workflow and can be visualized by anyone regardless of their level of experience with MD. The automated analysis, feature-rich visualization, database integration, and open-source distribution with an easy to install process, will allow ProLint to become a routine workflow in lipid–protein interaction studies.
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Tang, Ming, Xiaocong Wang, Neha S. Gandhi, Bethany Lachele Foley, Kevin Burrage, Robert J. Woods i YuanTong Gu. "Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study". Glycobiology 30, nr 10 (19.03.2020): 830–43. http://dx.doi.org/10.1093/glycob/cwaa026.
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Abstract Collagen undergoes many types of post-translational modifications (PTMs), including intracellular modifications and extracellular modifications. Among these PTMs, glycosylation of hydroxylysine (Hyl) is the most complicated. Experimental studies demonstrated that this PTM ceases once the collagen triple helix is formed and that Hyl-O-glycosylation modulates collagen fibrillogenesis. However, the underlying atomic-level mechanisms of these phenomena remain unclear. In this study, we first adapted the force field parameters for O-linkages between Hyl and carbohydrates and then investigated the influence of Hyl-O-glycosylation on the structure of type I collagen molecule, by performing comprehensive molecular dynamic simulations in explicit solvent of collagen molecule segment with and without the glycosylation of Hyl. Data analysis demonstrated that (i) collagen triple helices remain in a triple-helical structure upon glycosylation of Hyl; (ii) glycosylation of Hyl modulates the peptide backbone conformation and their solvation environment in the vicinity and (iii) the attached sugars are arranged such that their hydrophilic faces are well exposed to the solvent, while their hydrophobic faces point towards the hydrophobic portions of collagen. The adapted force field parameters for O-linkages between Hyl and carbohydrates will aid future computational studies on proteins with Hyl-O-glycosylation. In addition, this work, for the first time, presents the detailed effect of Hyl-O-glycosylation on the structure of human type I collagen at the atomic level, which may provide insights into the design and manufacture of collagenous biomaterials and the development of biomedical therapies for collagen-related diseases.
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Keten, Sinan, i Markus J. Buehler. "Nanostructure and molecular mechanics of spider dragline silk protein assemblies". Journal of The Royal Society Interface 7, nr 53 (2.06.2010): 1709–21. http://dx.doi.org/10.1098/rsif.2010.0149.
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Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3 1 -helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.
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Arnittali, Maria, Anastassia N. Rissanou, Maria Amprazi, Michael Kokkinidis i Vagelis Harmandaris. "Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments". International Journal of Molecular Sciences 22, nr 11 (31.05.2021): 5931. http://dx.doi.org/10.3390/ijms22115931.
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In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.
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Keskin i Alsoy Altinkaya. "A Review on Computational Modeling Tools for MOF-Based Mixed Matrix Membranes". Computation 7, nr 3 (18.07.2019): 36. http://dx.doi.org/10.3390/computation7030036.
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Computational modeling of membrane materials is a rapidly growing field to investigate the properties of membrane materials beyond the limits of experimental techniques and to complement the experimental membrane studies by providing insights at the atomic-level. In this study, we first reviewed the fundamental approaches employed to describe the gas permeability/selectivity trade-off of polymer membranes and then addressed the great promise of mixed matrix membranes (MMMs) to overcome this trade-off. We then reviewed the current approaches for predicting the gas permeation through MMMs and specifically focused on MMMs composed of metal organic frameworks (MOFs). Computational tools such as atomically-detailed molecular simulations that can predict the gas separation performances of MOF-based MMMs prior to experimental investigation have been reviewed and the new computational methods that can provide information about the compatibility between the MOF and the polymer of the MMM have been discussed. We finally addressed the opportunities and challenges of using computational studies to analyze the barriers that must be overcome to advance the application of MOF-based membranes.
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F. Garrido, Pablo, Martín Calvelo, Rebeca Garcia-Fandiño i Ángel Piñeiro. "Rings, Hexagons, Petals, and Dipolar Moment Sink-Sources: The Fanciful Behavior of Water around Cyclodextrin Complexes". Biomolecules 10, nr 3 (10.03.2020): 431. http://dx.doi.org/10.3390/biom10030431.
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The basket-like geometry of cyclodextrins (CDs), with a cavity able to host hydrophobic groups, makes these molecules well suited for a large number of fundamental and industrial applications. Most of the established CD-based applications rely on trial and error studies, often ignoring key information at the atomic level that could be employed to design new products and to optimize their use. Computational simulations are well suited to fill this gap, especially in the case of CD systems due to their low number of degrees of freedom compared with typical macromolecular systems. Thus, the design and validation of solid and efficient methods to simulate and analyze CD-based systems is key to contribute to this field. The behavior of supramolecular complexes critically depends on the media where they are embedded, so the detailed characterization of the solvent is required to fully understand these systems. In the present work, we use the inclusion complex formed by two α-CDs and one sodium dodecyl sulfate molecule to test eight different parameterizations of the GROMOS and AMBER force fields, including several methods aimed to increase the conformational sampling in computational molecular dynamics simulation trajectories. The system proved to be extremely sensitive to the employed force field, as well as to the presence of a water/air interface. In agreement with previous experiments and in contrast to the results obtained with AMBER, the analysis of the simulations using GROMOS showed a quick adsorption of the complex to the interface as well as an extremely exotic behavior of the water molecules surrounding the structure both in the bulk aqueous solution and at the water surface. The chirality of the CD molecule seems to play an important role in this behavior. All together, these results are expected to be useful to better understand the behavior of CD-based supramolecular complexes such as adsorption or aggregation driving forces, as well as to introduce new methods able to speed up general MD simulations.
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Wang, Bin, Jinyang Xu, Chengliang Duan, Jinpeng Li, Jinsong Zeng, Jun Xu, Wenhua Gao i Kefu Chen. "Regulatory Mechanism of Opposite Charges on Chiral Self-Assembly of Cellulose Nanocrystals". Molecules 28, nr 4 (15.02.2023): 1857. http://dx.doi.org/10.3390/molecules28041857.
