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Modelling infrared spectra of the O-H stretches in liquid H2O based on a deep learning potential, the importance of nuclear quantum effects Mol. Simulat. (IF 2.1) Pub Date : 2024-03-14 Dongyao Li, Dan Zhao, Yao Huang, Hujun Shen, Mingsen Deng
In this study, we have trained a deep learning (DL) potential for water using training datasets obtained from the DPLibrary (https://dplibrary.deepmd.net/). Subsequently, we conducted classical mol...
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In-silico design novel phenylsulfonyl furoxan and phenstatin derivatives as multi-target anti-cancer inhibitors based on 2D-QSAR, molecular docking, dynamics and ADMET approaches Mol. Simulat. (IF 2.1) Pub Date : 2024-03-13 Abdelmadjid Guendouzi, Lotfi Belkhiri, Farah Djelti, Zineddine Mohamed Zendaoui, Houari Brahim, Abdelkrim Guendouzi, Abdelhamid Djekoun, Abdou Boucekkine
A series of 31 hybrid of phenylsulfonyl furoxan and phenstatin (1a-j, 2a-j, 3a-j, 4 and 5) derivatives, were computationally studied as potential anti-cancer inhibitors against four cell lines, i.e...
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The identification of the generalised Maxwell fluid for n-hexadecane liquids via non-equilibrium molecular dynamics simulations Mol. Simulat. (IF 2.1) Pub Date : 2024-03-06 Huan-Chang Tseng
Linear viscoelasticity is very important for chain-molecular fluids. The generalised Maxwell constitutive equation is classical in which the linear viscoelastic fluids consist of a series of spring...
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Effects of waste wood oil content on thermodynamic and structural properties of bio-asphalt and interactions between components: a molecular dynamic simulation study Mol. Simulat. (IF 2.1) Pub Date : 2024-03-05 Zhi Zheng, Naisheng Guo, Yiqiu Tan, Zhanping You
This study fully intends to elucidate the mechanism of waste wood oil (WWO) modifier content on the microscopic action of bio-asphalt by utilising molecular dynamics simulations. Molecular models o...
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Monte Carlo study of magnetic behaviour of single Fe and Ni nanoparticles Mol. Simulat. (IF 2.1) Pub Date : 2024-03-02 Nasim Yousefpour Novini, Şahin Uyaver, S.H. Reza Shojaei, Kazem Jamshidi-Galeh, Tavakkol Tohidi
The exchange integral in the magnetic response of a spherical metallic iron (Fe) and nickel (Ni) nanoparticle is theoretically studied by using Monte Carlo simulations. To this end, using the nanop...
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Targeting MurB from Helicobacter pylori: insights from virtual screening, molecular docking and molecular dynamics simulation Mol. Simulat. (IF 2.1) Pub Date : 2024-02-28 Abhishek Sharma, Amit Kumar Singh, Jayaraman Muthukumaran, Monika Jain
Helicobacter pylori is a gram-negative, helical-shaped bacteria found in the mucus lining of the stomach of humans responsible for causing sores or an ulcer. H. pylori is becoming a multi-drug resi...
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Mutant anaplastic lymphoma kinase inhibitor identification by integrated in silico approaches Mol. Simulat. (IF 2.1) Pub Date : 2024-02-17 Nadeem Ahmad, Salman Ali Khan, Madiha Sardar, Mamona Mushtaq, Ali Raza Siddiqui, Sajida Munsif, Mohammad Nur-e-Alam, Dmitry Nerukh, Zaheer Ul-Haq
Non-small-cell lung cancer (NSCLC) is the primary form of lung cancer globally and remains a leading cause of mortality. Anaplastic lymphoma kinase (ALK) mutations, such as I1171N + L1198H, have be...
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Effects of fused thiophene Π-bridge on the electronic and optical properties of modified theaflavin natural dye Mol. Simulat. (IF 2.1) Pub Date : 2024-02-17 Syafri, Faozan Ahmad, Aditya Wibawa Sakti, Permono A. Putro, Alvius Tinambunan, Husin Alatas
Natural dye sensitizers are substances that are sensitive to light colour and can be classified into several classes based on their chemical structure. Theaflavin pigments are unexplored natural dy...
