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Journal articles on the topic 'Atomistix ToolKit'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Myasnikova, L. N., A. S. Istlyaup, D. M. Sergeyev, N. N. Zhanturina, K. Sh Shunkeyev, and A. I. Popov. "Computer Simulations of the Band Structure and Density of States of the Linear Chains of NaCl Ions." Latvian Journal of Physics and Technical Sciences 56, no. 4 (2019): 49–56. http://dx.doi.org/10.2478/lpts-2019-0024.

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Abstract The paper presents the results of first-principles computer simulations of the band structure, the density of states, and the total energy of NaCl (NaCl, Na2Cl2, Na3Cl3, Na4Cl4, Na6Cl6) linear chains of atoms. Modelling of the specified characteristics is realised in the computer code Atomistix ToolKit combined with Virtual NanoLab. The total energy depends on the number of ions in the nanoobject under study, but practically does not depend on the geometric arrangement of ions.

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WANG, X. F., L. N. ZHAO, Z. H. YAO, et al. "ATOMISTIC SIMULATION OF GATE EFFECT ON NANOSCALE INTRINSIC Si FIELD-EFFECT TRANSISTORS." International Journal of Nanoscience 08, no. 01n02 (2009): 113–17. http://dx.doi.org/10.1142/s0219581x09005827.

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We study the electrostatic and quantum transport properties of nanoscale double-gated Si -based field effect transistors within the framework of density functional theory combined with nonequilibrium Green's function approach. In our model device system, a Si slab is sandwiched between two insulator slabs and connected to two semi-infinite Si electrodes at its left and right ends. The effect of the double gates is taken into account by applying proper electrostatic boundary conditions and solving the Poisson equation self-consistently in the system. In the representation of localized SIESTA li

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Srivastava, Anurag, Mohammad Irfan Khan, Neha Tyagi, and Purnima Swaroop Khare. "Doping Induced Structural Stability and Electronic Properties of GaN Nanotubes." Scientific World Journal 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/984591.

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The present paper discusses the effect of manganese doping on the structural stability and electronic band gap of chiral (2, 1), armchair (3, 3), and zigzag ((6, 0) and (10, 0)) single walled GaN nanotube by using density functional theory based Atomistix Toolkit (ATK) Virtual NanoLab (VNL). The structural stability has been analyzed in terms of minimum ground state total energy, binding, and formation energy. As an effect of Mn doping (1–4 atoms), all the GaN nanotubes taken into consideration show semiconducting to metallic transition first and after certain level of Mn doping changes its tr

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SRIVASTAVA, ANURAG, BODDEPALLI SANTHIBHUSHAN, and PANKAJ DOBWAL. "CHARGE STABILITY AND CONDUCTANCE ANALYSIS OF ANTHRACENE-BASED SINGLE ELECTRON TRANSISTOR." International Journal of Nanoscience 12, no. 06 (2013): 1350045. http://dx.doi.org/10.1142/s0219581x13500452.

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The present paper discusses the investigation of electronic properties of anthracene-based single electron transistor (SET) operating in coulomb blockade region using Density Functional Theory (DFT) based Atomistix toolkit-Virtual nanolab. The charging energies of anthracene molecule in isolated as well as electrostatic SET environments have been calculated for analyzing the stability of the molecule for different charge states. Study also includes the analysis of SET conductance dependence on source/drain and gate potentials in reference to the charge stability diagram. Our computed charging

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Mao, Hong-Ying, Bao-Xing Li, Wang-Feng Ding, et al. "Theoretical Study on the Aggregation of Copper Clusters on a Liquid Surface." Materials 12, no. 23 (2019): 3877. http://dx.doi.org/10.3390/ma12233877.