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The charge plays an important role in cellulose nanocrystal (CNC) self-assembly to form liquid crystal structures, which has rarely been systematically explored. In this work, a novel technique combining atomic force microscopy force and atomistic molecular dynamics simulations was addressed for the first time to systematically investigate the differences in the CNC self-assembly caused by external positive and negative charges at the microscopic level, wherein sodium polyacrylate (PAAS) and chitosan oligosaccharides (COS) were used as external positive and negative charge additives, respectively. The results show that although the two additives both make the color of CNC films shift blue and eventually disappear, their regulatory mechanisms are, respectively, related to the extrusion of CNC particles by PAAS and the reduction in CNC surface charge by COS. The two effects both decreased the spacing between CNC particles and further increased the cross angle of CNC stacking arrangement, which finally led to the color variations. Moreover, the disappearance of color was proved to be due to the kinetic arrest of CNC suspensions before forming chiral nematic structure with the addition of PAAS and COS. This work provides an updated theoretical basis for the detailed disclosure of the CNC self-assembly mechanism.
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Filipovic, N., M. Kojic i A. Tsuda. "Modelling thrombosis using dissipative particle dynamics method". Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 366, nr 1879 (lipiec 2008): 3265–79. http://dx.doi.org/10.1098/rsta.2008.0097.
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Aim . Arterial occlusion is a leading cause of cardiovascular disease. The main mechanism causing vessel occlusion is thrombus formation, which may be initiated by the activation of platelets. The focus of this study is on the mechanical aspects of platelet-mediated thrombosis which includes the motion, collision, adhesion and aggregation of activated platelets in the blood. A review of the existing continuum-based models is given. A mechanical model of platelet accumulation onto the vessel wall is developed using the dissipative particle dynamics (DPD) method in which the blood (i.e. colloidal-composed medium) is treated as a group of mesoscale particles interacting through conservative, dissipative, attractive and random forces. Methods . Colloidal fluid components (plasma and platelets) are discretized by mesoscopic (micrometre-size) particles that move according to Newton's law. The size of each mesoscopic particle is small enough to allow tracking of each constituent of the colloidal fluid, but significantly larger than the size of atoms such that, in contrast to the molecular dynamics approach, detailed atomic level analysis is not required. Results . To test this model, we simulated the deposition of platelets onto the wall of an expanded tube and compared our computed results with the experimental data of Karino et al . ( Miscrovasc. Res. 17 , 238–269, 1977). By matching our simulations to the experimental results, the platelet aggregation/adhesion binding force (characterized by an effective spring constant) was determined and found to be within a physiologically reasonable range. Conclusion . Our results suggest that the DPD method offers a promising new approach to the modelling of platelet-mediated thrombosis. The DPD model includes interaction forces between platelets both when they are in the resting state (non-activated) and when they are activated, and therefore it can be extended to the analysis of kinetics of binding and other phenomena relevant to thrombosis.
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Buchete, Nicolae-Viorel. "Unlocking the Atomic-Level Details of Amyloid Fibril Growth through Advanced Biomolecular Simulations". Biophysical Journal 103, nr 7 (październik 2012): 1411–13. http://dx.doi.org/10.1016/j.bpj.2012.08.052.
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Seng, De Wen. "Simulation Techniques in the Research of Structure and Performance of Nanosized Materials". Applied Mechanics and Materials 189 (lipiec 2012): 457–60. http://dx.doi.org/10.4028/www.scientific.net/amm.189.457.
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Due to their unique structure and performance, great attention to nanosized materials has increased in past years. Advanced information and simulation technologies provide an understanding of nanosized materials at the atomic scale with an unprecedented level of detail and accuracy and make nanosized materials design and performance prediction possible. Computer simulation theory and methods in the research of nanosized materials are summarized. The progress in computer simulation of nanosized materials, especially their mircostructure, mechanical, thermodynamic, electric, magnetic properties, is discussed in detailed. Some basic problems in structure and performance research of nanosized materials are also elaborated.
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Dehghani, Ali, Ghasem Bahlakeh, Bahram Ramezanzadeh i Mohammad Ramezanzadeh. "Applying detailed molecular/atomic level simulation studies and electrochemical explorations of the green inhibiting molecules adsorption at the interface of the acid solution-steel substrate". Journal of Molecular Liquids 299 (luty 2020): 112220. http://dx.doi.org/10.1016/j.molliq.2019.112220.
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Li, Zeng Qiang, Jun Wang i Qi Wu. "Molecular Dynamics Simulation of the Ablation Process in Ultrashort Pulsed Laser Machining of Polycrystalline Diamond". Advanced Materials Research 500 (kwiecień 2012): 351–56. http://dx.doi.org/10.4028/www.scientific.net/amr.500.351.
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The mechanism of ultrashort pulsed laser ablation of polycrystalline diamond (PCD) is investigated using molecular dynamics simulation. The simulation model provides a detailed atomic-level description of the laser energy deposition to PCD specimens and is verified by an experiment using 300 fs laser irradiation of a PCD sample. It is found that grain boundaries play an important role in the laser ablation. Melting starts from the grain boundaries since the atoms in these regions have higher potential energy and are melted more easily than the perfect diamond. Non-homogeneous melting then takes place at these places, and the inner crystal grains melt more easily in liquid surroundings presented by the melting grain boundaries. Moreover, the interplay of the two processes, photomechanical spallation and evaporation, are found to account for material removal in ultrashort pulsed laser ablation of PCD.
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Duong, Vy T., Elizabeth M. Diessner, Gianmarc Grazioli, Rachel W. Martin i Carter T. Butts. "Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures". Biomolecules 11, nr 12 (30.11.2021): 1788. http://dx.doi.org/10.3390/biom11121788.
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Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly compressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs. This “neural upscaling” procedure exploits the constraints implied by PSNs on possible configurations, as well as differences in the likelihood of observing different configurations with the same PSN. Using a 1 μs atomistic molecular dynamics trajectory of Aβ1–40, we show that neural upscaling is able to effectively recapitulate detailed structural information for intrinsically disordered proteins, being particularly successful in recovering features such as transient secondary structure. These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates from PSNs.
