scholarly journals Experiment and simulation of single inhibitor SH110 for void-free TSV copper filling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fuliang Wang ◽  
Yuping Le
Keyword(s):  
Quantum Chemistry ◽  
Three Dimensional ◽  
Linear Sweep Voltammetry ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Quantum Chemistry Calculations ◽  
Silicon Vias ◽  
Expensive Process ◽  
Materials Studio ◽  
Main Factor

AbstractThree-dimensional integration with through-silicon vias (TSVs) is a promising microelectronic interconnection technology. Three-component additives are commonly used for void-free TSV filling. However, optimising the additive concentrations is an expensive process. To avoid this, a single-component additive was developed: 3-(2-(4,5-dihydrothiazol-2-yl) disulfanyl) propane-1-sulfonic acid/sulfonate (SH110). Sodium 3,3′-dithiodipropane sulfonate (SPS) and SH110 were used as additives for TSV electroplating copper filling. SH110 resulted in void-free filling, whereas large keyhole voids were found for SPS. To understand how the additives affect the filling mechanism, linear sweep voltammetry of the plating solutions was carried out. The interactions between the Cu surface and additives were simulated by molecular dynamics (MD) analysis using Materials Studio software, and quantum chemistry calculations were conducted using GAUSSIAN 09W. SH110 adsorbs to the Cu surface by both 4,5-dihydrothiazole (DHT) and 3-mercaptopropane sulfonate (MPS) moieties, while SPS is adsorbed only by MPS moieties. MD simulations indicated that the adsorption of the coplanar MPS moiety is the main factor governing acceleration. Quantum chemistry calculations showed that DHT provides an inhibitory effect for TSV filling, while MPS acts as an accelerator for SH110. SH110 is an excellent additive exhibiting both the acceleration and the suppression necessary for achieving void-free TSV filling.

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

Interactive visualization of electron density slices

2005 ◽  
Vol 38 (3) ◽  
pp. 563-565 ◽  
Author(s):  
Filipe R. N. C. Maia ◽  
Abraham Szöke ◽  
Warren DeLano ◽  
David van der Spoel
Keyword(s):  
High Resolution ◽  
Quantum Chemistry ◽  
Electron Density ◽  
Three Dimensional ◽  
Structure Model ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Molecular Visualization ◽  
Density Maps ◽  
Quantum Chemistry Calculations

A new tool has been developed to aid in the visualization of electron density in crystals or from quantum chemistry calculations. It displays the fine details of the electron density on a plane and the three-dimensional model of the molecule at the same time. The program enables the user to examine the details of weak or irregular features. Such features frequently occur in low-resolution maps, where they determine the correct tracing of a protein backbone. In high-resolution maps, solvent regions are difficult or impossible to observe using isosurfaces. The tool has been integrated into an existing molecular visualization package (PyMol) making it possible to observe and interact both with a structure model and the electron density slices freely, simultaneously and independently. This visualization model fills a gap in the visualization methods available to crystallographers and others who work with electron density maps.

scholarly journals Elucidating the enhancement in optical properties of low band gap polymers by tuning the structure of alkyl side chains

2015 ◽  
Vol 17 (14) ◽  
pp. 9541-9551 ◽  
Author(s):  
Jing Lu ◽  
Yao Yao ◽  
Prathamesh M. Shenai ◽  
Lipeng Chen ◽  
Yang Zhao
Keyword(s):  
Optical Properties ◽  
Quantum Chemistry ◽  
Band Gap ◽  
Md Simulations ◽  
Side Chains ◽  
Low Band Gap ◽  
Electronic And Optical Properties ◽  
Quantum Chemistry Calculations ◽  
Alkyl Side Chains ◽  
Low Band Gap Polymers

Quantum chemistry calculations in combination with MD simulations reveal the influence of alkyl side groups on electronic and optical properties of polymers.