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The ground state structures of copper clusters with different sizes along with their aggregation have been systematic investigated using Amsterdam Density Functional (ADF) and Atomistix ToolKit (ATK) programs. On the basis of geometry optimization, some Cu clusters with more stable structures which were not reported previously have been revealed. In most cases, these Cu clusters prefer to adopt icosahedral structures which originate from the 13-atom icosahedron. It has also been demonstrated that the interaction between two Cu clusters is anisotropic, which is attributed to their charge distri

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Mehrabova, M. А., N. T. Panahov, and N. H. Hasanov. "Ab initio calculations of electronic band structure of CdMnS semimagnetic semiconductors." Doklady BGUIR 19, no. 8 (2022): 45–49. http://dx.doi.org/10.35596/1729-7648-2021-19-8-45-49.

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This work is devoted to theoretical investigations of Cd1-xMnxS semimagnetic semiconductors (SMSC). The purpose of this work was to calculate the electronic band structure of ideal and defective Cd1- xMnxS SMSC in both antiferromagnetic (AFM) and ferromagnetic (FM) phases. Ab initio, calculations are performed in the Atomistix Toolkit (ATK) program within the Density Functional Theory (DFT) and Local Spin Density Approximation (LSDA) on Double Zeta Double Polarized (DZDP) basis. We have used Hubbard U potential UMn = 3.59 eV for 3d states for Mn atoms. Supercells of 8 and 64 atoms were constru

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Rashid, Muhammad Haroon, Ants Koel, and Toomas Rang. "Simulations of Heterostructures Based on 3C-4H and 6H-4H Silicon Carbide Polytypes." Materials Science Forum 924 (June 2018): 302–5. http://dx.doi.org/10.4028/www.scientific.net/msf.924.302.

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In the last decade, silicon carbide (SiC) has gained a remarkable position among wide bandgap semiconductors due to its high temperature, high frequency, and high power electronics applications. SiC heterostructures, based on the most prominent polytypes like 3C-SiC, 4H-SiC and 6H-SiC, exhibit distinctive electrical and physical properties that make them promising candidates for high performance optoelectronic applications. The results of simulations of nn-junction 3C-4H/SiC and 6H-4H/SiC heterostructures, at the nanoscale and microscale, are presented in this paper. Nanoscale devices are simu

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Refaat, Marjan, and Mohammad Reza Moslemi. "A simulation study of silver nanowire for water and ethane vapor sensing." Microelectronics International 33, no. 2 (2016): 73–78. http://dx.doi.org/10.1108/mi-03-2015-0024.

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Purpose Nanowires, nanostructures with the diameter of the order of a nanometer, have recently attracted as gas sensors because of their interesting properties such as high sensitivity, fast response and high selectivity and stability. Among the different types of gas sensors, metallic nanowires used in high frequency applications because of their long mean free path that make the conduction ballistic. Design/methodology/approach This paper presents the results of simulations to find the effects of adsorbing some molecules by silver Ag nanowires. The mechanisms of the simulated gas sensor are

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Istlyaup, Assel, Lyudmila Myasnikova, Daulet Sergeyev, Marina Konuhova, and Anatoli I. Popov. "Computer simulation of the density of states and band structure of NaF nanotubes." Low Temperature Physics 50, no. 7 (2024): 569–73. http://dx.doi.org/10.1063/10.0026283.

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Modern solid-state physics increasingly focuses on the study of nanomaterials and the development of nanotechnologies. Various theoretical methods and research technologies are actively used to elucidate the significance of experimental results related to the study of solid-state defects. Progress in this field is likely associated with advancements in computer technologies and the development of modern quantum-chemical packages. The obtained spectra reveal a certain number of energy levels in the energy range from –30 to 20 eV. We determine the band structure, density of states, and total ene

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Haroon Rashid, Muhammad, Ants Koel, and Toomas Rang. "First Principles Simulations of Phenol and Methanol Detector Based on Pristine Graphene Nanosheet and Armchair Graphene Nanoribbons." Sensors 19, no. 12 (2019): 2731. http://dx.doi.org/10.3390/s19122731.