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Rodríguez, R., R. Florido, J. M. Gil, J. G. Rubiano, P. Martel i E. Mínguez. "RAPCAL code: A flexible package to compute radiative properties for optically thin and thick low and high-Z plasmas in a wide range of density and temperature". Laser and Particle Beams 26, nr 3 (22.07.2008): 433–48. http://dx.doi.org/10.1017/s026303460800044x.
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AbstractRadiative properties are fundamental for plasma diagnostics and hydro-simulations. For this reason, there is a high interest in their determination and they are a current topic of investigation both in astrophysics and inertial fusion confinement research. In this work a flexible computation package for calculating radiative properties for low and high Z optically thin and thick plasmas, both under local thermodynamic equilibrium and non-local thermodynamic equilibrium conditions, named RAPCAL is presented. This code has been developed with the aim of providing accurate radiative properties for low and medium Z plasmas within the context of detailed level accounting approach and for heavy elements under the detailed configuration accounting approach. In order to show the capabilities of the code, there are presented calculations of some radiative properties for carbon, aluminum, krypton and xenon plasmas under local thermodynamic and non-local thermodynamic equilibrium conditions.
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Liu, Shuhui, i Yang Xu. "MD Investigation on the Interaction between Carbamazepine and Two CYP Isoforms, CYP3A4 and CYP3A5". International Journal of Molecular Sciences 24, nr 3 (22.01.2023): 2188. http://dx.doi.org/10.3390/ijms24032188.
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Carbamazepine (CBZ), a commonly prescribed antiepileptic drug, in human liver, is mainly metabolized by two isoforms of cytochrome P450 (CYP), CYP3A4 and CYP3A5. Therefore, the binding of CBZ with these two enzymes plays crucial role in the biotransformation of the drug into its active metabolite. In the present work, classical molecular dynamics (MD) simulation was used to investigate the detailed interaction mechanism between CBZ and these two CYP isoforms at the atomic level. The results revealed that although CBZ can bind with the two proteins, all kinds of the interactions, including hydrogen bonds, salt bridges, hydrophobic interaction, and π-π interaction, are isoform specific. The specificity directly leads to a binding environment difference at the active sites of the two isoforms, as represented by the electrostatic surface potential maps, which further results in the varied dynamic behavior of CBZ in the two isoforms. Our research will help to deepen the understanding of the physiological functions of CYP isoforms and opens the door for the rational design and development of isoform-specific inhibitors.
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Tsai, Ping Chi, i Yeau Ren Jeng. "A Review on Mechanical Properties of Deformation Mechanism of Tubular Nanostructures: Molecular Dynamics Simulations". Solid State Phenomena 329 (25.03.2022): 79–86. http://dx.doi.org/10.4028/p-4mm443.
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A molecular dynamic (MD) simulation, which is used for estimating mechanical properties of both microscopic and mesoscopic materials during loading/unloading processes. Understanding the deformation mechanisms of material's internal structure, shape and volume is a key step to enhance its strength and rigidity. Novel nanostructures, nanoparticles and nanocomposites, more efficient, selective, and environmental friendly can be developed and suggested. At the moment, few experimental methods can characterize molecular mechanisms due to their time-consuming and cost-intensive. Therefore, MD simulation allows to gain understanding in structure-to-function relationships involved in the low-dimensional materials. Specifically, MD simulation can be performed on the time scale of nanoseconds, and in three dimensions, it is thus sufficient for the study of the mechanical behaviors and deformation mechanisms at a molecular level. This work reviews the progress in MD simulation of the mechanical properties and structure deformations for various tubular nanomaterials including silicon, carbon and III-V compound nanotubes (NTs), respectively. In particular, we have a detailed description and analysis of the impacts of environmental and structural factors on material strength for the present nanostructures. It is hopeful that this review can provide certain reference for the follow-up research.
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Villalón, Ariel, Carlos Muñoz, Javier Muñoz i Marco Rivera. "A Detailed dSPACE-Based Implementation of Modulated Model Predictive Control for AC Microgrids". Sensors 23, nr 14 (11.07.2023): 6288. http://dx.doi.org/10.3390/s23146288.
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Microgrids represent a promising energy technology, because of the inclusion in them of clean and smart energy technologies. They also represent research challenges, including controllability, stability, and implementation. This article presents a dSPACE-control-platform-based implementation of a fixed-switching-frequency modulated model predictive control (M2PC) strategy, as an inner controller of a two-level, three-phase voltage source inverter (VSI) working in an islanded AC microgrid. The developed controller is hierarchical, as it includes a primary controller to share the load equally with the other power converter with its own local modulated predictive-based controller. All details of the implementation are given for establishing the dSPACE-based implementation of the control on a dSPACE ds1103 control platform, using MATLAB/Simulink for the controller design, I/O implementation and configuration with the embedded dSPACE’s real-time interface in Simulink, and then using the ControlDesk software for monitoring and testing of the real plant. The latter consists of the VSI operating with LCL filters, and sharing an RL load with a paralleled VSI with exactly the same controller. Finally, the obtained experimental waveforms are shown, with our respective conclusions representing this work, which is a very valuable tool for helping microgrid researchers implement dSPACE-based real-time simulations.
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Liu, Huicong, Jiangjun Geng, Qifeng Zhu, Lue Zhang, Fengxia Wang, Tao Chen i Lining Sun. "Flexible Ultrasonic Transducer Array with Bulk PZT for Adjuvant Treatment of Bone Injury". Sensors 20, nr 1 (22.12.2019): 86. http://dx.doi.org/10.3390/s20010086.
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Flexible electronic devices are developing rapidly, especially in medical applications. This paper reports an arrayed flexible piezoelectric micromachined ultrasonic transducer (FPMUT) with a sandwich structure for adjuvant treatment of bone injury. To make the device conformable and stretchable for attaching to the skin surface, the flexible substrate of polydimethylsiloxane (PDMS) was combined with the flexible metal line interconnection between the bulk lead zirconate titanate (PZT) arrays. Simulations and experiments were carried out to verify the resonant frequency and tensile property of the reported FPMUT device. The device had a resonant frequency of 321.15 KHz and a maximum sound pressure level (SPL) of 180.19 dB at the distance of 5 cm in water. In addition, detailed experiments were carried out to test its acoustic performance with different pork tissues, and the results indicated good ultrasound penetration. These findings confirm that the FPMUT shows unique advantages for adjuvant treatment of bone injury.
