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Journal articles on the topic 'Atomic-level detailed simulations'

Author: Grafiati

Published: 6 September 2023

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1

Chrobak, Artur, Grzegorz Ziółkowski, Dariusz Chrobak, and Grażyna Chełkowska. "From Atomic Level to Large-Scale Monte Carlo Magnetic Simulations." Materials 13, no. 17 (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 ana

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Bal, Kristof M., and Erik C. Neyts. "Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations." Chemical Science 7, no. 8 (2016): 5280–86. http://dx.doi.org/10.1039/c6sc00498a.

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Bottaro, Sandro, and Kresten Lindorff-Larsen. "Biophysical experiments and biomolecular simulations: A perfect match?" Science 361, no. 6400 (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, accu

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Mulholland, Adrian J. "Computational enzymology: modelling the mechanisms of biological catalysts." Biochemical Society Transactions 36, no. 1 (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, and Robert O. Ritchie. "On the question of fractal packing structure in metallic glasses." Proceedings of the National Academy of Sciences 114, no. 32 (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 p

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Comitani, Federico, Claudio Melis, and Carla Molteni. "Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations." Biochemical Society Transactions 43, no. 2 (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 th

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Artyukhov, Vasilii I., Yuanyue Liu, and Boris I. Yakobson. "Equilibrium at the edge and atomistic mechanisms of graphene growth." Proceedings of the National Academy of Sciences 109, no. 38 (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-

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Herasari, Dian, Rukman Hertadi, Fida M. Warganegara, and Akhmaloka Akhmaloka. "Stability and Mobility of Lid Lipmnk in Acetonitrile by Molecular Dynamics Simulations Approach." Biosciences, Biotechnology Research Asia 15, no. 2 (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 d

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Cayrel, Roger, and 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

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Pujol-Navarro, Neret, Karina Kubiak-Ossowska, Valerie Ferro, and Paul Mulheran. "Simulating Peptide Monolayer Formation: GnRH-I on Silica." International Journal of Molecular Sciences 22, no. 11 (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 deve

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Colvin, Michael E., Jennifer C. Sasaki, and Ngoc L. Tran. "Chemical Factors in the Action of Phosphoramidic Mustard Alkylating Anticancer Drugs: Roles for Computational Chemistry." Current Pharmaceutical Design 5, no. 8 (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

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Taddei, Mario, Marco Garavelli, Saeed Amirjalayer, Irene Conti, and Artur Nenov. "Modus Operandi of a Pedalo-Type Molecular Switch: Insight from Dynamics and Theoretical Spectroscopy." Molecules 28, no. 2 (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

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Nolden, Markus, Agnes Scaramus, Rahim Nabbi, Frank Charlier, and 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 (November 10, 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 wa

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Sejdiu, Besian I., and D. Peter Tieleman. "ProLint: a web-based framework for the automated data analysis and visualization of lipid–protein interactions." Nucleic Acids Research 49, W1 (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

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Tang, Ming, Xiaocong Wang, Neha S. Gandhi, et al. "Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study." Glycobiology 30, no. 10 (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 investiga

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Keten, Sinan, and Markus J. Buehler. "Nanostructure and molecular mechanics of spider dragline silk protein assemblies." Journal of The Royal Society Interface 7, no. 53 (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,

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Arnittali, Maria, Anastassia N. Rissanou, Maria Amprazi, Michael Kokkinidis, and 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, no. 11 (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 properti

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Keskin and Alsoy Altinkaya. "A Review on Computational Modeling Tools for MOF-Based Mixed Matrix Membranes." Computation 7, no. 3 (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 sp

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F. Garrido, Pablo, Martín Calvelo, Rebeca Garcia-Fandiño, and Ángel Piñeiro. "Rings, Hexagons, Petals, and Dipolar Moment Sink-Sources: The Fanciful Behavior of Water around Cyclodextrin Complexes." Biomolecules 10, no. 3 (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 desig

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Wang, Bin, Jinyang Xu, Chengliang Duan, et al. "Regulatory Mechanism of Opposite Charges on Chiral Self-Assembly of Cellulose Nanocrystals." Molecules 28, no. 4 (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, respectiv

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Filipovic, N., M. Kojic, and A. Tsuda. "Modelling thrombosis using dissipative particle dynamics method." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 366, no. 1879 (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. colloida

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Buchete, Nicolae-Viorel. "Unlocking the Atomic-Level Details of Amyloid Fibril Growth through Advanced Biomolecular Simulations." Biophysical Journal 103, no. 7 (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 (July 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,

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Dehghani, Ali, Ghasem Bahlakeh, Bahram Ramezanzadeh, and 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 (February 2020): 112220. http://dx.doi.org/10.1016/j.molliq.2019.112220.