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A comparative Monte Carlo simulation of HDPE synthesis with bimodal molecular weight distribution: evaluating slurry and solution processes using dual-site metallocene catalyst Mol. Simulat. (IF 2.1) Pub Date : 2024-02-15 Ramin Bairami Habashi, Mohammad Najafi, Reza Zarghami
This research employed Monte Carlo simulation as a computational technique to investigate the copolymerization of ethylene and 1-butene in the presence of hydrogen, utilizing slurry and solution pr...
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Influence of metal oxides on circumcorannulene for the design of new push-pull corannulene models: applications in nano-electronics, optoelectronics and non-linear optics Mol. Simulat. (IF 2.1) Pub Date : 2024-02-15 Barnabas Aloumko, Crevain Souop Tala Foadin, Sali Mohammadou, Fridolin Tchangnwa Nya, Geh Wilson Ejuh
The search for new high-performance push-pull materials for use in nonlinear optics (NLO) and optics is currently a popular area of research. In this study, the effects of metal oxides -(MO)n = 1,2...
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Carbon structural evolution and interfacial reaction mechanism investigation of the green anode in kneading and baking via ReaxFF-MD and force-biased Monte Carlo Mol. Simulat. (IF 2.1) Pub Date : 2024-02-15 Xiaoshuang Gan, Zhen Yao, Zihan You, Shangyuan Wu, Ye Wan, Qifan Zhong
Baking is the most costly and critical process in anode preparation, and the study from the microscopic scale is conducive to the optimisation of anode baking process. In this research, a hybrid si...
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Photomodulated phase-separation kinetics in block copolymer melts: a DPD simulation study Mol. Simulat. (IF 2.1) Pub Date : 2024-02-14 Avinash Chauhan, Ashish Kumar Singh, Awaneesh Singh
We study phase-separation kinetics of symmetric diblock copolymer (BCP) melt in 3d subjected to sequential light on/off cycles. The incompatible blocks of each BCP chain are connected by a photosen...
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Comparison of the effect of fluorinated aliphatic and aromatic amino acids on stability at a solvent-exposed position of a globular protein Mol. Simulat. (IF 2.1) Pub Date : 2024-02-10 Kyung-Hoon Lee, Krzysztof Kuczera
Rational protein engineering has often focused on increasing the thermal stability of proteins by incorporating stabilising mutations. Introducing fluorinated amino acids into proteins has been use...
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Quantum mechanical analysis of halogen-based ionic liquid crystal [C12MIM.X(where X = Cl, Br)] molecules Mol. Simulat. (IF 2.1) Pub Date : 2024-01-31 Varsha Gautam, Shivani Chaudhary, Jitendra Kumar, Devendra Singh, Devesh Kumar
The electrical and non-linear optical characteristics of 1-dodecyl 3-methyl-imidazolium chloride (C12MIM.Cl or DDMIM.Cl) and 1-dodecyl 3-methyl-imidazolium bromide (C12MIM.Br or DDMIM.Br) ionic liq...
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Cerebroprotective effects of khellin: validation through computational studies in a bilateral common carotid artery occlusion/reperfusion (BCCAO/R) model Mol. Simulat. (IF 2.1) Pub Date : 2024-01-25 Chakravarthi Guntupalli, Mounica Ponugoti, D. S. N. B. K. Prasanth, Narender Malothu
This study investigates the molecular interactions between khellin and nitric oxide synthase, which plays a significant role in the pathophysiology of acute ischemic stroke. Molecular docking, dyna...
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Pharmacophore-based computational study on inhibitor of TMPRSS6 as hepcidin modulator in an iron overload of beta-thalassaemia Mol. Simulat. (IF 2.1) Pub Date : 2024-01-17 Piyush Kumar Yadav, Suchitra Singh, Ajay Kumar Singh
TMPRSS6 (transmembrane protease, serine 6) plays an important role in the cleavage of hemojuvelin (HJV), a key protein involved in the regulation of hepcidin metabolism. TMPRSS6 cleaves HJV at spec...
