Superhydrophobic property of cement mortar with polydimethylsiloxane modifier and a rough surface by Siyu Yu, Li Li, Chao Zhou, Song Lan

“…Hydrophobic modified HUHPC has sufficient mechanical properties to meet engineering requirements. Molecular dynamics simulations validates the mechanism of superhydrophobicity. …”
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Binding Orientations and Lipid Interactions of Human Amylin at Zwitterionic and Anionic Lipid Bilayers by Zhenyu Qian, Yan Jia, Guanghong Wei

“…In this study, as a first step to understand the mechanism of membrane-mediated hIAPP aggregation, we investigate the binding behaviors of hIAPP monomer at zwitterionic palmitoyloleoyl-phosphatidylcholine (POPC) bilayer by performing atomistic molecular dynamics simulations. The results are compared with those of hIAPP at anionic palmitoyloleoyl-phosphatidylglycerol (POPG) bilayers. …”
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Interaction of toll-like receptors and ACE-2 with different variants of SARS-CoV-2: A computational analysis by Azadeh Zahmatkesh, Elham Salmasi, Reza Gholizadeh

“…Molecular docking and molecular dynamics (MD) simulations were performed to investigate receptor-ligand interactions. …”
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Study on Molecular Recognition between Euphorbia Factor L713283 and β-Tubulin via Molecular Simulation Methods by Shan Chang, Hong-qiu He, Ren Kong, Zhen-jian Xie, Jian-ping Hu

“…We further investigated the binding modes of L713283 with β-tubulin using molecular docking and molecular dynamics (MD) simulation methods. The results indicated that the binding site between β-tubulin and L713283 was composed of the four regions, that is, residues Phe20~Glu27, Leu225~Thr232, Phe270~Gly277, and Ile356~Met363. …”
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On the validity of some equilibrium models for thermodiffusion by Araujo-Rocha, Mario, Diaz-Marquez, Alejandro, Stirnemann, Guillaume

“…Notably, there have been some attempts to relate this non-equilibrium, steady-state manifestation, to equilibrium properties of these solutions, for example, to the temperature dependence of the self-diffusion coefficient or to the solvation free energies of each of their components. Here, we use molecular dynamics simulations on dilute solutions containing molecular-size solutes, both in a thermophoretic setting as well as under equilibrium conditions, to test the validity of such models. …”
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Detailed Photoisomerization Dynamics of a Green Fluorescent Protein Chromophore Based Molecular Switch by Chen-Wei Jiang, Ai-Ping Fang, Di Zhao, Hong-Rong Li, Rui-Hua Xie, Fu-Li Li

“…With density-functional-based nonadiabatic molecular dynamics simulations, trans-to-cis and cis-to-trans photoisomerizations of a green fluorescent protein chromophore based molecule 4-benzylidene-2-methyloxazol-5(4H)-one (BMH) induced by the excitation to its S1 excited state were performed. …”
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Insight into Anticorrosion Mechanism of Ampicillin on Mild Steel in Acidic Environment: A Combined Experimental and Theoretical Approach by Tuan Dinh, Nguyen Minh Thong, Dinh Quy Huong, Trinh Le Huyen, Tran Duc Manh, Phan Tu Quy, Tran Xuan Mau, Pham Cam Nam

“…Moreover, Monte Carlo and molecular dynamics simulations were used to analyze the absorption behavior of inhibitor on the surface of Fe(110), which supplies the mechanism of inhibition corrosion processes. …”
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Multipotent Effect of Clozapine on Lipopolysaccharide-Induced Acetylcholinesterase, Cyclooxygenase-2,5-Lipoxygenase, and Caspase-3: In Vivo and Molecular Modeling Studies by Minhajul Arfeen, Devendra Kumar Dhaked, Vasudevan Mani

“…Further, the results from molecular docking were validated using molecular dynamics simulation (MDS) studies, confirming the results from molecular docking. …”
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Effective anti-inflammatory phenolic compounds from dandelion: identification and mechanistic insights using UHPLC-ESI-MS/MS, fluorescence quenching and anisotropy, molecular docki... by Hui Zou, Tingting Ben, Ping Wu, Geoffrey I.N. Waterhouse, Yilun Chen

“…This novel study identifies the effective anti-inflammatory phenolic compounds in dandelion and provides mechanistic insights into their interactions with receptor proteins (toll‐like receptor 4, TLR4; co‐receptor myeloid differentiation protein-2, MD-2) using UHPLC-ESI-MS/MS, lipopolysaccharide (LPS)-stimulated THP-1 cell line, fluorescence quenching and anisotropy, molecular docking (single ligand and multi-ligand docking) and molecular dynamics simulation. A 50 % aqueous methanol extract had a greater anti-inflammatory effect and higher chicoric acid content, compared with the 100 % water and 100 % methanol extracts. …”
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Networking Salt Inducible Kinase 1 Regulatory Perturbations on Type 2 Diabetes- Breast Cancer Co-Morbidity Associated Molecular Bridge by Durrani I.A., John P., Bhatti A.