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Over the last decade graphene based electronic devices have attracted the interest of researchers due to their exceptional chemical, electrical and optical properties. Graphene is very sensitive to any physical changes in its surrounding environment and, inherently, has very low electronic noise. This property of graphene makes it a suitable candidate for sensor applications. The purpose of the work presented in this article is to demonstrate the ability of graphene derivatives to detect toxic organic compounds like phenol and methanol. A novel method for the detection of organic compounds (ph

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Rashid, Muhammad Haroon, Ants Koel, Toomas Rang, and Mehadi Hasan Ziko. "Simulations of Benzene and Hydrogen-Sulfide Gas Detector Based on Single-Walled Carbon Nanotube over Intrinsic 4H-SiC Substrate." Micromachines 11, no. 5 (2020): 453. http://dx.doi.org/10.3390/mi11050453.

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Carbon nanotubes (CNTs)-based sensors have gained significant importance due to their tremendous electrical and physical attributes. CNT-based gas sensors have high sensitivity, stability, and fast response time compared to that of solid-state sensors. On exposure to a large variety of organic and inorganic compounds, the conductivity of CNT changes. This change in electrical conductivity is being used as a detection signal to detect different target molecules. Hydrogen-sulfide and benzene are hazardous gases that can cause serious health issues in humans. Therefore, it is mandatory to detect

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Rashid, Muhammad Haroon, Ants Koel, and Toomas Rang. "Nano and Micro-Scale Simulations of Si/4H-SiC and Si/3C-SiC NN-Heterojunction Diodes." Materials Science Forum 963 (July 2019): 357–61. http://dx.doi.org/10.4028/www.scientific.net/msf.963.357.

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In the last decades, silicon carbide (SiC) based heterostructures have gained a remarkable place in research field due to their exceptional properties. These properties make SiC highly suitable for high temperature, high frequency, and high power electronics applications. The most prominent polytypes (among 200 types) of SiC like 3C-SiC, 4H-SiC and 6H-SiC, have distinctive electrical and physical attributes that make them promising candidates for high performance optoelectronic applications. Silicon (Si) also has been accepted as a promising material for wide range of electronic, optical and o

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Rahman, Fahrin, Md Saidur Rahman, Rubab Ahmmed, and Md Hazrat Ali. "Quantum Capacitance and Fermi Level Change in Graphene nanoribbons due to Gas Sensing." International Journal of Applied and Structural Mechanics, no. 31 (January 19, 2023): 1–9. http://dx.doi.org/10.55529/ijasm.31.1.9.

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Here we used semiempirical computations to examine the property of nanoribbon of Graphene as a gas sensor with interaction of H2O gas molecule for both pure and defective GNRs which has been generated in Atomistix Toolkit (ATK) software. Density of States GNR before and after the interaction is shown in a (DOS) diagram with gas particles was discovered to be different which has been observed in MATLAB software. It's vital to look at the quantum capacitance when examining Graphene’s electrical properties. So, this study looked at change in quantum capacitance and Fermi Level of Graphene before

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Rahman, Fahrin, Md Saidur Rahman, Rubab Ahmmed Ahmmed, and Md Hazrat Ali. "Quantum Capacitance and Fermi Level Change in Graphene nanoribbons due to Gas Sensing." International Journal of Applied and Structural Mechanics, no. 31 (January 19, 2023): 1–9. http://dx.doi.org/10.55529/ijasm31.1.9.

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Here we used semiempirical computations to examine the property of nanoribbon of Graphene as a gas sensor with interaction of H2O gas molecule for both pure and defective GNRs which has been generated in Atomistix Toolkit (ATK) software. Density of States GNR before and after the interaction is shown in a (DOS) diagram with gas particles was discovered to be different which has been observed in MATLAB software. It's vital to look at the quantum capacitance when examining Graphene’s electrical properties. So, this study looked at change in quantum capacitance and Fermi Level of Graphene before

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Rashid, Muhammad Haroon, Ants Koel, and Toomas Rang. "Effects of the Inclusion of Armchair Graphene Nanoribbons on the Electrical Conduction Properties of NN-Heterojunction 4H-6H/SiC Diodes." Materials Science Forum 962 (July 2019): 29–35. http://dx.doi.org/10.4028/www.scientific.net/msf.962.29.