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DFT study of sucrose hydrolysis by a GH32 cell-wall invertase, a key enzyme in carbohydrate metabolism Mol. Simulat. (IF 2.1) Pub Date : 2024-01-09 Wijitra Meelua, Jitrayut Jitonnom
The Arabidopsis thaliana cell-wall invertase 1 (AtCWIN1), a member of the family 32 glycoside hydrolase (GH32), hydrolyzes sucrose into fructose and glucose via a retaining mechanism. AtCWIN1 plays...
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Insights into role of synergistic interplay among collagen type I, collagen type II, and water on the structure and nanomechanics of collagen fibrils in annulus fibrosus: a molecular dynamics study Mol. Simulat. (IF 2.1) Pub Date : 2024-01-09 Shambo Bhattacharya, Devendra K. Dubey
Annulus Fibrosus’s (AF) multi-directional load-bearing ability manifests from Nature’s design wherein type I collagen (COL-I) dominates outer AF and type II collagen (COL-II) dominates inner AF wit...
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Molecular dynamic approach in the regulation of systemic XCT antiporter through biologically active molecules for ischemic stroke Mol. Simulat. (IF 2.1) Pub Date : 2024-01-05 Namrata Sangwan, Jitender Singh, Arushi Chauhan, Krishan L. Khanduja, Pramod K. Avti
The heterodimeric amino acid transporter systemic XCT plays a crucial role in redox balance regulation by facilitating L-cystine and L-glutamate import/export in a 1:1 ratio. Translating findings f...
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Thermodynamic properties of fluids with Mie n − m potentials and application to tune effective Mie potentials for simple real fluids Mol. Simulat. (IF 2.1) Pub Date : 2024-01-03 B. P. Akhouri, R. Perween, J. R. Solana
Monte Carlo computer simulations have been performed to obtain the equation of state and internal energy of fluids with Mie n − m potentials, with m = 6 and n = 9, 12 and 15, for different supercri...
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Self-assembly of macrocyclic oligofurans to create novel organic nanotubes through π–π stacking: a computational study Mol. Simulat. (IF 2.1) Pub Date : 2024-01-03 Hamid Reza Masoodi, Sotoodeh Bagheri, Masoud Rohani Moghadam
In this manuscript, the potential utility of 6CF macrocyclic oligofuran is theoretically investigated to create novel nanotubes. The energetic, electronic, structural and topological properties of ...
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Effect of kinetic properties of zeolites on the gas-sensing performance of zeolite-covered SnO2 sensors Mol. Simulat. (IF 2.1) Pub Date : 2024-01-03 Yanhui Sun, Tengyue Hou, Shupeng Sun, Shouhang Fu, Xue Wang
Zeolite additional layers coating on metal oxide surfaces to improve the selectivity and response values of the sensors are effective and widely used. The specific adsorption and diffusion of gas m...
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Molecular dynamics simulation studies on uptake of fipronil sulfone by gut microbiome and its influence on risk for cause of Parkinson’s disease Mol. Simulat. (IF 2.1) Pub Date : 2024-01-03 Abhay Bhat, Anushree M, Vivek Chandramohan, Sasmita Sabat
Biotransformation of Fipronil forms three metabolites: fipronil sulfone, fipronil sulfide and fipronil desulfinyl. Among the triad of metabolites, fipronil sulfone exhibits quantitatively predomina...
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ReaxFF study of the decarboxylation of methyl palmitate over binary metallic nickel-molybdenum catalysts Mol. Simulat. (IF 2.1) Pub Date : 2024-01-03 Maipelo Nyepetsi, Olayinka A. Oyetunji, Foster Mbaiwa
Biodiesel has emerged as a possible replacement for fossil-based fuels, particularly in the transportation industry. Because of its high oxygen content, it has several limitations including high vi...
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Statement of Retraction: Ir-decorated gallium nitride nanotubes as a chemical sensor for recognition of mesalamine drug: a DFT study Mol. Simulat. (IF 2.1) Pub Date : 2023-12-20
Published in Molecular Simulation (Vol. 50, No. 2, 2024)
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Effects of lattice orientation and defect degree on Si/Al solid interfacial structure and thermal resistance Mol. Simulat. (IF 2.1) Pub Date : 2023-12-20 Liying Wang, Jiansheng Wang, Xueling Liu, Xinli Lu
The effect of variation in the Si/Al interface structure on the thermal properties is explored with non-equilibrium molecular dynamics method in present work, and two distinct approaches are employ...