Acoustic and Photoacoustic Inspection of Through-Silicon Vias in the GHz-Frequency Band

2017 ◽  
Author(s):  
Sebastian Brand ◽  
Michael Kögel ◽  
Frank Altmann ◽  
Ingrid DeWolf ◽  
Ahmad Khaled ◽  
...  
Keyword(s):  
Quality Assessment ◽  
Frequency Band ◽  
Process Development ◽  
Three Dimensional ◽  
Non Destructive Testing ◽  
Destructive Testing ◽  
Vertical Interconnection ◽  
Testing Techniques ◽  
Silicon Vias ◽  
Non Destructive

Abstract Through Silicon Via (TSV) is the most promising technology for vertical interconnection in novel three-dimensional chip architectures. Reliability and quality assessment necessary for process development and manufacturing require appropriate non-destructive testing techniques to detect cracks and delamination defects with sufficient penetration and imaging capabilities. The current paper presents the application of two acoustically based methods operating in the GHz-frequency band for the assessment of the integrity of TSV structures.

scholarly journals Numerical simulation of the impact of an integrated renovation project on the Maowei Sea hydrodynamic environment

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cui Wang ◽  
Ling Cai ◽  
Yaojian Wu ◽  
Yurong Ouyang
Keyword(s):  
Water Exchange ◽  
Land Reclamation ◽  
Three Dimensional ◽  
Exchange Capacity ◽  
Reclamation Project ◽  
Hydrodynamic Environment ◽  
Sea Area ◽  
Water Quality Models ◽  
The Impact ◽  
Main Factor

AbstractIntegrated renovation projects are important for marine ecological environment protection. Three-dimensional hydrodynamics and water quality models are developed for the Maowei Sea to assess the hydrodynamic environment base on the MIKE3 software with high resolution meshes. The results showed that the flow velocity changed minimally after the project, decreasing by approximately 0.12 m/s in the east of the Maowei Sea area and increasing by approximately 0.01 m/s in the northeast of the Shajing Port. The decrease in tidal prism (~ 2.66 × 106 m3) was attributed to land reclamation, and accounted for just 0.86% of the pre-project level. The water exchange half-life increased by approximately 1 day, implying a slightly reduced water exchange capacity. Siltation occurred mainly in the reclamation and dredging areas, amounting to back-silting of approximately 2 cm/year. Reclamation project is the main factor causing the decrease of tidal volume and weakening the hydrodynamics in Maowei Sea. Adaptive management is necessary for such a comprehensive regulation project. According to the result, we suggest that reclamation works should strictly prohibit and dredging schemes should optimize in the subsequent regulation works.

Novel thermally activated delayed fluorescence materials by high-throughput virtual screening: going beyond donor–acceptor design

2021 ◽  
Vol 9 (9) ◽  
pp. 3324-3333 ◽  
Author(s):  
Ke Zhao ◽  
Ömer H. Omar ◽  
Tahereh Nematiaram ◽  
Daniele Padula ◽  
Alessandro Troisi
Keyword(s):  
Virtual Screening ◽  
Quantum Chemistry ◽  
High Throughput ◽  
Delayed Fluorescence ◽  
Thermally Activated Delayed Fluorescence ◽  
Thermally Activated ◽  
Quantum Chemistry Calculations ◽  
Donor Acceptor ◽  
Molecular Semiconductors ◽  
High Throughput Virtual Screening

125 potential TADF candidates are identified through quantum chemistry calculations of 700 molecules derived from a database of 40 000 molecular semiconductors. Most of them are new and some do not belong to the class of donor–acceptor molecules.

scholarly journals Deciphering the Role of Residues Involved in Disorder-To-Order Transition Regions in Archaeal tRNA Methyltransferase 5

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 399
Author(s):  
Ambuj Srivastava ◽  
Dhanusha Yesudhas ◽  
Shandar Ahmad ◽  
M. Michael Gromiha
Keyword(s):  
Three Dimensional ◽  
Md Simulations ◽  
Order Transition ◽  
Free Form ◽  
Wild Type ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Type Complex ◽  
In The Wild ◽  
Trna Methyltransferase

tRNA methyltransferase 5 (Trm5) enzyme is an S-adenosyl methionine (AdoMet)-dependent methyltransferase which methylates the G37 nucleotide at the N1 atom of the tRNA. The free form of Trm5 enzyme has three intrinsically disordered regions, which are highly flexible and lack stable three-dimensional structures. These regions gain ordered structures upon the complex formation with tRNA, also called disorder-to-order transition (DOT) regions. In this study, we performed molecular dynamics (MD) simulations of archaeal Trm5 in free and complex forms and observed that the DOT residues are highly flexible in free proteins and become stable in complex structures. The energetic contributions show that DOT residues are important for stabilising the complex. The DOT1 and DOT2 are mainly observed to be important for stabilising the complex, while DOT3 is present near the active site to coordinate the interactions between methyl-donating ligands and G37 nucleotides. In addition, mutational studies on the Trm5 complex showed that the wild type is more stable than the G37A tRNA mutant complex. The loss of productive interactions upon G37A mutation drives the AdoMet ligand away from the 37th nucleotide, and Arg145 in DOT3 plays a crucial role in stabilising the ligand, as well as the G37 nucleotide, in the wild-type complex. Further, the overall energetic contribution calculated using MMPBSA corroborates that the wild-type complex has a better affinity between Trm5 and tRNA. Overall, our study reveals that targeting DOT regions for binding could improve the inhibition of Trm5.