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In recent years, graphene has sparked the interest of researchers due to its promising electrical and physical attributes. These attributes make it highly suitable to develop electronic devices with ultra-high mobility of charge carriers. Meanwhile silicon carbide (SiC), a wide bandgap semiconductor material, is being used for high temperature optoelectronic applications. SiC has more than 250 different crystalline forms, these are called polytypes. Some of these polytypes (such as 4H-SiC, 6H-SiC and 3C-SiC) have exceptional physical and electrical properties. Electronic devices which have SiC

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Rashid, Muhammad Haroon, Ants Koel, and Toomas Rang. "Nano- and Micro-Scale Simulations of Ge/3C-SiC and Ge/4H-SiC NN-Heterojunction Diodes." Materials Science Forum 1004 (July 2020): 490–96. http://dx.doi.org/10.4028/www.scientific.net/msf.1004.490.

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During the last decade, silicon carbide (SiC) and its heterostructures with other semiconductors have gained a significant importance for wide range of electronics applications. These structures are highly suitable for high frequency and high power applications in extremely high temperature environments. SiC exists in more than 200 different polycrystalline forms, called polytypes. Among these 200 types, the most prominent polytypes with exceptional physical and electrical attributes are 3C-SiC, 4H-SiC and 6H-SiC. Heterostructures of these SiC polytypes with other conventional semiconductors (

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Wasfi, Asma, Ahmed Al Hamarna, Omar Mohammed Hasani Al Shehhi, Hazza Fahad Muhsen Al Ameri, and Falah Awwad. "Graphene Nanoribbon Field Effect Transistor Simulations for the Detection of Sugar Molecules: Semi-Empirical Modeling." Sensors 23, no. 6 (2023): 3010. http://dx.doi.org/10.3390/s23063010.

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Graphene has remarkable characteristics that make it a potential candidate for optoelectronics and electronics applications. Graphene is a sensitive material that reacts to any physical variation in its environment. Due to its extremely low intrinsic electrical noise, graphene can detect even a single molecule in its proximity. This feature makes graphene a potential candidate for identifying a wide range of organic and inorganic compounds. Graphene and its derivatives are considered one of the best materials to detect sugar molecules due to their electronic properties. Graphene has low intrin

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Mekhrabov, Amdulla, and Matanat Mehrabova. "Effect of Gamma Irradiation on Structural and Optical Properties of CdMnTe Epitaxial Thin Films." Materials Science Forum 1119 (March 29, 2024): 3–12. http://dx.doi.org/10.4028/p-but1qb.

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Cd1-0.06Mn0.06Te epitaxial thin films were synthesis on glass substrates by the Molecular Beam Condensation (MBC) method in the vacuum evaporation equipment УВН-71-ПЗ with steam-oil pumping and nitrogen trap at working pressure of residual gas (1÷2)x10-4 Pa. By using additional source of Te vapor and controlling temperature, it has been determined the optimum conditions for obtaining Cd1-0.06Mn0.06Te epitaxial films with a perfect structure, clean and smooth surface, without of second phase inclusions. XRD investigations showed that Cd1-0.06Mn0.06Te epitaxial films grow on glass substrates on

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Dec, Bartłomiej, and Robert Bogdanowicz. "DFT studies of refractive index of boron-doped diamond." Photonics Letters of Poland 10, no. 2 (2018): 39. http://dx.doi.org/10.4302/plp.v10i2.824.

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The density functional theory is one of the optimal solutions in calculation of optical properties of materials on the quantum scale. In this paper, we have investigated refractive index of a boron-doped diamond structure with the usage of Atomistic Toolkit software from Synopsys. During this study, various methods and pseudopotentials were checked to obtain an optimal performance-accuracy method for calculation of such materials. Leading method used in calculation was used meta-GGA with Fritz-Haber Institute pseudopotential. Full Text: PDF ReferencesW. Kohn and L. J. Sham, "Self-Consistent Eq

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Rashid, Muhammad Haroon, Ants Koel, and Toomas Rang. "Simulations of Graphene Nanoribbon Field Effect Transistor for the Detection of Propane and Butane Gases: A First Principles Study." Nanomaterials 10, no. 1 (2020): 98. http://dx.doi.org/10.3390/nano10010098.

