Yan liu¹, Chuanlong Xu¹, Xiaobao Tian¹, Wentao Jiang¹, Qingyuan Wang¹, Haidong Fan^1,*

The International Conference on Computational & Experimental Engineering and Sciences, Vol.25, No.2, pp. 1-1, 2023, DOI:10.32604/icces.2023.09982

Abstract Zirconium alloys were widely used as fuel cladding in nuclear reactors. Stacking fault pyramid (SFP) is an irradiation-induced defect in zirconium. In this work, the formation process of SFP from a hexagonal vacancy plate on basal plane is studied by molecular dynamics (MD) simulations. The results show that, during the SFP formation from a basal vacancy plate, the dislocation is firstly dissociated into two partial dislocations and . The former one resides on the basal plane, while the latter one glides on the first-order pyramidal plane. The … More >

Zikun Li¹, Jing Tang¹, Xiaobao Tian¹, Qingyuan Wang¹, Wentao Jiang¹, Haidong Fan^1,*

The International Conference on Computational & Experimental Engineering and Sciences, Vol.25, No.2, pp. 1-1, 2023, DOI:10.32604/icces.2023.09968

Abstract Magnesium is a lightweight structural metal but the industrial application is limited by its poor intrinsic ductility. Pyramidal dislocations are believed to be responsible for the ductility enhancement whereas the dislocation plasticity of magnesium was not well studied, especially the pyramidal dislocations. In this work, molecular dynamics simulations were performed to investigate the pyramidal disloation behaviors including the decomposition of pyramidal dislocations on both pyramidal-I and pyramidal-II planes and the interactions between themselves and other dislocations in Mg. The pyramidal-I dislocations are decomposed into and dislocations under shear stress at 0-400K, which all reside… More >

MOHAMAD ZULKEFLEE SABRI¹, JOANNA BOJARSKA², FAI-CHU WONG^3,4, TSUN-THAI CHAI^3,4,*

BIOCELL, Vol.47, No.8, pp. 1727-1742, 2023, DOI:10.32604/biocell.2023.029272 - 28 August 2023

Abstract Molecular dynamics (MD) simulation is a computational technique that analyzes the movement of a system of particles over a given period. MD can provide detailed information about the fluctuations and conformational changes of biomolecules at the atomic level over time. In recent years, MD has been widely applied to the discovery of peptides and peptide-like molecules that may serve as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibitors. This review summarizes recent advances in such explorations, focusing on four protein targets: angiotensin-converting enzyme 2 (ACE2), spike protein (S protein), main protease (M^pro), and papain-like protease (PL^pro).… More > Graphic Abstract

Hengjiao Gao¹, Yuqing Xiong^1,*, Kaifeng Zhang¹, Shengzhu Cao¹, Mingtai Hu¹, Yi Li¹, Ping Zhang², Xiaoli Liu³

Journal of Renewable Materials, Vol.11, No.4, pp. 1715-1729, 2023, DOI:10.32604/jrm.2022.024023 - 01 December 2022

Abstract The interface properties of Fe(101)/zinc silicate modified by organo-siloxane (KH-570) was studied by using the method of molecular dynamics simulation. By calculating the temperature and energy fluctuation of equilibrium state, equilibrium concentration distribution, MSD of layer and different groups, and interaction energy of two interface models, the influencing mechanism on the interface properties of adding organosiloxane into coating system was studied at the atomic scale. It shows that the temperature and energy of interface oscillated in a small range and it was exited in a state of dynamic equilibrium within the initial simulation stage (t More > Graphic Abstract

DIEGO MASONE^1,2,*

BIOCELL, Vol.47, No.1, pp. 1-14, 2023, DOI:10.32604/biocell.2023.024146 - 26 September 2022

Abstract The inflexible concept of membrane curvature as an independent property of lipid structures is today obsolete. Lipid bilayers behave as many-body entities with emergent properties that depend on their interactions with the environment. In particular, proteins exert crucial actions on lipid molecules that ultimately condition the collective properties of the membranes. In this review, the potential of enhanced molecular dynamics to address cell-biology problems is discussed. The cases of membrane deformation, membrane fusion, and the fusion pore are analyzed from the perspective of the dimensionality reduction by collective variables. Coupled lipid-protein interactions as fundamental determinants More >

