ABSTRACT Molecular dynamics simulations have been employed to investigate the transformation of structural units at the grain boundary under tensile conditions. A series of symmetric tilt-[110]-Σ27 bi-crystal Cu models are considered in this research. The findings indicate that atomic potential energy significantly influences the transformation of structural units. The potential energy of the common atom from two neighbouring structural units breaks through the threshold due to external loading, leading to its migration to adjacent atomic layers. This migration triggers the transformation of the structural unit and results in the nucleation of dislocations on the grain boundaries, which further leads to a precipitous decline in the potential energy of the grain boundaries.

ABSTRACT Structural and dynamical properties of cis-1,4-polyisoprene-graphite system were compared by four coarse-grained models. Coarse-graining of graphene layers replaced four carbon atoms by a single bead while four mapping schemes were used for the polymer. Pressure-correction was applied to the nonbonded part of the coarse-grained potential among coarse-grained polyisoprene beads. Among structural properties density profiles, bond orientation and conformation tensor as function of distance from the graphite surface were studied. Bulk values were achieved at around 2 nm from the graphite surface. Higher degree of coarse-graining showed comparatively larger fluctuations in data. Among dynamical properties mean square displacement and autocorrelation of end-to-end unit vectors for varied distances from the graphite surface were studied. Dynamics study indicated that pressure-correction method used to optimise pressure of the system resulted in slower dynamics for the higher degree of coarse-graining.

ABSTRACT Asphalt aging is a natural process that causes changes in the properties of asphalt, particularly in asphalt adhesion. Previous studies show that the effect of aging on asphalt adhesion performance is not uniform and depends on the asphalt source and aging conditions. To investigate the effects of different SARA (saturates, aromatics, resins, and asphaltenes) ratios and structural changes on the adhesive properties of asphalt after aging, this study employs molecular dynamics simulation to calculate asphalt properties such as density, viscosity, and work of adhesion. The above properties were computed for 12 categories of asphalt molecules, individual SARA components, and asphalt models characterised by diverse SARA ratios, followed by a correlation analysis. The study reveals that asphalt aging increases density, viscosity, and adhesion to silica. The increase in polar functional groups, namely ketone and sulfoxide, is responsible for the enhanced adhesion of asphalt to silica due to the resulting increase in electrostatic potential energy. Different SARA ratios lead to different asphalt properties, with the RA/SA index ((asphaltene%+resin%)/(saturate% + aromatic%)) showing a better correlation with the properties. Positive correlations were observed among density, viscosity, and work of adhesion. This study advances our understanding of chemical and structural effects on aged asphalt properties.

ABSTRACT In this numerical research, the proposed mechanism of contraction of an artificial muscle filament with regard to the performance of a natural filament and the possibility of industrial production is presented using the Dissipative Particle Dynamics (DPD) method. First, an artificial myosin component has been simulated, which includes a micro-nozzle with a thin fixed two-end polymer membrane in the middle. The swelling of the limited permeable membrane from one side results from moving the DPD fluid and, consequently, the fluid force will be transferred. Also, by changing the direction of the movement of the fluid, the swelling of the polymer membrane is reversed. It has been shown that the amount of swelling is directly dependent on the amount and direction of external force implementation ( F e = ± 0.001, ± 0.003, ± 0.005 and ± 0.007) and there is a delay (almost one DPD unit) in the amount of displacement when the direction of the flow is changed due to the inertia force effect. The proposed mechanism includes six double artificial myosins, whose myosin movement causes that actin to take contraction in a wave motion considering both forward and backward movements of the limited permeable thin membrane. Also, more artificial myosins may provide smoother contraction.

ABSTRACT Non-linear optical (NLO) parameter of a series of donor–acceptor substituted N-salicylidene-4-benzenesulfonylaniline (SBSA) derivatives with a contrast of first hyperpolarisability has been investigated using density functional-based theory. The derivative of SBSA with both the donor and acceptor substitution (NMe2-SBSA-NO2) exhibits the highest first hyperpolarisability ( ∼ 3 × 103 a.u in gas phase) value. Frequency and solvent polarity responsive behaviours of first hyperpolarisability are utilised to demonstrate the variation of NLO as switchable electrical parameter. Each of the studied compounds displays very high NLO response at frequency corresponding to the absorption maxima of their electronic state. Likewise, the increase of solvent polarity induces a substantial increase of first hyperpolarisability. The computation of NLO responsive first hyperpolarisability by varying the frequency and solvent dielectric constant within a wide domain is very tedious and time-consuming. To overcome the lacuna, we implemented machine learning tools such as artificial neural networks (ANNs), fuzzy logic (FL) and adaptive neuro-fuzzy inference system (ANFIS) to predict the computation data of the NMe2-SBSA-NO2 and moderately good results were obtained using ANFIS as soft computing tool.