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Computational and in vitro targeting of HUVECs by ARA-Linker-TGFαL3 through VEGFR2 Mol. Simulat. (IF 2.1) Pub Date : 2023-12-20 Abdolamir Ghadaksaz, Abbas Ali Imani Fooladi, Hamideh Mahmoodzadeh Hosseini, Mohsen Amin, Fatemeh Adami Ghamsari
Angiogenesis blockade represents a therapeutic strategy to inhibit the growth of the tumour and its progression and metastasis. Targeting the vascular endothelial growth factor receptor 2 (VEGFR2) ...
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A molecular dynamic simulation-based study on nanoscale friction stir welding between copper and aluminium Mol. Simulat. (IF 2.1) Pub Date : 2023-12-20 Roshan Kumar Jha, K. Vijay Reddy, Snehanshu Pal
The primary aim of this study is to enhance our understanding of friction stir welding (FSW) at the atomic level. To accomplish this, we utilised molecular dynamics simulations to examine the nanos...
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Hydrogen embrittlement of iron nanowires: investigating size and orientation dependence on loading behaviour Mol. Simulat. (IF 2.1) Pub Date : 2023-12-20 Liam S. Morrissey
With the ever-increasing use and applications of nanowires it has never been more imperative to understand how environmental interactions modify their unique mechanical properties and loading behav...
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Molecular dynamics study on friction of polymer material polyamide 6 (PA 6) Mol. Simulat. (IF 2.1) Pub Date : 2023-12-20 Xinmin Li, Zhengjie Qiu, Yonglong Wu, Feilong Li, Runzhi Zhang
The resin material PA6 has a wide range of application in engineering due to its excellent mechanical properties. The friction behaviour of PA 6 was studied using molecular dynamics simulation meth...
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Simulations of the thermodynamic properties of the helium fluid from the state-of-the-art ab initio potentials and their uncertainty estimation Mol. Simulat. (IF 2.1) Pub Date : 2023-12-20 Pan Xu, Qing-Yao Luo, Bo Dong, Bo Song
The molecular dynamics simulation method is used to study the internal energy, pressure, isochoric heat capacity, and sound speed of helium based on the state-of-the-art ab initio potentials. The s...
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DFT Study of adsorption and diffusion of CO2 on bimetallic surfaces Mol. Simulat. (IF 2.1) Pub Date : 2023-12-20 Hamideh Khodabandeh, Ali Nakhaei Pour, Ali Mohammadi
In this work, adsorption and diffusion of CO2 on the Cu (111) surface, and Cu (111) surface modified by tungsten (W) and platinum (Pt) were studied and their electronic properties were examined usi...
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Monte Carlo dynamics simulation of nanoparticles for enhanced oil recovery Mol. Simulat. (IF 2.1) Pub Date : 2023-12-19 Afeez Oluwatobi Yusuff, Beh Hoe Guan, Surajudeen Sikiru, Saba Ayub, Fatai Adisa Wahaab, Mudassir Hassan Yarima, Ahmed Abdullah Almalki
This research used density functional theory (DFT)-based simulation software to investigate the potential of emerging nanotechnology to alter the physical–chemical interactions of a reservoir syste...
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Assessing the structural dynamics of the glucose-6-phosphate dehydrogenase dimer interface using molecular dynamics simulation and ligand screening using computer aided drug discovery Mol. Simulat. (IF 2.1) Pub Date : 2023-12-11 Naveen Eugene Louis, Muaawia Ahmed Hamza, Puteri Nur Sarah Diana Engku Baharuddin, Shamini Chandran, Nurriza Ab Latif, Mona Awad Alonazi, Joazaizulfazli Jamalis, Arjumand Warsy, Syazwani Itri Amran
Glucose-6-phosphate-dehydrogenase deficiency is the most common enzymopathy. Current therapies for G6PD deficiency are unable to treat a broad range of pathogenic variants. In this study, we assess...