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During the last few years graphene has emerged as a potential candidate for electronics and optoelectronics applications due to its several salient features. Graphene is a smart material that responds to any physical change in its surrounding environment. Graphene has a very low intrinsic electronic noise and it can detect even a single gas molecule in its proximity. This property of graphene makes is a suitable and promising candidate to detect a large variety of organic/inorganic chemicals and gases. Typical solid state gas sensors usually requires high operating temperature and they cannot

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Chan, Henry, Badri Narayanan, Mathew Cherukara, et al. "BLAST: bridging length/timescales via atomistic simulation toolkit." MRS Advances 6, no. 2 (2021): 21–31. http://dx.doi.org/10.1557/s43580-020-00002-z.

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Dec, Bartłomiej, Robert Bogdanowicz, and Krzysztof Pyrchla. "Ab-initio study of electrical and optical properties of allylamine." Photonics Letters of Poland 10, no. 3 (2018): 94. http://dx.doi.org/10.4302/plp.v10i3.847.

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The Density functional theory is one of most promising methodology in fast and accurate calculations of electrical and optical properties from the atomic basis. In this paper, we calculate electrical and optical properties of allylamine (2-propen 1- amine) in terms of accuracy and speed of calculations obtained by selection of DFT-1/2 method with ultrasoft Vanderbilt pseudopotentials. Comparison of density of states between molecule and bulk configuration shows great agreement between them, therefore we calculated refractive index which showed even better agreement with experimental data. Full

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Mayeshiba, Tam, Henry Wu, Thomas Angsten, et al. "The MAterials Simulation Toolkit (MAST) for atomistic modeling of defects and diffusion." Computational Materials Science 126 (January 2017): 90–102. http://dx.doi.org/10.1016/j.commatsci.2016.09.018.

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de-Córdoba, Gonzalo F., Benedetto Molinari, and José L. Torres. "Public Debt Frontier: A Python Toolkit for Analyzing Public Debt Sustainability." Sustainability 13, no. 23 (2021): 13260. http://dx.doi.org/10.3390/su132313260.

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This study proposes a synthetic visual indicator with which to perform debt sustainability analysis using dynamic general equilibrium models. In a single diagram, we summarized the general equilibrium relationships among economic activity, government budget, and the maximum amount of sustainable public debt. Then, we measured sustainability using the distance of actual debt from the model-consistent maximum debt. This indicator can be implemented with any DSGE model; as a backing theory, we used a neoclassical model augmented with endogenous tax revenues, disaggregated public spending, differe

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Jafarova, Vusala N., and Aynur N. Jafarova. "Ferromagnetism in silver-doped single-walled zinc oxide nanotubes." Journal of Physics: Conference Series 2699, no. 1 (2024): 012015. http://dx.doi.org/10.1088/1742-6596/2699/1/012015.

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Abstract In this paper, the electronic and magnetic properties of single-walled ZnO:Ag nanotubes with a chirality of (6,0) were investigated. Ab initio simulations were carried out using Atomistic ToolKit computer code implementing density functional theory within the local spin density approximation. To obtain an accurate energy band gap for related systems, we used the Hubbard U semiempirical corrections. The introduction of the Ag atom into the ZnO nanotube structure changes the electronic structure, the energy gap decreases with the silver concentration. The calculated value of total magne

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Chen, Junliang, Sujun Yun, Tiekuang Dong, Zhongzhou Ren, and Xiaoping Zhang. "Investigate the radiation-induced damage on an atomistic DNA model by using Geant4-DNA toolkit." Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 494-495 (May 2021): 59–67. http://dx.doi.org/10.1016/j.nimb.2021.03.010.