Pravej Alam^*, Thamer H. Al balawi

Phyton-International Journal of Experimental Botany, Vol.91, No.9, pp. 1923-1931, 2022, DOI:10.32604/phyton.2022.021334 - 13 May 2022

Abstract Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most damaging diseases to rice across the world. Various chemicals have been employed so far for the management of bacterial leaf blight. On the other hand, these compounds are damaging to the ecosystem and have an impact on non-target species such as humans and animals. As a result, there is a need to create a new natural inhibitor for BLB management. Deformylase (PDF) enzyme is present in all eubacteria and its necessity in bacterial protein synthesis reveals it as an attractive target… More >

Xiaoxia Liu^1,2,*

CMES-Computer Modeling in Engineering & Sciences, Vol.131, No.2, pp. 919-927, 2022, DOI:10.32604/cmes.2022.017756 - 14 March 2022

Abstract Magnesium (Mg) and its composites have been widely used in different fields, but the mechanical properties and deformation mechanisms of polycrystalline Mg (polyMg) at the atomic scale are poorly understood. In this paper, the effects of grain size, temperature, and strain rate on the tensile properties of polyMg are explored and discussed by the Molecular dynamics (MD) simulation method. The calculated results showed that there exists a critical grain size of 10 nm for the mechanical properties of polyMg. The flow stress decreases with the increase of grain size if the average grain size is… More >

Nada M. Mostafa^1,5,#, Muhammad I. Ismail^2,#, Amr M. El-Araby³, Dina M. Bahgat¹, Ahmed M. Elissawy^1,5, Ahmed M. Mostafa⁴, Omayma A. Eldahshan^1,5,*, Abdel Nasser B. Singab^1,5,*

Phyton-International Journal of Experimental Botany, Vol.91, No.5, pp. 1089-1104, 2022, DOI:10.32604/phyton.2022.018239 - 24 January 2022

Abstract Coronaviruses caused an outbreak pandemic disease characterized by a severe acute respiratory distress syndrome leading to the infection of more than 200 million patients and the death of more than 4 million individuals. The primary treatment is either supportive or symptomatic. Natural products have an important role in the development of various drugs. Thus, screening of natural compounds with reported antiviral activities can lead to the discovery of potential inhibitory entities against coronaviruses. In the current study, an in-silico molecular docking experiment was conducted on the effects of some of these natural antiviral phytoconstituents, (e.g.,… More >

Reza Khademi Zahedi¹, Naif Alajlan², Hooman Khademi Zahedi³, Timon Rabczuk^2,*

CMC-Computers, Materials & Continua, Vol.70, No.3, pp. 4635-4655, 2022, DOI:10.32604/cmc.2022.017682 - 11 October 2021

Abstract The outstanding thermal, optical, electrical and mechanical properties of molybdenum disolphide (MoS₂) heterostructures make them exceptional candidates for an extensive area of applications. Nevertheless, despite considerable technological and academic interest, there is presently a few information regarding the mechanical properties of these novel two-dimensional (2D) materials in the presence of the defects. In this manuscript, we performed extensive molecular dynamics simulations on pre-cracked and pre-notched all-molybdenum disolphide (MoS₂) heterostructure systems using ReaxFF force field. Therefore, we study the influence of several central-crack lengths and notch diameters on the mechanical response of 2H phase, 1T phase and… More >

Yun Wang¹, Tiantian Wang², Bei Wang¹, Wei Chang³, Jiangli Cao¹, Lihua Hu³, Minxu Lu¹, Lei Zhang^1,*

Journal of Renewable Materials, Vol.10, No.2, pp. 301-327, 2022, DOI:10.32604/jrm.2021.015518 - 30 August 2021

Abstract A novel and effective water-soluble aldehydes (β-HA) as corrosion inhibitor was synthesized for N80 steel corrosion in 15% HCl solution, and the corrosion inhibition performance was evaluated by using weight loss, electrochemical measurements, scanning electron microscope (SEM), quantum chemical calculation and molecular dynamics simulation (MDS). The results show that synthesized β-HA showed excellent corrosion performance compared with MHB and PE for carbon steel in 15% HCl solution compared with MHB and PE, and the inhibition efficiency increased with increasing concentration of the inhibitor. The inhibition efficiency of β-HA at 8 mmol/L reached the maximum value 94.08%. The More >