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Effect of methanol on the pyrolysis behaviour of kerogen by ReaxFF molecular dynamics simulations Mol. Simulat. (IF 2.1) Pub Date : 2023-12-11 Mingyue Yu, Jin-Hui Zhan, Xiang Li, Wen He, Xiaoxing Liu
A series of molecular dynamics simulations were performed using the ReaxFF reactive force field to investigate the pyrolysis of Longkou oil shale kerogen in the presence of methanol. The roles of m...
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Effects of attractive inter-particle interaction on cross-transport coefficient between mass and heat in binary fluids Mol. Simulat. (IF 2.1) Pub Date : 2023-12-11 Tatsuma Oishi, Yuya Doi, Yuichi Masubuchi, Takashi Uneyama
In some binary fluids, mass transport is observed under a temperature gradient. This phenomenon is called the Soret effect. In this study, we discuss the influence of inter-particle interaction. We...
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Molecular dynamics and integral equation study of the structure and dynamics of solid and liquid magnesium phosphide Mol. Simulat. (IF 2.1) Pub Date : 2023-12-11 Yenal Aydın, Seçkin D. Günay, Ünsal Akdere, Çetin Taşseven
The static structure and self-ionic transport in solid and molten magnesium phosphide (Mg3P2) are investigated by means of the molecular dynamics simulation and the hypernetted-chain theory of liqu...
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Molecular dynamics investigation of the interaction between volatile organic compounds and deep eutectic solvents Mol. Simulat. (IF 2.1) Pub Date : 2023-12-11 Deepak Kumar Panda, B. L. Bhargava
Mixtures of tetrabutylammonium-chloride-based deep eutectic solvent (DES) and three volatile organic compounds (VOCs) – butanal, ethanol, and toluene – have been investigated using classical molecu...
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Rapid screening of gas solubility in ionic liquids using biased particle insertions with pre-sampled liquid trajectories Mol. Simulat. (IF 2.1) Pub Date : 2023-12-11 Ryan W. Smith, Edward J. Maginn
We present an efficient, general-purpose variant of the Widom test particle insertion method for computing chemical potentials of gaseous solutes in fluids or porous solids. The method is implement...
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Lasioglossin-1 peptide inhibits binding of spike protein of SARS-CoV-2 to ACE2 receptor: an in silico approach of some bee venom peptides Mol. Simulat. (IF 2.1) Pub Date : 2023-11-30 Karim Mahnam, Mahtab Zarean, Zahra Ghobadi
The coronavirus prevalent, initiated by the SARS-CoV-2 virus, has induced a global health crisis, recently. Coronavirus can bind to ACE2 receptors on the surface of human cells and infect them thro...
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pH-Dependent conformational stability of SpeB from Thermus thermophilus HB8: insights from molecular dynamics simulation Mol. Simulat. (IF 2.1) Pub Date : 2023-11-20 Malaisamy Veerapandian, Nagarajan Hemavathy, Alagesan Karthika, Jayaraman Manikandan, Umashankar Vetrivel, Jeyaraman Jeyakanthan
N(1)-aminopropyl agmatine ureohydrolase (SpeB) is considered an essential enzyme for the growth and survival of thermophiles, it is involved in the biosynthesis of polyamines. The present study inv...
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Proposed modification to a muscle-like acid-base switchable [2](2)rotaxane for improved force delivery Mol. Simulat. (IF 2.1) Pub Date : 2023-10-27 Tina T. Dinh, Gloria Bazargan, Karl Sohlberg
Switchable rotaxanes are good candidates for molecular machines because of their ability to undergo reversible and repeatable co-conformational isomerism in response to an external stimulus. An aci...
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Effect of sliding velocity on the nanoscale friction behaviour of articular cartilage contact interface: insights from all-atom molecular dynamics investigation Mol. Simulat. (IF 2.1) Pub Date : 2023-10-22 Abhinava Chatterjee, Sujeet K. Sinha, Devendra K. Dubey
This study employs molecular dynamics simulations to explore nanoscale friction behaviour as a function of varying loading and sliding speeds on a developed top-layer articular cartilage contact in...