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Ahmed Jamal, G. R., M. Rezanur Islam, M. Adnan Rahman, J. Ferdous Meem, and R. Akter Sathie. "Chirality Dependence of Gas Adsorption Property of Single Wall Carbon Nanotubes." Materials Science Forum 889 (March 2017): 248–52. http://dx.doi.org/10.4028/www.scientific.net/msf.889.248.

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In this work, effect of chirality on gas adsorption property of semiconducting single-wall carbon nanotubes (SWCNTs) is reported for the first time. First principles simulation of the interaction of three different chirality SWCNTs with different gas molecules is performed maintaining equilibrium tube–molecule distance. Results are obtained employing density functional theory, using the Atomistic toolkit simulation package (ATK-DFT). Nanotube density of states is observed to vary significantly due to interaction with different types of gases as well as for same gas if chirality of SWCNTs varie

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Jagga, Deepali, Vitaly I. Korepanov, Daria M. Sedlovets, and Artur Useinov. "Spin-Induced Switching of Electronic State Populations in Transition Metal Polyphthalocyanines." Materials 15, no. 22 (2022): 8098. http://dx.doi.org/10.3390/ma15228098.

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Polyphthalocyanines (PPCs) are a new and promising class of two dimensional materials offering versatile avenues for next generation electronic devices. For organic spintronic devices, PPCs can be engineered to tailor the electric and magnetic properties. In this work, we investigate PPC’s monolayers with embedded transition metal atoms (TM = Fe, Ni, Cu), utilizing first principle calculations based on spin-polarized generalized gradient approximation (SGGA). PPC sheets with central TM atoms are simulated for the dispersion curves, electronic density of states (DOS), and projected density of s

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Hassani-Ardekani, Hajar, Hanieh Niroomand-Oscuii, Ehsan Nikbin, and Amir Shamloo. "Molecular dynamics simulation of the dissociation mechanism of P-selectin from PSGL-1." Journal of Theoretical and Computational Chemistry 16, no. 04 (2017): 1750035. http://dx.doi.org/10.1142/s0219633617500353.

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Interactions between P-selectin, expressed on activated endothelium, and its counterpart P-selectin glycoprotein ligand-1 (PSGL-1), expressed on leukocytes, play a pivotal role in adhesive events that recruit circulating leukocytes toward inflamed or injured tissues. Atomistic understanding of the association and dissociation of these bonds under blood flow is necessary to define the underlying mechanism. In this study, steered molecular dynamics (SMD) simulations were applied to investigate the conformational changes of P-LE/SGP-3 construct (an effective binding unit of the P-selectin/PSGL-1

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Nahlik, Josef, Jan Voves, Alexandr Laposa, and Jiri Kroutil. "The Study of Graphene Gas Sensor." Key Engineering Materials 605 (April 2014): 495–98. http://dx.doi.org/10.4028/www.scientific.net/kem.605.495.

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The graphene is suitable for gas sensing applications for its two dimensional char-acter which gives the best possible ratio between sensor surface and volume. The interactionbetween graphene surface and gas molecules can signicantly change the graphene layer trans-port properties. Therefore graphene can serve as a sensitive layer in a gas sensor. This work isconcentrated on the analysis of the conductivity of graphene layer exposed to dierent gases(NH3, CO2 ...). Together with the electrical measurement on the interdigital graphene sensora simulation based on quantum atomistic approach has be

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Salih, Ehab, and Ahmad I. Ayesh. "Enhancing the Sensing Performance of Zigzag Graphene Nanoribbon to Detect NO, NO2, and NH3 Gases." Sensors 20, no. 14 (2020): 3932. http://dx.doi.org/10.3390/s20143932.