scholarly journals Adsorption and Desorption Mechanisms of Rare Earth Elements (REEs) by Layered Double Hydroxide (LDH) Modified with Chelating Agents

2019 ◽  
Vol 9 (22) ◽  
pp. 4805 ◽  
Author(s):  
Shuang Zhang ◽  
Naoki Kano ◽  
Kenji Mishima ◽  
Hirokazu Okawa
Keyword(s):  
Rare Earth ◽  
Quantum Chemistry ◽  
Rare Earth Elements ◽  
Adsorption Capacity ◽  
Density Functional ◽  
Stable State ◽  
Experimental Result ◽  
Adsorption And Desorption ◽  
Adsorption Affinity ◽  
Quantum Chemistry Calculations

In order to obtain the adsorption mechanism and adsorption structures of Rare Earth Elements (REEs) ions adsorbed onto layered double hydroxides (LDH), the adsorption performance of LDH and ethylenediaminetetraacetic acid (EDTA) intercalated LDH for REEs was investigated by batch experiments and regeneration studies. In addition to adsorption capacity, the partition coefficient (PC) was also evaluated to assess their true performance metrics. The adsorption capacity of LDH increases from 24.9 μg·g−1 to 145 μg·g−1 for Eu, and from 20.8 μg·g−1 to 124 μg·g−1 for La by intercalating EDTA in this work; and PC increases from 45.5 μg·g−1·uM−1 to 834 μg·g−1·uM−1 for Eu, and from 33.6 μg·g−1·μM−1 to 405 μg·g−1·μM−1 for La. Comparison of the data indicates that the adsorption affinity of EDTA-intercalated LDH is better than that of precursor LDH no matter whether the concept of adsorption capacity or that of the PC was used. The prepared adsorbent was characterized by XRD, SEM-EDS and FT-IR techniques. Moreover, quantum chemistry calculations were also performed using the GAUSSIAN09 program package. In this calculation, the molecular locally stable state structures were optimized by density functional theory (DFT). Both the quantum chemistry calculations and the experimental data showed that REEs ions adsorbed by EDTA-intercalated LDH are more stable than those adsorbed by precursor LDH. Furthermore, the calculation results of adsorption and desorption rates show that adsorption rates are larger for Eu(III) than for La(III), which agrees with the experimental result that Eu(III) has a higher adsorption ability under the same conditions. The LDHs synthesized in this work have a high affinity for removing REEs ions.

scholarly journals Porous Characteristics of Three-Dimensional Disordered Graphene Networks

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 127
Author(s):  
YongChao Wang ◽  
YinBo Zhu ◽  
HengAn Wu
Keyword(s):  
Pore Size ◽  
Low Temperatures ◽  
Gas Adsorption ◽  
Three Dimensional ◽  
Md Simulations ◽  
Structural Features ◽  
Atomic Scale ◽  
Critical Factors ◽  
Chlorination Process ◽  
Porous Morphology

The porous characteristics of disordered carbons are critical factors to their performance on hydrogen storage and electrochemical capacitors. Even though the porous information can be estimated indirectly by gas adsorption experiments, it is still hard to directly characterize the porous morphology considering the complex 3D connectivity. To this end, we construct full-atom disordered graphene networks (DGNs) by mimicking the chlorination process of carbide-derived carbons using annealing-MD simulations, which could model the structure of disordered carbons at the atomic scale. The porous characteristics, including pore volume, pore size distribution (PSD), and specific surface area (SSA), were then computed from the coordinates of carbon atoms. From the evolution of structural features, pores grow dramatically during the formation of polyaromatic fragments and sequent disordered framework. Then structure is further graphitized while the PSD shows little change. For the obtained DGNs, the porosity, pore size, and SSA increase with decreasing density. Furthermore, SSA tends to saturate in the low-density range. The DGNs annealed at low temperatures exhibit larger SSA than high-temperature DGNs because of the abundant free edges.

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