This work reviews self-guided (SG) molecular simulation methods and illustrates the characteristics and applications of these methods through several example simulations. The main characteristic of SG methods is that past motion in simulations is use...
Surfaces and interfaces are ubiquitous in nature and are involved in many biological processes. Due to this, natural organisms have evolved a number of methods to control interfacial and surface properties. Many of these methods involve the use of sp...
In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecu...
Self-guided (SG) molecular simulation methods, namely self-guided molecular dynamics (SGMD) and self-guided Langevin dynamics (SGLD), enhance conformational search by promoting low-frequency motion. A simple local time averaging scheme is used to ext...
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study p...
Lubricating oils play a crucial role in modern industrial production, mechanical manufacturing, aerospace, and other fields. This paper provides a review and summary of the entire workflow for molecular simulations of lubricating oils, from molecular...
With the rising performance demands in road engineering, traditional experiments often fail to reveal the microscopic mechanisms behind asphalt behavior. Molecular dynamics (MD) simulation has emerged as a valuable complement, enabling molecular-leve...
In this work, through experiments and molecular dynamics simulations, it was found that the viscosity of heavy oil decreased significantly after ultrasonic treatment, and the viscosity reduction rate can be up to 60%. The simulation results show that...
Superspreading is the rapid and complete spreading of surfactant-laden droplets on hydrophobic substrates. This phenomenon has been studied for many decades by experiment, theory, and simulation, but it has been only recently that molecular-level sim...
Molecular dynamics (MD) simulation is a particularly useful technique in food processing. Normally, food processing techniques can be optimized to favor the creation of higher-quality, safer, more functional, and more nutritionally valuable food prod...
We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local mini...
The scission rates of polystyrene and fluorinated polystyrene irradiated in an irradiation facility with Co-60 γ-rays were determined using molecular dynamics simulation and gel permeation chromatography (GPC) molecular weight distributions. Th...
We review the studies on the thermophysical properties of undercooled metals and alloys by molecular simulations in recent years. The simulation methods of melting temperature, enthalpy, specific heat, surface tension, diffusion coefficient and visco...
(1) Background: In the quest to accurately model the radiolysis of water in its supercritical state, a detailed understanding of water’s molecular structure, particularly how water molecules are arranged in this unique state, is essential. (2)...
As an important target for the development of novel antibiotics, UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) has been widely studied. Pyridone methylsulfone hydroxamate (PMH) compounds can effectively inhibit the catalytic a...
Channelrhodopsin-2 (ChR2) is a light-activated and non-selective cationic channel protein that can be easily expressed in specific neurons to control neuronal activity by light. Although ChR2 has been extensively used as an optogenetic tool in neuros...
Molecular dynamics (MD) simulation is a powerful tool to study the molecular level working mechanism of corrosion inhibitors in mitigating corrosion. In the past decades, MD simulation has emerged as an instrument to investigate the interactions at t...
In poorly consolidated carbonate rock reservoirs, solids production risk, which can lead to increased environmental waste, can be mitigated by injecting formation-strengthening chemicals. Classical atomistic molecular dynamics (MD) simulation is empl...
Acrylamide polymers with a high degree of polymerization are widely used in petroleum production. It is of great significance to study the oil displacement mechanism of acrylamide polymers with a high degree of polymerization from the micro level. In...
The preparation of solid dispersions (SDs) of emodin (EMO) represents an effective strategy for enhancing its limited water solubility. However, there is a lack of effective strategies for carrier screening. The molecular mechanism underlying EMO-SDs...
Gas adsorption in the porous shale matrix is critical for gas-in-place (GIP) evaluation and exploration. Adsorption investigations benefit significantly from the use of molecular simulation. However, modelling adsorption in a realistic shale topology...
Malaria remains a global health challenge, with increasing resistance to frontline antimalarial treatments such as artemisinin (ART) threatening the efficacy of current therapies. In this study, we investigated the potential of FDA-approved drugs to...
Background/Objectives: Hepatocellular carcinoma (HCC) is a primary malignancy often driven by metabolic syndrome, fatty liver disease, and chronic hepatitis. These conditions foster a pro-inflammatory microenvironment that promotes tumor progression....
In this study, homoisoflavone methylophiopogonanone A (MOA) was investigated for its inhibitory effect on ferroptosis of H9c2 cells using a set of cellular assays, such as BODIPY-probed and H2DCFDA-probed flow cytometry analyses, cell counting kit-8...
A profound comprehension of friction and wear mechanisms is essential for the design and development of high-performance polymeric materials for tribological application. However, it is difficult to deeply investigate the polymer friction process in...
Catechins, a class of polyphenolic compounds found in tea, have attracted significant attention due to their numerous health benefits, particularly for the treatment and protection of hypertension. However, the potential targets and mechanisms of act...
