Molecular Dynamics Model Research Articles

Boroxol ring dissolution in molten and glassy B2O3 by neutron and x-ray diffraction difference methods.

The structure of 11B2O3 boron oxide glass and its liquid have been measured over a wide temperature range by pulsed neutron diffraction, from T = 14K up to 1500K. Contrary to prior neutron scattering results in the literature, thermal expansion of the B-O bond is resolved, with a coefficient of αBO = 4.1(3) ppm K-1, in quantitative agreement with the result previously derived by high-energy x-ray diffraction. Exploiting the scattering contrast between neutrons and x rays, difference functions are derived that eliminate contributions due to O-O pairs, revealing, for the first time, the nearest-neighbor B-B peak in the pair distribution function. This peak occurs at rBB = 2.430(1) Å in B2O3 glass, consistent with a mean B-O-B bond angle β ≃ 124° and a large boroxol ring fraction. In the liquid, a much larger rBB ≃ 2.54Å and β ≃ 134° are indicative of either a much lower ring fraction f, a larger non-ring B-O-B bond angle, βNR, or a combination of both. The latter scenario is supported by comparison to a range of molecular dynamics models with varying boroxol ring fractions.

Synergistic lubrication effect of graphene oxide and MoS2 nanoparticles in water-based fluid: Experiment and humid-environmental MD simulation study

In this study, a lubricant was synthesized using water-based hybrid nanofluid containing graphene oxide (GO) and MoS2 nanoparticles. Pin-on-disk tribology tests and molecular dynamics (MD) simulations under humid environment were conducted. It was discovered that the GO-MoS2 hybrid nanofluid, at the optimal concentration combination (0.3wt.% GO + 0.1wt.% MoS2), demonstrated a notably enhanced synergistic lubrication effect, resulting in a reduction of approximately 14.6% in the average friction coefficient and 14.4% in the wear rate when compared to the single nanofluid. Through interfacial tribochemical analysis, a protective polycrystalline tribofilm in the thickness of about 18.6nm was formed on metal surface, consisting of ultra-fine GO, MoS2 crystals and amorphous substances derived from the organic matters of nanofluids. Besides, from humid-environmental MD simulation results, there were lower friction force, normal force and peak temperature values in MD model containing both GO and MoS2 nanosheets, meanwhile the lattice mismatch between different nanosheets led to high interlamellar repulsion, further mitigating the pressure and friction. By analyzing the absorption behavior of dispersant molecules, sodium dodecylbenzene sulfonate and triethanolamine molecules partially transferred from nanosheets to Fe surface. Based on the experiment and humid-environmental MD simulation results, the excellent tribological behavior of nanofluid was attributed to the polishing, mending, interlayer sliding effect of nanoparticles and the tribofilm induced by interfacial tribochemistry.

Molecular dynamics study on the edge effect of single crystal Ni with two indenters nanoindentation

The edge effect and the formation and evolution of dislocations in nanoindentation were studied using molecular dynamics methods. A series of molecular dynamics models of two indenter nanoindentation was constructed, and diamond indenters were used for indentation simulation. This paper analyzes the effects of two indenters distance and indentation depth on the edge side extrusion, surface collapse, indentation force, internal defects, and stress of single crystal Ni workpieces. The results show that the number of particles extruded from the side does not increase linearly with the indentation distance increasing, the magnitude of indentation force changes with the increase of indentation depth and is influenced by the distance between the indenters, and the internal defects of single crystal nickel workpieces change with the change of indentation distance and increase with the increase of indentation depth. This work has a positive impact on understanding the nanoindentation processing of single crystal Ni and can help to understand the mechanism of internal dislocation formation in workpieces under multiple indenters indentation.