“…Prospective studies on potentiating these hub genes particularly TP53, in context to SIK1 molecular dynamics may provide further insights into the molecular links tying T2DM to BC.…”
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Investigating the functional and structural effect of non-synonymous single nucleotide polymorphisms in the cytotoxic T-lymphocyte antigen-4 gene: An in-silico study. by Md Mostafa Kamal, Kazi Fahmida Haque Shantanu, Shamiha Tabassum Teeya, Md Motiar Rahman, A K M Munzurul Hasan, Douglas P Chivers, Tanveer A Wani, Atekah Hazzaa Alshammari, Mahesh Rachamalla, Francisco Carlos da Silva Junior, Md Munnaf Hossen

“…Thus, uncovering the molecular dynamics of single nucleotide polymorphisms (SNPs) within the CTLA4 gene is critical. …”
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The future of plant lectinology: Advanced technologies and computational tools by Vinicius J.S. Osterne, Kyria S. Nascimento, Benildo S. Cavada, Els J.M. Van Damme

“…Additionally, computational methods—including molecular docking, molecular dynamics simulations, and machine learning pipelines—support predictions of lectin structures and binding properties, underpinning experimental efforts. …”
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A Structural Effect of the Antioxidant Curcuminoids on the Aβ(1–42) Amyloid Peptide by Angelo Santoro, Antonio Ricci, Manuela Rodriquez, Michela Buonocore, Anna Maria D’Ursi

“…The results suggest that the synthetic tetrahydrocurcumin (THC) derivative interacts with the amyloid peptide in all the systems presented, while cyclocurcumin (CYC) and bisdemethoxycurcumin (BMDC) only interact when the peptide is in a less stable conformation. Molecular dynamics simulations helped visualise the curcuminoids’ effect in an aqueous system and hypothesise the importance of the peptide surface exposition to the solvent, differently modulated by the curcumin derivatives.…”
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Immunoinformatics Approach to Design a Chimeric CD70-Peptide Vaccine against Renal Cell Carcinoma by Haideh Namdari, Farhad Rezaei, Fatemeh Heidarnejad, Mohammad Yaghoubzad-Maleki, Maryam Karamigolbaghi

“…The chosen vaccine construct underwent diverse assessments such as molecular dynamics simulation, immune response simulation, and in silico cloning. …”
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AI-enhanced 3D-QSAR screening of fragment-based novel designed molecules targeting Phalaris minor ACCase by Bikash Kumar Rajak, Priyanka Rani, Durg Vijay Singh, Nitesh Singh

“…The selected herbicide-like molecules are further processed through fragment-based design to generate a library of new compounds, refined using binding affinity thresholds (-8.5 kcal/mol) and Quantitative Structure-Activity Relationship (QSAR) models. Finally, molecular dynamics (MD) simulations validated the interaction stability of these potential herbicides over 100 ns, yielding four promising candidates optimized for ACCase inhibition. …”
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Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes by Reiner Ribarics, Michael Kenn, Rudolf Karch, Nevena Ilieva, Wolfgang Schreiner

“…To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices. …”
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Machine learning-assisted design of Ti–V–Nb–Mo refractory high-entropy alloys with higher ductility and specific yield strength by Yan Li, Junjie Gong, Shilong Liang, Wei Wu, Yongxin Wang, Zheng Chen

“…A dataset of the alloys' performance parameters was established by applying first-principles and molecular dynamics calculations. The combination of the aforementioned dataset with the solid solution strengthening (SSH) model and the D (γs/γusf) parameter enabled the construction of a highly accurate strength-ductility prediction model for the alloys through the use of an XGBoost algorithm. …”
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2-Amino-6-methylbenzothiazole as corrosion inhibitor for low carbon steel in acidic solution: Experimental and theoretical studies by Klodian Xhanari, Muhamed Farruku, Avni Berisha, Bujar Seiti, Kledi Xhaxhiu, Efrosini Kokalari, Alketa Lame

“…Density Functional Theory (DFT) calculations, along with Monte Carlo (MC) and Molecular Dynamics (MD) simulations, were employed to investigate AMBT’s corrosion inhibition behaviour at the molecular level. …”
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Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG1 antibody by Jing Dai, Saeed Izadi, Jonathan Zarzar, Patrick Wu, Angela Oh, Paul J. Carter

“…An extensive mutational analysis was undertaken of the complementarity-determining region residues residing in hydrophobic surface patches predicted by spatial aggregation propensity, in conjunction with residue-level solvent accessibility, averaged over conformational ensembles from molecular dynamics simulations. Dynamic light scattering (DLS) was used as a medium throughput screen for self-interaction of ~ 200 anti-GCGR IgG1 variants. …”
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Simulations of pH and thermal effects on SARS-CoV-2 spike glycoprotein by Ziyuan Niu, Georgios Kementzidis, Miriam Rafailovich, Marcia Simon, Evangelos Papadopoulos, Bertal H. Aktas, Yuefan Deng

“…We performed triplicate and long-time all-atom molecular dynamics simulations to investigate the structures and dynamics of the SARS-CoV-2 spike glycoprotein (S-protein) for a broad range of pH = 1 through 11 and temperatures of 3°C through 75°C. …”
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