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In this article, a zigzag graphene nanoribbon (ZGNR)-based sensor was built utilizing the Atomistic ToolKit Virtual NanoLab (ATK-VNL), and used to detect nitric oxide (NO), nitrogen dioxide (NO2), and ammonia (NH3). The successful adsorption of these gases on the surface of the ZGNR was investigated using adsorption energy (Eads), adsorption distance (D), charge transfer (∆Q), density of states (DOS), and band structure. Among the three gases, the ZGNR showed the highest adsorption energy for NO with −0.273 eV, the smallest adsorption distance with 2.88 Å, and the highest charge transfer with

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ЕРМИЛОВ Н, В., Н. БИККУЛОВА Н, Р. КУРБАНГУЛОВ А, Р. АКМАНОВА Г та М. МУНАСЫПОВ И. "ИССЛЕДОВАНИЕ ЗОННЫХ СТРУКТУР КВАНТОВЫХ ТОЧЕК PBS С ЛИГАНДАМИ CL И FA". Инженерная физика, № 2 (28 лютого 2025). https://doi.org/10.25791/infizik.2.2025.1457.

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Сульфид цинка PbS - полупроводник с узкой шириной запрещенной зоны, который является перспективным термоэлектрическим материалом. В работе представлены высокопроизводительные вычисления электронной структуры и оптических свойств квантовых точек PbS с лигандами Cl и FA с использованием метода теории функционала плотности - линейной комбинации атомных орбиталей(DFT-LCAO), встроенного в программное обеспечение Atomistix ToolKit. Рассмотрено применение высокопроизводительных вычислений для исследования зонных структур квантовых точек PbS с лигандами Cl и FA. Zinc sulfide PbS is a narrow band gap s

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Zeinab, Jokar, and Reza Moslemi Mohammad. "Effects of Position and Shape of Atomic Defects on the Band Gap of Graphene Nano Ribbon Superlattices." January 1, 2015. https://doi.org/10.5281/zenodo.1099172.

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In this work, we study the behavior of introducing atomic size vacancy in a graphene nanoribbon superlattice. Our investigations are based on the density functional theory (DFT) with the Local Density Approximation in Atomistix Toolkit (ATK). We show that, in addition to its shape, the position of vacancy has a major impact on the electrical properties of a graphene nanoribbon superlattice. We show that the band gap of an armchair graphene nanoribbon may be tuned by introducing an appropriate periodic pattern of vacancies. The band gap changes in a zig-zag manner similar to the variation of ba

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Jafarova, V. N. "Ab-initio calculation of structural and electronic properties of ZnO and ZnSe compounds with wurtzite structure." International Journal of Modern Physics B, July 19, 2022. http://dx.doi.org/10.1142/s0217979222501569.

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Some physical properties (structural and electronic) of Zn-based wurtzite structures have been theoretically studied by the density functional theory (DFT). Ab-initio calculations were done using the plane-wave pseudo-potential method within the Atomistix ToolKit (ATK) software package. Detailed investigations on the structural and electronic properties of the binary bulk compounds, ZnO and ZnSe, have been conducted and compared with the obtained studies. Using the modified Becke–Johnson potential has successfully improved the calculated bandgap. From the first-principles calculations for inve

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Wasfi, Asma, Mawahib Sulieman, Ziad Sefelnasr, et al. "Detection of butane and propane gases via C2N sensors: first principles modeling." Scientific Reports 13, no. 1 (2023). http://dx.doi.org/10.1038/s41598-023-46870-x.

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AbstractGas sensing is a critical research area in aerospace, military, medical, and industrial environments, as it helps prevent risks to human health and the environment caused by toxic gases. Propane and butane, commonly used as fuels in household and industrial settings, are toxic and flammable gases that need to be effectively detected to avoid leakage or explosion accidents. To address this, nanomaterial-based gas sensors are being developed with low power consumption and operating temperatures. In this study, two-dimensional nitrogenated holey graphene (C2N) based sensors are used for t

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Gelžinytė, Elena, Simon Wengert, Tamás K. Stenczel, et al. "wfl Python toolkit for creating machine learning interatomic potentials and related atomistic simulation workflows." Journal of Chemical Physics 159, no. 12 (2023). http://dx.doi.org/10.1063/5.0156845.