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Geiger, Martin, Christian Wegner, Winfried Mayer i Christian Waldschmidt. "A Wideband Dielectric Waveguide-Based 160-GHz Radar Target Generator". Sensors 19, nr 12 (22.06.2019): 2801. http://dx.doi.org/10.3390/s19122801.
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The increasing number of radar sensors in commercial and industrial products leads to a growing demand for system functionality tests. Conventional test procedures require expensive anechoic chambers to provide a defined test environment for radar sensors. In this paper, a compact and low cost dielectric waveguide radar target generator for level probing radars is presented. The radar target generator principle is based on a long dielectric waveguide as a one-target scenery. By manipulating the field distribution of the waveguide, a specific reflection of a radar target is generated. Two realistic scenarios for a tank level probing radar are investigated and suitable targets are designed with full wave simulations. Target distances from 13 cm to at least 9 m are realized with an extruded dielectric waveguide with dielectric losses of 2 dB/m at 160 GHz. Low loss (0.5 dB) and low reflection holders are used to fix the waveguide. Due to the dispersion of the dielectric waveguide, a detailed analysis of its impact on frequency-modulated continuous wave (FMCW) radars is given and compared to free-space propagation. The functionality of the radar target generator is verified with a 160-GHz FMCW radar prototype.
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Muhseen, Ziyad Tariq, Salim Kadhim, Yahiya Ibrahim Yahiya, Eid A. Alatawi, Faris F. Aba Alkhayl i Ahmad Almatroudi. "Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches". Biology 10, nr 12 (10.12.2021): 1310. http://dx.doi.org/10.3390/biology10121310.
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Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein’s receptor-binding domain (RBD) has been reported in Europe. In order to design therapeutic strategies suitable for B.1.620, further studies are required. A detailed investigation of the structural features and variations caused by these substitutions, that is, a molecular level investigation, is essential to uncover the role of these changes. To determine whether and how the binding affinity of ACE2–RBD is affected, we used protein–protein docking and all-atom simulation approaches. Our analysis revealed that B.1.620 binds more strongly than the wild type and alters the hydrogen bonding network. The docking score for the wild type was reported to be −122.6 +/− 0.7 kcal/mol, while for B.1.620, the docking score was −124.9 +/− 3.8 kcal/mol. A comparative binding investigation showed that the wild-type complex has 11 hydrogen bonds and one salt bridge, while the B.1.620 complex has 14 hydrogen bonds and one salt bridge, among which most of the interactions are preserved between the wild type and B.1.620. A dynamic analysis of the two complexes revealed stable dynamics, which corroborated the global stability trend, compactness, and flexibility of the three essential loops, providing a better conformational optimization opportunity and binding. Furthermore, binding free energy revealed that the wild type had a total binding energy of −51.14 kcal/mol, while for B.1.628, the total binding energy was −68.25 kcal/mol. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity. In conclusion, the current study presents distinguishing features of B.1.620, which can be used to design structure-based drugs against the B.1.620 variant.
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Parvini, Cameron H., M. A. S. R. Saadi i Santiago D. Solares. "Extracting viscoelastic material parameters using an atomic force microscope and static force spectroscopy". Beilstein Journal of Nanotechnology 11 (16.06.2020): 922–37. http://dx.doi.org/10.3762/bjnano.11.77.
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Atomic force microscopy (AFM) techniques have provided and continue to provide increasingly important insights into surface morphology, mechanics, and other critical material characteristics at the nanoscale. One attractive implementation involves extracting meaningful material properties, which demands physically accurate models specifically designed for AFM experimentation and simulation. The AFM community has pursued the precise quantification and extraction of rate-dependent material properties, in particular, for a significant period of time, attempting to describe the standard viscoelastic response of materials. AFM static force spectroscopy (SFS) is one approach commonly used in pursuit of this goal. It is capable of acquiring rich temporal insight into the behavior of a sample. During AFM-SFS experiments the cantilever base approaches samples with a nearly constant velocity, which is manipulated to investigate different timescales of the mechanical response. This manuscript seeks to build upon our previous work and presents an approach to extracting useful linear viscoelastic information from AFM-SFS experiments. In addition, the basis for selecting and restricting the model parameters for fitting is discussed from the perspective of applying this technique on a practical level. This work begins with a guided discussion that develops a fit function from fundamental laws, continues with conditioning a raw SFS experimental dataset, and concludes with the fit and prediction of viscoelastic response parameters such as storage modulus, loss modulus, loss angle, and compliance. These steps constitute a complete guide to leveraging AFM-SFS data to estimate key material parameters, with a series of detailed insights into both the methodology and supporting analytical choices.
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Lin, Yiqi, Mengxue Zhang, Patricio S. La Rosa, James D. Wilson i Arye Nehorai. "Electro-Mechanical Ionic Channel Modeling for Uterine Contractions and Oxytocin Effect during Pregnancy". Sensors 19, nr 22 (9.11.2019): 4898. http://dx.doi.org/10.3390/s19224898.