Investigating new drugs from marine seaweed metabolites for cervical cancer therapy by molecular dynamic modeling approach

The etiology of cervical cancer in women is attributed to the continuous infection of the human papillomavirus (HPV). The high costs and side effects of standard treatments and the limited efficacy of HPV vaccination have led to a quest for novel, cost-effective cervical cancer treatments, particularly in middle- and low-income countries. Therefore, our objective was to evaluate the capacity of marine seaweed compounds to hinder the activity of the cervical cancer E6 Oncoprotein. The Seaweed Metabolite Database was evaluated for its ability to inhibit E6 Oncoprotein functions by high throughput virtual screening. The investigations included molecular docking, ADMET test, MD simulation, and MM/GBSA analysis to identify three lead seaweed drug-like compounds: BC008 (-8.9 kcal/mol), RL379 (-8.9 kcal/mol), and BC014 (-8.7 kcal/mol). All of the leading candidates had positive characteristics in terms of pharmacokinetics, pharmacodynamics, and toxicity. The molecular dynamics simulation of the apoprotein, control drug, and lead compounds revealed the superior structural stability and uniformity of the main drug candidates. The MM/GBSA study revealed that the BC008-protein complex exhibited the most significant free binding energy, with a value of -57.41 kcal/mol. In the end, the findings derived from this investigation might provide a basis for developing innovative anticancer treatments.

A perspective on describing nucleonic flow and pionic observables within the ultra-relativistic quantum molecular dynamics model

A perspective on describing nucleonic flow and pionic observables within the ultra-relativistic quantum molecular dynamics model

Experimental and molecular dynamics simulation investigation on the CaO-based gelling process of waste MgCl2-riched brine

ABSTRACT The alkaline gelling backfilling technique is an important potential method for processing the brine tailings in the salt ore potash industry. It involves complicated reactions and products, which have direct influences on the backfilling process. In this study, the gelling material of the potash tailings was experimentally determined to be a 318-phase crystal structure and a corresponding molecular dynamics model was developed. The effect of proportion and crystal cluster size on the properties of paste was theoretically predicted based on the Compass II force field. The qualitative and quantitative comparison with the experimental results indicates that the model can reproduce the properties of the gelling process reasonably. Besides, the molecular diffusion, hydrogen bond network and interaction were clarified further based on the calculation results. The result indicates that the number of Mg2+ has a significant effect on the molecular diffusion of the system. The interaction energy between short-chain clusters and the other components is smaller than the energy between long-chain clusters and the other components so that the long-chain clusters can be more stable than the short-chain structures. The related results are expected to provide support for the development of low-cost gelling reagents and optimisation of the gelling backfill process.

Disassembly of Virus-Like Particles and the Stabilizing Role of the Nucleic Acid Cargo.

In many simple viruses and virus-like particles, the protein capsid self-assembles around a nucleic-acid genome. Although the assembly process has been studied in detail, relatively little is known about how the capsid disassembles, a potentially important step for infection (in viruses) or cargo delivery (in virus-like particles). We investigate capsid disassembly using a coarse-grained molecular dynamics model of a T = 1 dodecahedral capsid and an RNA-like polymer. We alter the interactions between the subunits of the capsid as well as the ionic strength of the solution to induce partial or complete disassembly of self-assembled particles. We find that disassembly follows nucleation-and-growth kinetics, where the nucleation barrier is related to the interaction strengths as well as to the conformation of the polymer. In particular, we find that polymer segments that interact with adjacent subunits reinforce the subunit-subunit contacts. These results have implications for the design of virus-like particles for applications such as drug delivery. A cargo designed with reinforcement in mind might be used to control the stability of such particles and mediate disassembly.

Kinetics of Macroion Adsorption on Silica: Complementary Theoretical and Experimental Investigations for Poly-l-arginine.

A comprehensive approach enabling a quantitative interpretation of poly-l-arginine (PARG) adsorption kinetics at solid/electrolyte interfaces was developed. The first step involved all-atom molecular dynamics (MD) modeling of physicochemical characteristics yielding PARG molecule conformations, its contour length, and the cross-section area. It was also shown that PARG molecules, even in concentrated electrolyte solutions (100 mM NaCl), assume a largely elongated shape with an aspect ratio of 36. Using the parameters derived from MD, the PARG adsorption kinetics at the silica/electrolyte interface was calculated using the random sequential adsorption approach. These predictions were validated by optical reflectometry measurements. It was confirmed that the molecules irreversibly adsorbed in the side-on orientation and their coverage agreed with the elongated shape of the PARG molecule predicted from the MD modeling. These theoretical and experimental results were used for the interpretation of the quartz crystal microbalance measurements carried out under various pH conditions. A comprehensive analysis unveiled that the results stemming from the hydrodynamic theory postulating a lubrication-like (soft) contact of the macroion molecules with the sensor adequately reflect the adsorption kinetics. The range of validity of the intuitively used Sauerbrey model was also estimated. It was argued that acquired results can be exploited to control macroion adsorption at solid/liquid interfaces. This is essential for the optimum preparation of their supporting layers used for bioparticle immobilization and shell formation at nanocapsules in targeted drug delivery.