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Li, Zeng Qiang, Jun Wang, and Qi Wu. "Molecular Dynamics Simulation of the Ablation Process in Ultrashort Pulsed Laser Machining of Polycrystalline Diamond." Advanced Materials Research 500 (April 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 take

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Duong, Vy T., Elizabeth M. Diessner, Gianmarc Grazioli, Rachel W. Martin, and Carter T. Butts. "Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures." Biomolecules 11, no. 12 (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 netwo

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Rodríguez, R., R. Florido, J. M. Gil, J. G. Rubiano, P. Martel, and 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, no. 3 (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 prope

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Liu, Shuhui, and Yang Xu. "MD Investigation on the Interaction between Carbamazepine and Two CYP Isoforms, CYP3A4 and CYP3A5." International Journal of Molecular Sciences 24, no. 3 (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 hydr

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Tsai, Ping Chi, and Yeau Ren Jeng. "A Review on Mechanical Properties of Deformation Mechanism of Tubular Nanostructures: Molecular Dynamics Simulations." Solid State Phenomena 329 (March 25, 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 simul

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Villalón, Ariel, Carlos Muñoz, Javier Muñoz, and Marco Rivera. "A Detailed dSPACE-Based Implementation of Modulated Model Predictive Control for AC Microgrids." Sensors 23, no. 14 (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 wi

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Liu, Huicong, Jiangjun Geng, Qifeng Zhu, et al. "Flexible Ultrasonic Transducer Array with Bulk PZT for Adjuvant Treatment of Bone Injury." Sensors 20, no. 1 (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

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Geiger, Martin, Christian Wegner, Winfried Mayer, and Christian Waldschmidt. "A Wideband Dielectric Waveguide-Based 160-GHz Radar Target Generator." Sensors 19, no. 12 (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 reali

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Muhseen, Ziyad Tariq, Salim Kadhim, Yahiya Ibrahim Yahiya, Eid A. Alatawi, Faris F. Aba Alkhayl, and 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, no. 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

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Parvini, Cameron H., M. A. S. R. Saadi, and Santiago D. Solares. "Extracting viscoelastic material parameters using an atomic force microscope and static force spectroscopy." Beilstein Journal of Nanotechnology 11 (June 16, 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 viscoelast

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Lin, Yiqi, Mengxue Zhang, Patricio S. La Rosa, James D. Wilson, and Arye Nehorai. "Electro-Mechanical Ionic Channel Modeling for Uterine Contractions and Oxytocin Effect during Pregnancy." Sensors 19, no. 22 (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 mo

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González-López, Jorge, Jeremy K. Cockcroft, Ángeles Fernández-González, Amalia Jimenez, and 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, no. 5 (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 c

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Zvorykin, V. D., N. V. Didenko, A. A. Ionin, et al. "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, no. 3 (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

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Kumar, M. Santhosh, and Ganesh Reddy Karri. "EEOA: Cost and Energy Efficient Task Scheduling in a Cloud-Fog Framework." Sensors 23, no. 5 (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 t

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Zubair, Muhammad, and Robert Dickinson. "Calculating the Effect of Ribs on the Focus Quality of a Therapeutic Spherical Random Phased Array." Sensors 21, no. 4 (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 ra

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Yurtsever, Ayhan, Pei-Xi Wang, Fabio Priante, et al. "Molecular insights on the crystalline cellulose-water interfaces via three-dimensional atomic force microscopy." Science Advances 8, no. 41 (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

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Coopmans, Tim, Robert Knegjens, Axel Dahlberg, et al. "NetSquid, a NETwork Simulator for QUantum Information using Discrete events." Communications Physics 4, no. 1 (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 ap

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Bogetti, Xiaowei, Anthony Bogetti, Joshua Casto, Gordon Rule, Lillian Chong, and Sunil Saxena. "Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by EPR and simulation." Protein Science, August 26, 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. EP

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Pan, Dongqing, Dongsheng Guan, Tien-Chien Jen, and Chris Yuan. "Atomic Layer Deposition Process Modeling and Experimental Investigation for Sustainable Manufacturing of Nano Thin Films." Journal of Manufacturing Science and Engineering 138, no. 10 (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 essenc

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LI, Yuhai, Qingshun Bai, Yuheng Guan, et al. "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, April 22, 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 th

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Theiss, Silva K., M. J. Caturla, T. Diaz de la Rubia, M. C. Johnson, Ant Uralt, and 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

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Qin, Jie, Yang Liu, and Jun Li. "Quantitative Dynamics of Paradigmatic S_N2 reaction OH⁻ + CH₃F on Accurate Full-Dimensional Potential Energy Surface." Journal of Chemical Physics, August 29, 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 com

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Kim, Byungjo, Jinkyu Bae, Hyunhak Jeong, Seung Ho Hahn, Suyoung Yoo, and 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, June 12, 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

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Schnedermann, Christoph, Antonios M. Alvertis, Torsten Wende, et al. "A molecular movie of ultrafast singlet fission." Nature Communications 10, no. 1 (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

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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 effectiv

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Simpkins, Blake S., Edward T. Yu, Patrick Waltereit, and 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 es

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