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Uterine contractions during normal pregnancy and preterm birth are an important physiological activity. Although the cause of preterm labor is usually unknown, preterm birth creates very serious health concerns in many cases. Therefore, understanding normal birth and predicting preterm birth can help both newborn babies and their families. In our previous work, we developed a multiscale dynamic electrophysiology model of uterine contractions. In this paper, we mainly focus on the cellular level and use electromyography (EMG) and cell force generation methods to construct a new ionic channel model and a corresponding mechanical force model. Specifically, the ionic channel model takes into consideration the knowledge of individual ionic channels, which include the electrochemical and bioelectrical characteristics of individual myocytes. We develop a new sodium channel and a new potassium channel based on the experimental data from the human myometrium and the average correlations are 0.9946 and 0.9945, respectively. The model is able to generate the single spike, plateau type and bursting type of action potentials. Moreover, we incorporate the effect of oxytocin on changing the properties of the L-type and T-type calcium channels and further influencing the output action potentials. In addition, we develop a mechanical force model based on the new ionic channel model that describes the detailed ionic dynamics. Our model produces cellular mechanical force that propagates to the tissue level. We illustrate the relationship between the cellular mechanical force and the intracellular ionic dynamics and discuss the relationship between the application of oxytocin and the output mechanical force. We also propose a simplified version of the model to enable large scale simulations using sensitivity analysis method. Our results show that the model is able to reproduce the bioelectrical and electromechanical characteristics of uterine contractions during pregnancy.
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González-López, Jorge, Jeremy K. Cockcroft, Ángeles Fernández-González, Amalia Jimenez i Ricardo Grau-Crespo. "Crystal structure of cobalt hydroxide carbonate Co2CO3(OH)2: density functional theory and X-ray diffraction investigation". Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 73, nr 5 (15.09.2017): 868–73. http://dx.doi.org/10.1107/s2052520617007983.
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The cobalt carbonate hydroxide Co2CO3(OH)2is a technologically important solid which is used as a precursor for the synthesis of cobalt oxides in a wide range of applications. It also has relevance as a potential immobilizer of the toxic element cobalt in the natural environment, but its detailed crystal structure is so far unknown. The structure of Co2CO3(OH)2has now been investigated using density functional theory (DFT) simulations and powder X-ray diffraction (PXRD) measurements on samples synthesizedviadeposition from aqueous solution. Two possible monoclinic phases are considered, with closely related but symmetrically different crystal structures, based on those of the minerals malachite [Cu2CO3(OH)2] and rosasite [Cu1.5Zn0.5CO3(OH)2], as well as an orthorhombic phase that can be seen as a common parent structure for the two monoclinic phases, and a triclinic phase with the structure of the mineral kolwezite [Cu1.34Co0.66CO3(OH)2]. The DFT simulations predict that the rosasite-like and malachite-like phases are two different local minima of the potential energy landscape for Co2CO3(OH)2and are practically degenerate in energy, while the orthorhombic and triclinic structures are unstable and experience barrierless transformations to the malachite phase upon relaxation. The best fit to the PXRD data is obtained using a rosasite model [monoclinic with space groupP1121/nand cell parametersa= 3.1408 (4) Å,b= 12.2914 (17) Å,c= 9.3311 (16) Å and γ = 82.299 (16)°]. However, some features of the PXRD pattern are still not well accounted for by this refinement and the residual parameters are relatively poor. The relationship between the rosasite and malachite phases of Co2CO3(OH)2is discussed and it is shown that they can be seen as polytypes. Based on the similar calculated stabilities of these two polytypes, it is speculated that some level of stacking disorder could account for the poor fit of the PXRD data. The possibility that Co2CO3(OH)2could crystallize, under different growth conditions, as either rosasite or malachite, or even as a stacking-disordered phase intermediate between the two, requires further investigation.
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Zvorykin, V. D., N. V. Didenko, A. A. Ionin, I. V. Kholin, A. V. Konyashchenko, O. N. Krokhin, A. O. Levchenko i in. "GARPUN-MTW: A hybrid Ti:Sapphire/KrF laser facility for simultaneous amplification of subpicosecond/nanosecond pulses relevant to fast-ignition ICF concept". Laser and Particle Beams 25, nr 3 (20.07.2007): 435–51. http://dx.doi.org/10.1017/s0263034607000559.
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The first stage of the petawatt excimer laser project started at the P.N. Lebedev Physical Institute, implements a development of multiterawatt hybrid GARPUN-MTW laser facility for generation of ultra-high intensity subpicosecond ultraviolet (UV) laser pulses. Under this project, a multi-stage e-beam-pumped 100-J, 100-ns GARPUN KrF laser was upgraded with a femtosecond Ti:Sapphire front-end, to produce combined subpicosecond/nanosecond laser pulses with variable time delay. Attractive possibility to amplify simultaneously short and long pulses in the same large-scale KrF amplifiers is analyzed with regard to the fast-ignition, inertial confinement fusion problem. Detailed description of hybrid laser system is presented with synchronized KrF and Ti:Sapphire master oscillators. Based on gain and absorption measurements at GARPUN amplifier and numerical simulations with a quasi-stationary code, we are predicting that 1.6 J can be obtained in a short pulse at hybrid GARPUN-MTW Ti:Sapphire/KrF laser facility, combined with several tens of joules in nanosecond pulse. Amplified spontaneous emission, which is responsible for the pre-pulse formation on a target, was also investigated: its acceptable level can be provided by properly choosing staged gain or loading the amplifiers by quasi-steady laser radiation. Fluorescence and transient absorption spectra of Ar/Kr/F2 mixtures conventionally used in KrF amplifiers were recorded to find out the possibility for femtosecond pulse amplification at the broadband Kr2F (42Γ → 1,2 2Γ) transition, which benefits in 100 times higher saturation energy density than for KrF (B → X) transition.
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Kumar, M. Santhosh, i Ganesh Reddy Karri. "EEOA: Cost and Energy Efficient Task Scheduling in a Cloud-Fog Framework". Sensors 23, nr 5 (22.02.2023): 2445. http://dx.doi.org/10.3390/s23052445.