Dinitrogen Activation: A Novel Approach with P/B Intermolecular FLP.

This study explores the reactivity of a new intermolecular P/B frustrated Lewis pair in the context of dinitrogen activation through a push-pull mechanism. The ab initio molecular dynamics model known as atom-centered density matrix propagation plays a pivotal role in elucidating the weakly associated encounter complex. In-depth analysis, mainly through intrinsic reaction coordinate calculations, supports a single-step mechanism. Notably, N2 activation is observed to proceed through a concerted mechanism, proving slightly endergonic in solvents like toluene and hexane. Furthermore, density functional theory calculations reveal that the N2 activation reaction becomes kinetically and thermodynamically favorable when it is subjected to a moderately oriented external electric field of 2.57 V nm-1 along the reaction axis. In addition, natural bonding orbital and extended transition state-natural orbitals for chemical valence analyses contribute to a more profound comprehension of the electron-transfer processes integral to the chemical reaction.

Mechanism and Characterization of Bicomponent-Filler-Reinforced Natural Rubber Latex Composites: Experiment and Molecular Dynamics (MD).

The incorporation of reinforcing fillers into natural rubber latex (NR) to achieve superior elasticity and mechanical properties has been widely applied across various fields. However, the tendency of reinforcing fillers to agglomerate within NR limits their potential applications. In this study, multi-walled carbon nanotube (MWCNT)-silica (SiO2)/NR composites were prepared using a solution blending method, aiming to enhance the performance of NR composites through the synergistic effects of dual-component fillers. The mechanical properties, dispersion behavior, and Payne effect of three types of composites-SiO2/NR (SNR), MWCNT/NR (MNR), and MWCNT-SiO2/NR (MSNR)-were investigated. In addition, the mean square displacement (MSD), fractional free volume (FFV), and binding energy of the three composites were simulated using molecular dynamics (MD) models. The results showed that the addition of a two-component filler increased the tensile strength, elongation at break, and Young's modulus of NR composites by 56.4%, 72.41%, and 34.44%, respectively. The Payne effect of MSNR was reduced by 4.5% compared to MNR and SNR. In addition, the MD simulation results showed that the MSD and FFV of MSNR were reduced by 21% and 17.44%, respectively, and the binding energy was increased by 69 times, which was in agreement with the experimental results. The underlying mechanisms between the dual-component fillers were elucidated through dynamic mechanical analysis (DMA), a rubber process analyzer (RPA), and field emission scanning electron microscopy (SEM). This study provides an effective reference for broadening the application fields of NR.

Ethosuximide: Subunit- and Gβγ-dependent blocker and reporter of allosteric changes in GIRK channels.

The antiepileptic drug ethosuximide (ETX) suppresses epileptiform activity in a mouse model of GNB1 syndrome, caused by mutations in Gβ1 protein, likely through the inhibition of G-protein gated K+ (GIRK) channels. Here, we investigated the mechanism of ETX inhibition (block) of different GIRKs. We studied ETX inhibition of GIRK channels expressed in Xenopus oocytes with or without their physiological activator, the G protein subunit dimer Gβγ. ETX binding site and mode of action were analysed using molecular dynamic (MD) simulations and kinetic modelling, and the predictions were tested by mutagenesis and functional testing. We show that ETX is a subunit-selective, allosteric blocker of GIRKs. The potency of ETX block is increased by Gβγ, in parallel with channel activation. MD simulations and mutagenesis locate the ETX binding site in GIRK2 to a region associated with phosphatidylinositol-4,5-bisphosphate (PIP2) regulation, and suggest that ETX acts by closing the helix bundle crossing (HBC) gate and altering channel's interaction with PIP2. The apparent affinity of ETX block is highly sensitive to changes in channel gating caused by mutations in Gβ1 or GIRK subunits. ETX block of GIRKs is allosteric, subunit-specific, and enhanced by Gβγ through an intricate network of allosteric interactions within the channel molecule. Our findings pose GIRK as a potential therapeutic target for ETX and ETX as a potent allosteric GIRK blocker and a tool for probing gating-related conformational changes in GIRK.

