The crosslinked binders formed by using glycidyl azide polymer (GAP) as the binder matrix and bis-propargyl succinate (BPS) as the curing agent have good application prospects in the field of solid propellants. Aiming at the shortcomings of tradition...
Natural rubber (NR), with its excellent mechanical properties, has been attracting considerable scientific and technological attention. Through molecular dynamics (MD) simulations, the effects of key structural factors on tensile stress at the molecu...
Alkaptonuria (AKU) is a rare metabolic disorder characterized by the accumulation of homogentisic acid (HGA), leading to progressive ochronosis and joint degeneration. While much is known about HGA’s role in tissue damage, the molecular mechani...
Temperature dependence of solid–liquid interfacial properties during crystal growth in nickel was investigated by ensemble Kalman filter (EnKF)-based data assimilation, in which the phase-field simulation was combined with atomic configurations of mo...
This study developed and validated a new simple and improved two-parameter high-quality equation of state (EOS) for hydrogen that can be used with less computational burden for the accurate description of various processes regarding underground hydro...
The collection of reliable data is an important and time-consuming part of the life cycle inventory (LCI) phase. Automation of individual steps can help to obtain a higher volume of or more realistic data. The aim of this paper is to survey the curre...
Respiratory diseases represent a persistent global health challenge, underscoring the need for intelligent, accurate, and personalized diagnostic and therapeutic systems. Existing methods frequently suffer from limitations in diagnostic precision, la...
Alzheimer’s disease, the most common form of dementia, currently has no cure. There are only temporary treatments that reduce symptoms and the progression of the disease. Alzheimer’s disease is characterized by the prevalence of plaques of aggregated...
Calmodulin (CaM) is a multifunctional calcium-binding protein, which regulates a variety of biochemical processes. CaM acts through its conformational changes and complex formation with its target enzymes. CaM consists of two globular domains (N-lobe...
The rational design of molecularly imprinted polymers has evolved along with state-of-the-art experimental imprinting strategies taking advantage of sophisticated computational tools. In silico methods enable the screening and simulation of innovativ...
We have performed molecular dynamics (MD) simulations of melt systems consisting of a small number of long ring poly(ethylene oxide) (PEO) probes immersed in a host matrix of linear PEO chains and have studied their microscopic dynamics and topology...
The freeze-drying of complex formulations, such as liposomes, is challenging, particularly if dispersions contain residual organic solvents. This work aimed to investigate the effects of possible protectants, namely sucrose, trehalose and/or poly(vin...
ORF2p (open reading frame 2 protein) is a multifunctional multidomain enzyme that demonstrates both reverse transcriptase and endonuclease activities and is associated with the pathophysiology of cancer. The 3D structure of the entire seven-domain OR...
Molecular dynamics simulations take advantage of supercomputing environments, e.g., to solve molecular systems composed of millions of atoms. Supercomputers are increasing their computing and memory power while they are becoming more complex with the...
In this study, the molecular structure models of four ionic liquids were created, the reverse nonequilibrium molecular dynamics simulation (RNEMD) approach was used to predict their densities and viscosities, and their thermal conductivity was simula...
Using reactive atomistic molecular dynamics, we simulate the network formation and bulk properties of chemically identical liquid crystal elastomers (LCEs) and isotropic elastomers. The nematic elastomer is from a family of materials that have been s...
The estimation of the binding of a set of molecules against BRD9 protein was carried out through an in silico molecular dynamics-driven exhaustive analysis to guide the identification of potential novel ligands. Starting from eight crystal structures...
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...
The thermal conductivities of untreated polyisoprene and polybutadiene were calculated by molecular dynamics (MD) simulations using a Green-Kubo approach between −10 °C and 50 °C at atmospheric pressure. For comparison, the thermal cond...
This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other h...
The hyaluronate molecule is a negatively charged polysaccharide that performs a plethora of physiological functions in many cell tissues depending on its conformation. In the present paper, molecular modeling at three levels of theory and two basis s...
Synthetic cannabinoid receptor agonists (SCRAs) have become a wide group of new psychoactive substances since the 2010s. For the last few years, the X-ray structures of the complexes of cannabinoid receptor I (CB1) with SCRAs as well as the complexes...
Neuropsychiatric diseases are characterized by complex molecular underpinnings that remain challenging to fully elucidate. Molecular dynamics (MD) simulations have emerged as a powerful computational tool, providing a crucial bridge between static ge...
This study investigated the effect of interactive computer simulation-supported inquiry on South African grade 8 learners’ comprehension of atoms and molecular structures. Two sample groups of 34 learners per sample group were used, one acting...
The thermal energy storage properties of a working fluid can be modified by the exothermic and endothermic adsorption and desorption of fluid molecules in the micro/nanoporous materials. In this study, thermogravimetric (TG) analysis experiments and...