This study provides a comprehensive review of ultrasonic welding research in molecular dynamics simulations, encompassing the latest advancements by scholars worldwide. Compared to traditional welding methods, ultrasonic welding offers advantages suc...
While the economy is rapidly expanding in most emerging countries, issues coupled with a higher population has created foreseeable tension among food, water, and energy. It is crucial for more sustainable valorization of resources, for instance, nano...
The interfacial interaction between asphalt binder and mineral aggregate makes different components have different diffusion behavior. It influences the performance of interface and consequently that of the mix. In this research, the models of four a...
Elucidating the underlying mechanisms of molecular solidification in both homo- and hetero-geneous systems is of paramount importance for a large swathe of natural phenomena (whether on Earth or throughout the Universe), as well as a whole litany of...
Scutellaria baicalensis is often used to treat breast cancer, but the molecular mechanism behind the action is unclear. In this study, network pharmacology, molecular docking, and molecular dynamics simulation are combined to reveal the most active c...
This study investigates the efficacy of polyacrylamide-based polymers, specifically hydrolysed polyacrylamide (HPAM), in reducing solids production within carbonate reservoirs. Building on our earlier simulation approach, molecular simulations were c...
In recent years, simulation studies have emerged as valuable tools for understanding processes. In particular, molecular dynamic simulations hold great significance when it comes to the adsorption process. However, comprehensive studies on molecular...
Over the last decade, the availability of computer time, together with new algorithms capable of exploiting parallel computer architectures, has opened up many possibilities in molecularly modelling liquid crystalline systems. This perspective articl...
Alzheimer’s disease is an irreversible neurological disorder for which there are no effective small molecule therapeutics. A phosphodiesterase 5 (PDE5) inhibitor is a candidate medicine for the treatment of Alzheimer’s disease. Rutaecarpi...
γ-Aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that degrades γ-aminobutyric (GABA) in the brain. GABA is an important inhibitory neurotransmitter that plays important neurological r...
Channelrhodopsin-2 (ChR2) has been one of the most important objects in the study of optogenetics. The retinal chromophore molecule absorbs photons and undergoes an isomerization reaction, which triggers the photocycle, resulting in a series of confo...
The adsorption of three typical polycyclic aromatic hydrocarbons (PAHs), naphthalene, phenanthrene, and pyrene with different ring numbers, on a common mesoporous material (MCM-41) was simulated based on a well-validated model. The adsorption equilib...
In cancer immunotherapy, an emerging approach is to block the interactions of programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) using small-molecule inhibitors. The food-derived polyphenols curcumin (CC), resveratrol (RSV) and...
Background: Colorectal cancer is the third most common cancer worldwide, accounting for about 10% of all cancer cases. There is an urgent need to improve treatment outcomes and survival rates for colorectal cancer. Juglone is an anthraquinone with an...
Introduction: Tumor necrosis factor-α (TNF-α) is a key regulator of inflammatory responses, and its biological activity is dependent on proteolytic processing by the tumor necrosis factor-α-converting enzyme (TACE), also known as AD...
By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-calle...
Herein, the toughening mechanism and effects of 3-(aminopropyl)triethoxysilane (3-APTES) intercalation in calcium–silicate–hydrate (CSH) structures were investigated through molecular dynamics simulations. CSH established a model using 11...
A series of commercial difunctional benzoxazine monomers are characterized using thermal and thermo-mechanical techniques before constructing representative polymer networks using molecular simulation techniques. Good agreement is obtained between re...
In the process of the exploitation of deep oil and gas resources, shale wellbore stability control faces great challenges under complex temperature and pressure conditions. It is difficult to reflect the micro mechanism and process of the action of i...
Measuring molecular mobility (Mm) in solid food is challenging due to the rigid and heterogeneous nature of these matrices. The thermodynamic parameter Strength (S) fails to account for molecular displacement distances. This study emphasizes the role...
By using molecular dynamics simulation, we investigate the wettability of a surface texturized with a periodic array of hierarchical pillars. By varying the height and spacing of the minor pillars on top of major pillars, we investigate the wetting t...
Gas membrane separation technology is widely applied in different industry processes because of its advantages relating to separation performance and economic efficiency. It is usually difficult and time consuming to determine the suitable membrane m...
20 September 2024
The study aims to investigate the effects of curcumin on radiation/chemotherapy-induced oral mucositis (R/CIOM) and preliminarily explore its mechanism. Randomized controlled trials were identified from the PubMed, Embase, Web of Science, Cochrane Li...
Soluble sulfur (S8) and insoluble sulfur (IS) have different application fields, and molecular dynamics simulation can reveal their differences in solubility in solvents. It is found that in the simulated carbon disulfide (CS2) solvent, soluble sulfu...
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