Noncatalytic Reduction of Nitrogen Oxide and Soot Inhibition during Cocombustion with Biotar: The Molecular Dynamics Modeling Approach.

Cocombustion with biomass tar is a potential method for NO reduction during fossil fuel combustion. In this work, the molecular dynamic method based on the reactive force field was used to study the NO reduction by phenol, which is a typical tar model compound. Results indicate that phenol undergoes significant decomposition at 3000 K, resulting in the formation of small molecular fragments accompanied by the generation of large molecular, network-structured soot particles. At higher temperatures (3500 K), the morphology of the soot produced from phenol decomposition undergoes a certain degree of change. It evolves from a two-dimensional network structure to a three-dimensional particulate structure. Soot particles are significant products of the thermal decomposition process of phenol. NO acts as an oxidant during the phenol decomposition process, significantly inhibiting the formation of soot particles during this process. Phenol also promotes the reduction of NO. The corresponding NO reduction ratios of NO are 52%, 76%, and 89% for 1500, 2000, and 2500 K respectively. CO, H2O, and N2 were the three most important reaction products during phenol-NO interaction. HNO is an important intermediate during the reduction of NO by phenol. The combination of the H radical and NO is the main route for HNO. It can be seen that HNO is quickly produced at the initial stage. The calculated activated energies for NO reduction and phenol oxidation are 30.47 and 50.85 kJ/mol, respectively.

The Dps Protein Protects Escherichia coli DNA in the Form of the Trimer.

The Dps protein is the major DNA-binding protein of prokaryotes, which protects DNA during starvation by forming a crystalline complex. The structure of such an intracellular DNA-Dps complex is still unknown. However, the phenomenon of a decrease in the size of the Dps protein from 90 Å to 69-75 Å during the formation of a complex with DNA has been repeatedly observed, and no explanation has been given. In this work, we show that during the formation of intracellular DNA-Dps crystals, the protein transitions to another oligomeric form: from a dodecameric (of 12 monomers), which has an almost spherical shape with a diameter of 90 Å, to a trimeric (of three monomers), which has a shape close to a torus-like structure with a diameter of 70 Å and a height of 40 Å. The trimer model was obtained through the molecular dynamic modeling of the interaction of the three monomers of the Dps protein. Placement of the obtained trimer in the electron density of in vitro DNA-Dps crystal allowed for the determination of the lattice parameters of the studied crystal. This crystal model was in good agreement with the SAXS data obtained from intracellular crystals of 2-day-old Escherichia coli cells. The final crystal structure contains a DNA molecule in the through channel of the crystal structure between the Dps trimers. It was discussed that the mechanism of protein transition from one oligomeric form to another in the cell cytoplasm could be regulated by intracellular metabolites and is a simple and flexible mechanism of prokaryotic cell transition from one metabolic state to another.

Ionization calculations using classical molecular dynamics

By performing an ensemble of molecular dynamics simulations, the model-dependent ionization state is computed for strongly interacting systems self-consistently. This is accomplished through a free energy minimization framework based on the technique of thermodynamic integration. To illustrate the method, two simple models applicable to partially ionized hydrogen plasma are presented in which pair potentials are employed between ions and neutral particles. Within the models, electrons are either bound in the hydrogen ground state or distributed in a uniform charge-neutralizing background. Particular attention is given to the transition between atomic gas and ionized plasma, where the effect of neutral interactions is explored beyond commonly used models in the chemical picture. Furthermore, pressure ionization is observed when short-range repulsion effects are included between neutrals. The developed technique is general, and we discuss the applicability to a variety of molecular dynamics models for partially ionized warm dense matter. Published by the American Physical Society 2025

Effects of Machining Parameters on Abrasive Flow Machining of Single Crystal γ-TiAl Alloy Based on Molecular Dynamics.