Methods to predict the equilibrium solubility of nonelectrolyte solids are indispensable for early-stage process development, design, and feasibility studies. Conventional analytic methods typically require reference data to regress parameters, which...
Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a p...
To predict the favorable thermodynamical conditions and characterize cryogenic pellet formations for applications in nuclear fusion reactors, a high–throughput molecular dynamics study based on a unified framework to simulate the growth process...
(1) Background: We developed an algorithm to perform interactive molecular simulations (IMS) of protein alignment in membranes, allowing on-the-fly monitoring and manipulation of such molecular systems at various scales. (2) Methods: UnityMol, an adv...
Cellulosic insulation paper is usually used in oil-immersed transformer insulation systems. In this study, the molecular dynamics method based on reaction force field (ReaxFF) was used to simulate the pyrolysis process of a cellobiose molecular model...
Data science and machine learning (ML) techniques are employed to shed light into the molecular mechanisms that affect fluid-transport properties at the nanoscale. Viscosity and thermal conductivity values of four basic monoatomic elements, namely, a...
Molecular dynamic simulations of Li+, and Br− ions in acetonitrile were carried out. The simulated structural properties were compared to experimental data. The solvent potentials of Li+-Br−, Li+-Li+, and Br−-Br− were evaluated using constrained mole...
Antimicrobial peptides are highly dynamic entities that acquire structure upon binding to a membrane interface. To better understand the structure and the mechanism for the molecular recognition of dodecylphosphocholine (DPC) micelles by the anticocc...
To enhance quantitativeness and interpretability in identifying the mechanisms of complex oil–mineral–surfactant systems, this paper introduces an algorithmic molecular simulation analysis approach, transforming molecular dynamics traject...
This paper presents a coarse-grained molecular simulation for fullerenes based on a multipolar expansion method developed previously. The method is enabled by the construction of transferable united atoms potentials that approximate the full atomisti...
Osteoarthritis (OA) is one of the most common forms of arthritis and is commonly characterized by the breakdown of the hyaline cartilage and synovial fluid in joints. The body naturally responds by releasing proteins with specific functions to combat...
The melting behavior of alkanes plays a critical role in a wide field of applications. While experimental studies have established the occurrence of premelting phenomena in both short- and long-chain alkanes, molecular-level insights remain limited....
Snake venom is comprised of a combination of different proteins and peptides with a wide range of molecular weights and different disposition processes inherent to each compound. This causes venom to have a complex exposure profile. Our study investi...
In this work, the effect of molecular cosolvents tetraethylene glycol dimethyl ether (TEGDME) on the structure and versatile nature of mixtures of these compounds with imidazolium-based ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([b...
Intrinsically disordered proteins (IDPs) are molecules without a fixed tertiary structure, exerting crucial roles in cellular signalling, growth and molecular recognition events. Due to their high plasticity, IDPs are very challenging in experimental...
Capillary condensation phenomena are important in various technological and environmental processes. Using molecular simulations, we study the confined phase behavior of fluids relevant to carbon sequestration and shale gas production. As a first ste...
A molecular-level insight into phase transformations is in great demand for many molecular systems. It can be gained through computer simulations in which cooling is applied to a system at a constant rate. However, the impact of the cooling rate on t...
Numerical simulations of hotwire anemometers in low-speed, high-altitude conditions have been carried out using the direct simulation Monte Carlo (DSMC) method. Hotwire instruments are commonly used for in-situ turbulence measurements because of thei...
Amyloid fibrils are thought to grow by a two-step dock-lock mechanism. However, previous simulations of fibril formation (i) overlook the bi-molecular nature of the docking step and obtain rates with first-order units, or (ii) superimpose the docked...
We investigated the performance of the computationally effective GFN2-xTB approach in molecular dynamics (MD) simulations of liquid electrolytes for lithium/sodium batteries. The studied systems were LiTFSI and NaTFSI solutions in ethylene carbonate...
Aβ (1-40) can transfer from the aqueous phase to the bilayer and thus form stable ion-channel-like pores where the protein has alpha-helical conformation. The stability of the pores is due to the presence of the GXXXG motif. It has been reported...
In this article, two main approaches to the prediction of thermal conductivities by molecular dynamics (MD) simulations are discussed, namely non-equilibrium molecular dynamics simulations (NEMD) and the application of the Green–Kubo formula, i...
Molecular dynamics simulations were performed on 27 deep eutectic solvents (DESs) composed of various hydrogen bond acceptors (HBAs)—tetrabutylammonium bromide (TBAB), tetrabutylammonium chloride (TBAC), and tetraethylammonium chloride (TEAC)&m...
The four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the mos...
G protein-coupled receptors (GPCRs) play a key role in many cellular signaling mechanisms, and must select among multiple coupling possibilities in a ligand-specific manner in order to carry out a myriad of functions in diverse cellular contexts. Muc...
of 33