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Predictive atomistic simulations are increasingly employed for data intensive high throughput studies that take advantage of constantly growing computational resources. To handle the sheer number of individual calculations that are needed in such studies, workflow management packages for atomistic simulations have been developed for a rapidly growing user base. These packages are predominantly designed to handle computationally heavy ab initio calculations, usually with a focus on data provenance and reproducibility. However, in related simulation communities, e.g., the developers of machine l

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Wang, Weiwei, Boyao Lyu, Lingyao Kong, Hans Fangohr, and Haifeng Du. "MicroMagnetic.jl: A Julia package for micromagnetic and atomistic simulations with GPU support." Chinese Physics B, September 3, 2024. http://dx.doi.org/10.1088/1674-1056/ad766f.

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Abstract MicroMagnetic.jl is an open-source Julia package for micromagnetic and atomistic simulations. Using the features of the Julia programming language, MicroMagnetic.jl supports CPU and various GPU platforms, including NVIDIA, AMD, Intel, and Apple GPUs. Moreover, MicroMagnetic.jl supports Monte Carlo simulations for atomistic models and implements the Nudged-Elastic-Band method for energy barrier computations. With built-in support for double and single precision modes and a design allowing easy extensibility to add new features, MicroMagnetic.jl provides a versatile toolset for research

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Oues, Namir, Sarath Chandra Dantu, Riktaben Jigarkumar Patel, and Alessandro Pandini. "MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations." Bioinformatics, July 7, 2023. http://dx.doi.org/10.1093/bioinformatics/btad427.

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Abstract Motivation Molecular dynamics (MD) simulations have become routine tools for the study of protein dynamics and function. Thanks to faster GPU-based algorithms, atomistic and coarse-grained simulations are being used to explore biological functions over the microsecond timescale, yielding terabytes of data spanning multiple trajectories, thereby extracting relevant protein conformations without losing important information is often challenging. Results We present MDSubSampler, a Python library and toolkit for a posteriori subsampling of data from multiple trajectories. This toolkit pro

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Vizoso, Daniel, and Chaitanya Deo. "Determination of Vacancy Formation Energies in Binary UZr Alloys Using Special Quasirandom Structure Methods." Frontiers in Materials 8 (July 6, 2021). http://dx.doi.org/10.3389/fmats.2021.692660.

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The use of predictive models to examine defect production and migration in metallic systems requires a thorough understanding of the energetics of defect formation and migration. In fully miscible alloys, atomistic properties will all have a range of values that are heavily dependent on local atomic configurations. In this work we have used the atomistic simulation tool Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to investigate the impact of first nearest neighbor configuration on vacancy formation energies at 0 K in γ-U-Zr alloys of varying Zr concentrations. The proper

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Hatch, Harold W., Christina Bergonzo, Marco A. Blanco, et al. "Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models." Journal of Chemical Physics 161, no. 9 (2024). http://dx.doi.org/10.1063/5.0224809.

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We develop a multiscale coarse-grain model of the NIST Monoclonal Antibody Reference Material 8671 (NISTmAb) to enable systematic computational investigations of high-concentration physical instabilities such as phase separation, clustering, and aggregation. Our multiscale coarse-graining strategy captures atomic-resolution interactions with a computational approach that is orders of magnitude more efficient than atomistic models, assuming the biomolecule can be decomposed into one or more rigid bodies with known, fixed structures. This method reduces interactions between tens of thousands of

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"First Principles Calculations of Carbon-Nanotube and Boron-Nanotube Based Single Electron Transistors." East European Journal of Physics, no. 1 (2020). http://dx.doi.org/10.26565/2312-4334-2020-1-05.

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Low power consumption, small device size and better controlled onto the charge carriers are the factors, that made Single-electron transistor (SET) a suitable candidate for molecular electronics; yet there are some improvements that can be done in order to use it practically. The single electron transistor (SET) operates through the tunnelling of electron via two tunnel junctions. Choosing a suitable island material plays a key role in the tunnelling of electron through the tunnel junctions. In the present work, the First principle calculations of carbon-nanotube and boron-nanotube based Singl

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