Observing the intricate microstructure changes in abrasive flow machining with traditional experimental methods is difficult. Molecular dynamics simulations are used to look at the process of abrasive flow processing from a microscopic scale in this work. A molecular dynamics model for micro-cutting a single crystal γ-TiAl alloy with a rough surface in a fluid medium environment is constructed, which is more realistic. The evolution of material removal, cutting force, temperature, energy, and dislocation during micro-cutting are analyzed. The impact of cutting depth, abrasive particle sizes, and abrasive material on the micro-cutting process are analyzed. The analysis shows that the smaller cutting depth and abrasive particle sizes are beneficial to obtain a better machining surface, and the cubic boron nitride (CBN) abrasive is an effective substitute material for diamonds. The purpose of this study is to provide unique insights for improving the material removal rate and subsurface quality by adjusting machining parameters in actual abrasive flow precision machining.

Experimental investigation and molecular dynamics simulations of plasma treatment on the interface properties of carbon fiber-reinforced PI resin composites

ABSTRACT This paper examines surface modification of carbon fibers using low-temperature plasma and investigates the temperature-dependent interfacial properties of high-performance polyimide-based composites. Additionally, the mechanisms by which air and argon plasma treatments enhance the high-temperature interfacial properties of carbon fiber-reinforced polymers (CFRP) are examined. First, the changes in physical morphology and surface structural defects of carbon fibers under different plasma atmospheres are discussed: carbon fibers develop surface protrusions after various plasma treatments, and a grooved morphology forms after argon plasma treatment. The ID/IG ratio (R value) of the carbon fiber surface increased from 1.25 in untreated fibers to 1.37 after air plasma treatment, and further to 1.60 after argon plasma treatment. The short-beam shear strength test results show that at 300°C, the ILSS (interlaminar shear strength) of argon plasma-treated laminates increased from 67.70 MPa to 87.69 MPa, a 29.53% improvement. The ILSS of air plasma-treated laminates reached 81.46 MPa, a 20.33% improvement. Argon plasma-treated laminates showed more stable interlaminar shear performance at high temperatures, maintaining an interfacial retention rate of 85.11% at 300°C. Secondly, the mechanisms by which air and argon plasma modification enhance the high-temperature interface performance of CFRP are as follows: Air treatment, due to the dual effects of chemical bonding and physical etching, allows the laminated plates to exhibit excellent performance at room temperature. However, in high-temperature environments, the chemical bonding effect is easily affected and damaged, significantly reducing the interface retention rate of the laminated plates. The etching effect of argon treatment is quite significant, which means that the improvement effect of argon mainly manifests in the mechanical interlocking action, with the chemical bonding effect being relatively small. The physical effect of mechanical interlocking is less influenced by temperature, thus the high-temperature retention rate of the laminate is relatively high. Furthermore, molecular dynamics models of the interface were built using atomic simulation to explore how plasma modification introduces active groups that enhance the interface at the molecular level. The impact of these modifications on interfacial structure and energy was analyzed using molecular dynamics metrics. Both experimental and molecular dynamics simulation results confirm that plasma treatment has a positive regulatory effect on the interface.

No Bridge between Us: EXAFS and Computations Confirm Two Distant Iron Ions Comprise the Active Site of Alkane Monooxygenase (AlkB).

Alkane monooxygenase (AlkB) is the dominant enzyme that catalyzes the oxidation of liquid alkanes in the environment. Two recent structural models derived from cryo-electron microscopy (cryo-EM) reveal an unusual active site: a histidine-rich center that binds two iron ions without a bridging ligand. To ensure that potential photoreduction and radiation damage are not responsible for the absence of a bridging ligand in the cryo-EM structures, spectroscopic methods are needed. We present the results of extended X-ray absorption fine structure (EXAFS) experiments collected under conditions where photodamage was avoided. Careful data analysis reveals an active site structure consistent with the cryo-EM structures in which the two iron ions are ligated by nine histidines and separated by at least 5 Å. The EXAFS data were used to inform structural models for molecular dynamics (MD) simulations. The MD simulations corroborate EXAFS observations that neither of the two conserved carboxylate-containing residues (E281 and D190) near the active site are likely candidates for metal ion bridging. Mutagenesis experiments, spectroscopy, and additional MD simulations were used to further explore the role of these carboxylate residues. A variant in which a carboxylate containing residue (E281) was changed to a methyl residue (E281A) showed little change in pre-edge features, consistent with the observation that it is not essential for activity and hence unlikely to serve as a bridging ligand at any point in the catalytic cycle. D190 variants had substantially diminished activity, suggesting an important role in catalysis not yet fully understood.