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Cloud-fog computing is a wide range of service environments created to provide quick, flexible services to customers, and the phenomenal growth of the Internet of Things (IoT) has produced an immense amount of data on a daily basis. To complete tasks and meet service-level agreement (SLA) commitments, the provider assigns appropriate resources and employs scheduling techniques to efficiently manage the execution of received IoT tasks in fog or cloud systems. The effectiveness of cloud services is directly impacted by some other important criteria, such as energy usage and cost, which are not taken into account by many of the existing methodologies. To resolve the aforementioned problems, an effective scheduling algorithm is required to schedule the heterogeneous workload and enhance the quality of service (QoS). Therefore, a nature-inspired multi-objective task scheduling algorithm called the electric earthworm optimization algorithm (EEOA) is proposed in this paper for IoT requests in a cloud-fog framework. This method was created using the combination of the earthworm optimization algorithm (EOA) and the electric fish optimization algorithm (EFO) to improve EFO’s potential to be exploited while looking for the best solution to the problem at hand. Concerning execution time, cost, makespan, and energy consumption, the suggested scheduling technique’s performance was assessed using significant instances of real-world workloads such as CEA-CURIE and HPC2N. Based on simulation results, our proposed approach improves efficiency by 89%, energy consumption by 94%, and total cost by 87% over existing algorithms for the scenarios considered using different benchmarks. Detailed simulations demonstrate that the suggested approach provides a superior scheduling scheme with better results than the existing scheduling techniques.
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Zubair, Muhammad, i Robert Dickinson. "Calculating the Effect of Ribs on the Focus Quality of a Therapeutic Spherical Random Phased Array". Sensors 21, nr 4 (9.02.2021): 1211. http://dx.doi.org/10.3390/s21041211.
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The overlaying rib cage is a major hindrance in treating liver tumors with high intensity focused ultrasound (HIFU). The problems caused are overheating of the ribs due to its high ultrasonic absorption capability and degradation of the ultrasound intensity distribution in the target plane. In this work, a correction method based on binarized apodization and geometric ray tracing approach was employed to avoid heating the ribs. A detailed calculation of the intensity distribution in the focus plane was undertaken to quantify and avoid the effect on HIFU beam generated by a 1-MHz 256-element random phased array after the ultrasonic beam passes through the rib cage. Focusing through the ribs was simulated for 18 different idealized ribs-array configurations and 10 anatomically correct ribs-array configurations, to show the effect of width of the ribs, intercostal spacing and the relative position of ribs and array on the quality of focus, and to identify the positions that are more effective for HIFU applications in the presence of ribs. Acoustic simulations showed that for a single focus without beam steering and for the same total acoustic power, the peak intensity at the target varies from a minimum of 211 W/cm2 to a maximum of 293 W/cm2 for a nominal acoustic input power of 15 W, whereas the side lobe level varies from 0.07 Ipeak to 0.28 Ipeak and the separation between the main lobe and side lobes varies from 2.5 mm to 6.3 mm, depending on the relative positioning of the array and ribs and the beam alignment. An increase in the side lobe level was observed by increasing the distance between the array and the ribs. The parameters of focus splitting and the deterioration of focus quality caused by the ultrasonic propagation through the ribs were quantified in various possible different clinical scenarios. In addition to idealized rib topology, anatomical realistic ribs were used to determine the focus quality of the HIFU beam when the beam is steered both in axial and transverse directions and when the transducer is positioned at different depths from the rib cage.
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Yurtsever, Ayhan, Pei-Xi Wang, Fabio Priante, Ygor Morais Jaques, Keisuke Miyazawa, Mark J. MacLachlan, Adam S. Foster i Takeshi Fukuma. "Molecular insights on the crystalline cellulose-water interfaces via three-dimensional atomic force microscopy". Science Advances 8, nr 41 (14.10.2022). http://dx.doi.org/10.1126/sciadv.abq0160.
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Cellulose, a renewable structural biopolymer, is ubiquitous in nature and is the basic reinforcement component of the natural hierarchical structures of living plants, bacteria, and tunicates. However, a detailed picture of the crystalline cellulose surface at the molecular level is still unavailable. Here, using atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we revealed the molecular details of the cellulose chain arrangements on the surfaces of individual cellulose nanocrystals (CNCs) in water. Furthermore, we visualized the three-dimensional (3D) local arrangement of water molecules near the CNC surface using 3D AFM. AFM experiments and MD simulations showed anisotropic water structuring, as determined by the surface topologies and exposed chemical moieties. These findings provide important insights into our understanding of the interfacial interactions between CNCs and water at the molecular level. This may allow the establishment of the structure-property relationship of CNCs extracted from various biomass sources.
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Coopmans, Tim, Robert Knegjens, Axel Dahlberg, David Maier, Loek Nijsten, Julio de Oliveira Filho, Martijn Papendrecht i in. "NetSquid, a NETwork Simulator for QUantum Information using Discrete events". Communications Physics 4, nr 1 (16.07.2021). http://dx.doi.org/10.1038/s42005-021-00647-8.
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AbstractIn order to bring quantum networks into the real world, we would like to determine the requirements of quantum network protocols including the underlying quantum hardware. Because detailed architecture proposals are generally too complex for mathematical analysis, it is natural to employ numerical simulation. Here we introduce NetSquid, the NETwork Simulator for QUantum Information using Discrete events, a discrete-event based platform for simulating all aspects of quantum networks and modular quantum computing systems, ranging from the physical layer and its control plane up to the application level. We study several use cases to showcase NetSquid’s power, including detailed physical layer simulations of repeater chains based on nitrogen vacancy centres in diamond as well as atomic ensembles. We also study the control plane of a quantum switch beyond its analytically known regime, and showcase NetSquid’s ability to investigate large networks by simulating entanglement distribution over a chain of up to one thousand nodes.
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Bogetti, Xiaowei, Anthony Bogetti, Joshua Casto, Gordon Rule, Lillian Chong i Sunil Saxena. "Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by EPR and simulation". Protein Science, 26.08.2023. http://dx.doi.org/10.1002/pro.4770.