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Effect of twin boundary spacing on the mechanical properties of nano-columnar crystalline Cu-Ni alloy Mol. Simulat. (IF 2.1) Pub Date : 2023-10-22 Xuefeng Lu, Xu Yang, Wei Zhang, Xin Guo, Junqiang Ren, Hongtao Xue, Junchen Li, Fu Ling Tang
Nanotwinned exist in crystals as coherent interfaces with low interfacial energy, which can not only improve the strength of metal materials, but also increase the ductility. In this manuscript, we...
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Modulation of ion transport through nanopores in water desalination: a molecular dynamics study Mol. Simulat. (IF 2.1) Pub Date : 2023-10-22 Lanlan Qin, Haiou Huang, Jian Zhou
A good understanding of ion transport mechanisms through nanopores is an important issue for the development of advanced water desalination technologies. We use the molecular dynamics simulation me...
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Probing the mechanical and deformation behaviour of CNT-reinforced AlCoCrFeNi high-entropy alloy – a molecular dynamics approach Mol. Simulat. (IF 2.1) Pub Date : 2023-10-22 Subrata Barman, Sudip Dey
This present study investigates the mechanical and deformation behaviour of pristine and carbon nanotube (CNT)-reinforced AlCoCrFeNi high-entropy alloys (HEAs) using molecular dynamics (MD) simulat...
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Molecular dynamic simulations of deformation behaviour of blended polyethylene Mol. Simulat. (IF 2.1) Pub Date : 2023-10-22 Jingfu Shi, Jia Zhou, Lei Liu, Wenxiang Liu, Changqing Miao
The tensile deformation behaviour of blended polyethylene (PE) was studied using molecular dynamic methods. The blended PE was modeled by blending linear chains with different molecular weights bas...
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Size effects on dislocation starvation in Cu nanopillars: a molecular dynamic simulations study Mol. Simulat. (IF 2.1) Pub Date : 2023-10-22 G. Sainath, Vani Shankar, A. Nagesha
Size plays an important role on the deformation mechanism of nanopillars. With decreasing size, many FCC nanopillars exhibit dislocation starvation which is responsible for their high strength. How...
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Host–guest interactions of Crizotinib with natural and modified cyclodextrins: a combined molecular docking and molecular dynamics simulation approaches Mol. Simulat. (IF 2.1) Pub Date : 2023-10-22 Elham Mohebbi, Leila Hokmabady, Fatemeh Ravari
In this work, molecular docking and molecular dynamics (MD) simulation were applied to investigate the ability of natural cyclodextrins (CDs; Alpha, Beta and Gamma Cyclodextrins) and modified CDs (...
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Molecular insights into the corrosion inhibition mechanism of omeprazole and tinidazole: a theoretical investigation Mol. Simulat. (IF 2.1) Pub Date : 2023-09-30 Savaş Kaya, Hassane Lgaz, Abhinay Thakkur, Ashish Kumar, Dilara Özbakır Işın, Nihat Karakuş, Samia Ben Ahmed
In many studies published in recent years, corrosion scientists proved that various drug molecules can exhibit high inhibition performance against the corrosion of metal surfaces and alloys. This s...
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Exploration of anti-tumour inhibitors from colchicine derivatives based on 3D-QSAR, molecular docking and molecular dynamics simulations Mol. Simulat. (IF 2.1) Pub Date : 2023-09-30 Jian-Bo Tong, Yuan Liu, Xue-chun Xiao, Peng Gao, Hai-yin Xu
Microtubulin is an important research target for anti-tumour drugs, which can be used to inhibit microtubulin polymerisation and improve the efficacy of tumour therapy. In this paper, 61 microtubul...
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In-silico and in-vitro identification of triazole based compounds as potential EGFR inhibitors targeting lung cancer Mol. Simulat. (IF 2.1) Pub Date : 2023-09-15 Sunil Kumar, Monu Kumar Shukla, Iqra Ali, Faheem Abbas, Rachna Verma, Girish Chandra, Deepak Kumar
The use of FDA-approved drugs for the therapy of lung cancer through drug repurposing is a noteworthy approach. We retrieved all the FDA-approved triazole-based drugs from Drugbank and conducted do...