How cells align to structured collagen fibrils: a hybrid cellular Potts and molecular dynamics model with dynamic mechanosensitive focal adhesions.

Many mammalian cells, including endothelial cells and fibroblasts, align and elongate along the orientation of extracellular matrix (ECM) fibers in a gel when cultured in vitro. During cell elongation, clusters of focal adhesions (FAs) form near the poles of the elongating cells. FAs are mechanosensitive clusters of adhesions that grow under mechanical tension exerted by the cells' pulling on the ECM and shrink when the tension is released. In this study, we use mathematical modeling to study the hypothesis that mechanical reciprocity between cells and the ECM is sufficient for directing cell shape changes and orientation. We show that FAs are preferentially stabilized along the orientation of ECM fibers, where cells can generate higher tension than in directions perpendicular to the ECM fibers. We present a hybrid computational model coupling three mathematical approaches: first, the cellular Potts model (CPM) describes an individual contractile cell; second, molecular dynamics (MD) represent the ECM as a network of cross-linked, deformable fibers; third, a set of ordinary differential equations (ODEs) describes the dynamics of the cell's FAs, in terms of a balance between assembly and a mechanoresponsive disassembly. The resulting computational model shows that mechanical reciprocity suffices for stiffness-dependent cell spreading, local ECM remodeling, and ECM-alignment-dependent cell elongation. These combined effects are sufficient to explain how cell morphology is influenced by the local ECM structure and mechanics.

Silicene-Based Quantum Dots Nanocomposite Coated Functional UV Protected Textiles With Antibacterial and Antioxidant Properties: A Versatile Solution for Healthcare and Everyday Protection.

The predominant adverse health effects in care delivery result from hospital-acquired (nosocomial) infections, which impose a substantial financial burden on global healthcare systems. Integrating contact-killing antibacterial action, gas permeability, and antioxidant properties into textile coatings offers a transformative solution, significantly enhancing both medical and everyday protective applications. This study presents an innovative, pollution-free physical compounding method for creating a fluorescent biopolymer composite embedded with silicene-based heteroatom-doped carbon quantum dots for the production of functional textiles. The resulting coated fabric shows superior ultraviolet (UV) protection behavior (UVA and UVB), thermal stability, breathability, mechanical strength, and antioxidant capabilities as demonstrated by the 2,2-diphenyl-1-picrylhydrazyl(DPPH) experiment (>78%) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) ABTS assay (>90%). Rigorous testing against both gram positive and gram negative bacteria confirms that the coated fabric has excellent antibacterial activity. Results from time-dependent antibacterial assays indicate that the nanocomposite can markedly inhibit bacterial proliferation within a few hours. Molecular dynamics modeling, in conjunction with experimental investigations, is employed to elucidate the intermolecular interactions influencing the components of the treated cotton fabrics. The ongoing research can result in the creation of cost-effective smart textile substrates aimed at inhibiting microbial contamination in healthcare and medical applications, possibly rendering them commercially viable.

Molecular dynamics model of mechanophore sensors for biological force measurement.

Cellular forces regulate an untold spectrum of living processes, such as cell migration, gene expression, and ion conduction. However, a quantitative description of mechanical control remains elusive due to the lack of general, live-cell tools to measure discrete forces between biomolecules. Here we introduce a computational pipeline for force measurement that leverages well-defined, tunable release of a mechanically activated small molecule fluorophore. These sensors are characterized using a multiscale approach combining equilibrium and steered QM/MM molecular dynamics models to capture the chemical, mechanical, and conformational transitions underlying force activation thresholds on a nano Newton scale. We find that chemical modification of the mechanophore and variation of its biomolecular tethers can tune the rate-determining step for fluorophore release and adjust the mechanochemical activation barrier. The models offer a new molecular framework for calibrated, programmable biomolecular force reporting within the live-cell regime, opening new opportunities to study mechanical phenomena in biological systems.