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AbstractThe catalytic activity of human glutathione S‐transferase A1‐1 (hGSTA1‐1), a homodimeric detoxification enzyme, is dependent on the conformational dynamics of a key C‐terminal helix α9 in each monomer. However, the structural details of how the two monomers interact upon binding of substrates is not well understood and the structure of the ligand‐free state of the hGSTA1‐1 homodimer has not been resolved. Here, we used a combination of EPR distance measurements and weighted ensemble simulations to characterize the conformational ensemble of the ligand‐free state at the atomic level. EPR measurements reveal a broad distance distribution between a pair of Cu(II) labels in the ligand‐free state that gradually shifts and narrows as a function of increasing ligand concentration. These shifts suggest changes in the relative positioning of the two α9 helices upon ligand binding. Weighted ensemble simulations generated unbiased pathways for the seconds‐timescale transition between alternate states of the enzyme, leading to the generation of atomically detailed structures of the ligand‐free state. Notably, the simulations provide direct observations of negative cooperativity between the monomers of hGSTA1‐1, which involve the mutually exclusive docking of α9 in each monomer as a lid over the active site. We identify key interactions between residues that lead to this negative cooperativity. Negative cooperativity may be essential for interaction of hGSTA1‐1 with a wide variety of toxic substrates and their subsequent neutralization. More broadly, this work demonstrates the power of integrating EPR distances with weighted ensemble rare‐events sampling strategy to gain mechanistic information on protein function at the atomic level.This article is protected by copyright. All rights reserved.
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Pan, Dongqing, Dongsheng Guan, Tien-Chien Jen i Chris Yuan. "Atomic Layer Deposition Process Modeling and Experimental Investigation for Sustainable Manufacturing of Nano Thin Films". Journal of Manufacturing Science and Engineering 138, nr 10 (13.09.2016). http://dx.doi.org/10.1115/1.4034475.
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This paper studies the adverse environmental impacts of atomic layer deposition (ALD) nanotechnology on manufacturing of Al2O3 nanoscale thin films. Numerical simulations with detailed ALD surface reaction mechanism developed based on density functional theory (DFT) and atomic-level calculations are performed to investigate the effects of four process parameters including process temperature, pulse time, purge time, and carrier gas flow rate on ALD film deposition rate, process emissions, and wastes. Full-cycle ALD simulations reveal that the depositions of nano thin films in ALD are in essence the chemisorption of the gaseous species and the conversion of surface species. Methane emissions are positively proportional to the film deposition process. The studies show that process temperature fundamentally affects the ALD chemical process by changing the energy states of the surface species. Pulse time is directly related to the precursor dosage. Purge time influences the ALD process by changing the gas–surface interaction time, and a higher carrier gas flow rate can alter the ALD flow field by accelerating the convective heat and mass transfer in ALD process.
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LI, Yuhai, Qingshun Bai, Yuheng Guan, Hao Liu, Peng Zhang, Buerlike Batelibieke, Rongqi Shen i in. "The mechanism study of low-pressure air plasma cleaning on large-aperture optical surface unraveled by experiment and reactive molecular dynamics simulation". Plasma Science and Technology, 22.04.2022. http://dx.doi.org/10.1088/2058-6272/ac69b6.
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Abstract The low-pressure air plasma cleaning is an effective method for removing the organic contaminants on large-aperture optical components in-situ in the inertial confinement fusion facility. Chemical reactions play a significant role in plasma cleaning, which is a complex process involving abundant bonds cleavage and species generation. In this work, experiments and reactive molecular dynamics simulations were carried out to unravel the reaction mechanism between the benchmark organic contaminants of dibutyl phthalate and air plasma. The optical emission spectroscopy was used to study the overall evolution behaviors of excited molecular species and radical signals from air plasma as a reference to simulations. Detailed reaction pathways were revealed and characterized, and specific intermediate radicals and products were analyzed during experiments and simulation. The reactive species in the air plasma, such as O, HO2 and O3 radicals, played a crucial role in cleaving organic molecular structures. Together, our findings provide an atomic-level understanding of complex reaction processes of low-pressure air plasma cleaning mechanisms and are essential for its application in industrial plasma cleaning.
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Theiss, Silva K., M. J. Caturla, T. Diaz de la Rubia, M. C. Johnson, Ant Uralt i P. B. Griffin. "Linking ab initio Energetics to Experiment: Kinetic Monte Carlo Simulation of Transient Enhanced Diffusion of B in Si". MRS Proceedings 538 (1998). http://dx.doi.org/10.1557/proc-538-291.
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AbstractWe have developed a kinetic Monte Carlo (kMC) simulator that links atomic migration and binding energies determined primarily from first principles calculations to macroscopic phenomena and laboratory time scales. Input for the kMC simulation is obtained from a combination of ab initio planewave pseudopotential calculations, molecular dynamics simulations, and experimental data. The simulator is validated against an extensive series of experimental studies of the diffusion of B spikes in self-implanted Si. The implant energy, dose, and dose rate, as well as the detailed thermal history of the sample, are included. Good agreement is obtained with the experimental data for temperatures between 750 and 950°C and times from 15 to 255 s. At 1050°C we predict too little diffusion after 105 s compared to experiment: apparently, some mechanism which is not adequately represented by our model becomes important at this temperature. Below 1050°C, the kMC simulation produces a complete description over macroscopic time scales of the atomic level diffusion and defect reaction phenomena that operate during the anneals. This simulator provides a practical method for predicting technologically interesting phenomena, such as transient enhanced diffusion of B, over a wide range of conditions, using energetics determined from first-principles approaches.
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Qin, Jie, Yang Liu i Jun Li. "Quantitative Dynamics of Paradigmatic SN2 reaction OH− + CH3F on Accurate Full-Dimensional Potential Energy Surface". Journal of Chemical Physics, 29.08.2022. http://dx.doi.org/10.1063/5.0112228.
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The bimolecular reaction between OH− and CH3F is not just a prototypical SN2 process but also has three other product channels. Here, we develop an accurate full-dimensional potential energy surface (PES) based on 191 193 points calculated at the level CCSD(T)-F12a/aug-cc-pVTZ. A detailed dynamics and mechanism analysis were carried out on this PES by using the quasi-classical trajectory approach. It is verified that the trajectories do not follow the minimum energy path (MEP) but directly dissociate to F− and CH3OH. In addition, a new transition state for proton exchange and a new product complex CH2F−‧‧‧H2O for proton abstraction were discovered. The trajectories avoid the transition state or this complex, instead dissociate to H2O and CH2F− directly through the ridge regions of the MEP before the transition state. These non-MEP dynamics become more pronounced at high collision energies. Detailed dynamics simulations provide new insights into the atomic-level mechanisms of the title reaction thanks to the new chemically accurate PES with the aid of the machine learning.