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Identification of small-molecule glucokinase activator for type-2-diabetes treatment: a structure-based virtual screening approach Mol. Simulat. (IF 2.1) Pub Date : 2023-09-14 Manokaran Malini, Ramasamy Thilagavathi, Jannet Vennila, Beutline Malgija, Gandhi Praveena, Chelliah Selvam
Glucokinase (GK, EC 2.7.1.2) is a crucial enzyme that catalyses the conversion of glucose to glucose-6-phosphate. It is used to treat type-2 diabetes (T2D), a serious metabolic disorder that is sti...
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Nanoindentation simulation study on mechanical properties and microstructure evolution of twin γ-TiAl alloy Mol. Simulat. (IF 2.1) Pub Date : 2023-09-11 Junye Li, Jiaxu Tang, Junwei Li, Rongxian Qiu, Fujun Xiao, Xiwei Dong, Lei Zhang
To explore the mechanical properties and deformation mechanism of twin γ-TiAl alloy under load and impact, based on the special interface structure in polycrystals, twinning at room temperature is ...
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Atomistic and molecular level portrayal of DNA – 1,8-napthalimide interaction Mol. Simulat. (IF 2.1) Pub Date : 2023-09-07 R. Radhika, R. Shankar
ABSTRACT The present work reports the physicochemical interaction between DNA and 1,8-napthalimide drugs to enlighten the field of drug discovery. Molecular dynamic studies of 1,8-napthalimide interacted DNA revealed distortions and destabilisation of the DNA. Among the drugs (Amonafide Azonafide and NNM-25), NNM-25 is found to have a strong interaction with DNA in gas and water phases by using the
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Effect of endohedral nickel atoms on the hydrophilicity of carbon nanotubes Mol. Simulat. (IF 2.1) Pub Date : 2023-09-06 Shakhrizoda Matnazarova, Umedjon Khalilov, Maksudbek Yusupov
Carbon nanotubes (CNTs) have been successfully used in biomedicine, including cancer therapy, due to their unique physico-chemical properties. Because pristine CNTs exhibit hydrophobic behaviour, t...
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First-principles calculations to investigate structural, mechanical, electronic, optical, and thermoelectric properties of novel cubic double Perovskites X2AgBiBr6 (X=Li, Na, K, Rb, Cs) for optoelectronic devices Mol. Simulat. (IF 2.1) Pub Date : 2023-08-29 Nabil Al Aqtash, Said M. Al Azar, Anas Y. Al-Reyahi, Ahmad Mufleh, Mufeed Maghrabi, Saber Saad Essaoud, Khadidja Berarma, Ahmad A. Mousa
Structural, elastic, electronic, optical, and thermoelectric properties of cubic double perovskites X2AgBiBr6 (X = Li, Na, K, Rb, Cs) were investigated using the density functional theory (DFT) met...
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Effects of externally-applied static electric fields on hydrogen hydrates: a molecular dynamics study Mol. Simulat. (IF 2.1) Pub Date : 2023-08-25 D. P. Luis, A. González-Calderón, J. López-Lemus
ABSTRACT Extensive molecular dynamics simulations in the equilibrium isobaric -isothermal (NPT) ensemble were developed to examine the strength of an external electric field required to dissociate the hydrogen clathrate hydrates using the direct coexistence method. The water molecules were modelled using the four-site TIP4P/Ice empirical potential, and the hydrogen molecules were described using a
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Transient of flow regimes and slip boundary analysis of water and gas in nano clay pores Mol. Simulat. (IF 2.1) Pub Date : 2023-08-20 Ying Bi, Xiaotian Jia, Youzhi Hao, Xin Du, Detang Lu
ABSTRACT Nanoscale two-phase flow is important during shale gas production. In this work, molecular dynamics simulations are employed to investigate fluid flow regimes of water and methane under different pressure gradients inside the nanoscale slit pores. The illite mineral is selected to model the clay pores based on the Small-Angle X-ray Diffraction (SAXD) experiment. The different flow regimes
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Temperature evolution in abandoned mines and the effect on gas adsorption properties of residual coal Mol. Simulat. (IF 2.1) Pub Date : 2023-08-18 San Zhao, Xiangjun Chen, Ningning Kang, Xinjian Li, Lin Wang
Abandoned mines contain a large amount of residual coal and gas resources for development and utilization. In order to accurately establish the calculation model of gas reserves and lay a foundatio...