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Kim, Byungjo, Jinkyu Bae, Hyunhak Jeong, Seung Ho Hahn, Suyoung Yoo i Sang K. Nam. "Deep neural network-based reduced-order modeling of ion–surface interactions combined with molecular dynamics simulation". Journal of Physics D: Applied Physics, 12.06.2023. http://dx.doi.org/10.1088/1361-6463/acdd7f.
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Abstract With the advent of complex and sophisticated architectures in semiconductor device manufacturing, atomic-resolution accuracy and precision are commonly required for industrial plasma processing. This demands a comprehensive understanding of the plasma–material interactions—particularly for forming fine high-aspect ratio (HAR) feature patterns with sufficiently high yield in wafer-level processes. In particular, because the shape distortion in HAR pattern etching is attributed to the deviation of the energetic ion trajectory, the detailed ion–surface interactions need to be thoroughly investigated. In this study, molecular dynamics (MD) simulations were utilized to obtain a fundamental understanding of the collisional nature of accelerated Ar ions on the fluorinated Si surface that may appear on the sidewall of the HAR etched hole. High-fidelity data for ion–surface interaction features representing the energy and angle distributions (EADs) of sputtered atoms for varying degrees of surface F coverage and ion incident angles were obtained via extensive MD simulations. A deep learning-based reduced-order modeling (DL-ROM) framework was developed for efficiently predicting the characteristics of the ion–surface interactions. In the ROM framework, a conditional variational autoencoder (CVAE) was implemented to obtain regularized latent representations of the distributional data with the condition of the governing factors of the physical system. The proposed ROM framework accurately reproduced the MD simulation results and significantly outperformed various DL-ROMs, such as autoencoder (AE), sparse AE (SAE), contractive AE (CAE), denoising AE (DAE), and variational AE (VAE). From the inferred features of the sputtering yield and EADs of sputtered/scattered species, significant insights can be obtained regarding the ion interactions with the fluorinated surface. As the ion incident angle deviated from the glancing-angle range (incident angle > 80°), diffuse reflection behavior was observed, which can substantially affect the ion transport in the HAR patterns. Moreover, it was hypothesized that a shift in sputtering characteristics occurs as the surface F coverage varies, based on the inferred EADs. This conjecture was confirmed through detailed MD simulations that demonstrated the fundamental relationship between surface atomic conformations and their sputtering behavior. Combined with additional atomistic-scale investigations, this framework can provide an efficient way to reveal various fundamental plasma–material interactions which are highly demanded for the future development of semiconductor device manufacturing.
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Schnedermann, Christoph, Antonios M. Alvertis, Torsten Wende, Steven Lukman, Jiaqi Feng, Florian A. Y. N. Schröder, David H. P. Turban i in. "A molecular movie of ultrafast singlet fission". Nature Communications 10, nr 1 (16.09.2019). http://dx.doi.org/10.1038/s41467-019-12220-7.
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Abstract The complex dynamics of ultrafast photoinduced reactions are governed by their evolution along vibronically coupled potential energy surfaces. It is now often possible to identify such processes, but a detailed depiction of the crucial nuclear degrees of freedom involved typically remains elusive. Here, combining excited-state time-domain Raman spectroscopy and tree-tensor network state simulations, we construct the full 108-atom molecular movie of ultrafast singlet fission in a pentacene dimer, explicitly treating 252 vibrational modes on 5 electronic states. We assign the tuning and coupling modes, quantifying their relative intensities and contributions, and demonstrate how these modes coherently synchronise to drive the reaction. Our combined experimental and theoretical approach reveals the atomic-scale singlet fission mechanism and can be generalized to other ultrafast photoinduced reactions in complex systems. This will enable mechanistic insight on a detailed structural level, with the ultimate aim to rationally design molecules to maximise the efficiency of photoinduced reactions.
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Rentsch, R. "Atomistic Simulation and Experimental Investigation of Ultra Precision Cutting Processes". MRS Proceedings 578 (1999). http://dx.doi.org/10.1557/proc-578-261.
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AbstractTypical applications for components and equipment with extreme quality requirements regarding surface roughness, shape accuracy and integrity of the generated surface structure can be found in optical and semiconductor industry. Ultra precision machine tools equipped with sharp, single crystalline diamond provide the necessary machining accuracy. Here the actual cutting process can take place at atomic level, which makes the acquisition of typical cutting process data difficult or impossible. However a detailed characterization and understanding of the process is vital for its effective control as well as for further tool and process development.Therefore an approach is made that focuses on linking results from atomistic simulations with results and observations from cutting experiments. In this work the potential of molecular dynamics (MD) modeling for studying phenomena related to ultra precision cutting processes will be demonstrated. Observations and first results for machining copper will be presented.
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Simpkins, Blake S., Edward T. Yu, Patrick Waltereit i James S. Speck. "Distinguishing negatively-charged and highly conductive dislocations in gallium nitride using scanning Kelvin probe and conductive atomic force microscopy". MRS Proceedings 743 (2002). http://dx.doi.org/10.1557/proc-743-l2.4.
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ABSTRACTScanning Kelvin probe microscopy (SKPM) and conductive atomic force microscopy (C-AFM) are used to image surfaces of GaN grown by molecular beam epitaxy (MBE). Numerical simulations are used to assist in the interpretation of SKPM images. Detailed analysis of the same area using both techniques allows imaging of surface potential variations arising from the presence of negatively charged dislocations and dislocation-related current leakage paths. Correlations between the charge state of dislocations, conductivity of leakage current paths, and possibly dislocation type can thereby be established. Approximately 25% of the leakage paths appear to be spatially correlated with negatively charged dislocation features. This is approximately the level of correlation expected due to spatial overlap of randomly distributed, distinct features of the size observed, suggesting that the negatively charged dislocations are distinct from those responsible for localized leakage paths found in GaN. The effects of charged dislocation networks on the local potential profile is modeled and discussed.