ABSTRACT The aim of this investigation is to design a novel drug, screened through various computational methods, that harnesses the historical evidence of plant products inhibiting viral infections. The beta-roll domain of Flavivirus NS1, crucial for its stability, membrane interaction and viral RNA replication, underscores its significance in disease pathogenesis, being the sole non-structural protein detected in the sera of DENV-infected patients. Our goal is to develop optimised compounds that disrupt NS1 β-roll domain polymerisation, mitigating hydrophobic core formation, to effectively inhibit DENV2 cytopathic infection by leveraging natural interference with viral replication. We created 10 plant-based ligand libraries and applied scaffold hopping and bioisosteric replacement to improve them. Computational methodologies, including virtual screening, molecular dynamics simulation, contact matrix and dynamic cross correlation matrix, were employed for analysing the dynamics of the protein with the association of ligand. ADMET analysis of ligand 126 revealed a favourable ADME profile with no observed toxicity properties. Calculations of pKd, pKi and pIC50 values indicated a heightened affinity of the ligand for the receptor protein, suggesting enhanced inhibitory action and a reduced dissociation rate. These encouraging findings suggest a greater potency of the drug, warranting further in vitro testing for validation.

ABSTRACT Resusciative endovascular balloon aortic occlusion (REBOA) can be used in various surgical operations, especially in patients with hypotension and shock caused by traumatic main vascular rupture and massive haemorrhage. However, the hydrodynamic effects of surgery on aortic haemodynamics and organ perfusion are still unclear. Herein, computational fluid dynamic methods were used to evaluate the effect of balloon expansion and that of balloon-occluded aortic ratios on haemodynamics. The simulation shows that the balloon reduces the flow rate from the heart to the ruptured aorta. While reducing the flow rate of the aortic branches downstream of the balloon under conditions with fixed cardiac output, the balloon will increase the flow rate of the aortic branches upstream of the balloon. And the flow in the diastolic phase is more complicated than that of the systolic phase, and the vortex generated upstream of the balloon is more evident than that of the formed downstream. Moreover, when the inflation rate of the balloon changes rapidly, the flow rate of blood at the balloon changes suddenly accordingly, which generates a large additional pressure on the balloon. The pressure will spread upstream, thereby generating a blood hammer effect on the blood vessel wall.

ABSTRACT It is demonstrated that the substitution of Cl, B, and I at different concentrations in TlCaF3 significantly alters the phase, electronic band structure and optical, elastic, mechanical and anisotropic properties of the material. At 2.81% and 5.63% concentrations of all substituted elements, the cubic phase of TlCaF3 transforms into a pseudo-cubic tetragonal phase. With the addition of substitutional atoms, a systematic considerable narrowing of the bandgap is seen, and it can be either direct or indirect depending on the symmetrical positions. The bandgap shrinking can be addressed, in part, via the total/partial/elemental density of states (DOS) in line with structural variations. From the optical response, the refractive index rises with substitution atoms. According to the mechanical stability requirements for each substitution, the determined elastic constants for cubic and tetragonal structures match. Additionally, using elastic parameters, it is possible to estimate the unique mechanical features to evaluate the ductility and brittleness of pure and substituted compounds. Furthernore, Cl, Br and I-atoms’ substitution would make them a suitable choice for improved optimisation in ultraviolet filters (UVF) due to the existence of their absorption spectra in the ultra-violet region and the modification in structural, electrical, optical, elastic and mechanical properties.

ABSTRACT Tuberculosis, one of the most ancient and formidable infectious diseases, primarily arises from the pathogenic bacterium Mycobacterium tuberculosis (Mtb). Phosphoenolpyruvate carboxykinase (Pck), a potential drug target, is essential for the growth of Mtb that involves in the pathway of gluconeogenesis at the centre of phosphoenolpyruvate-pyruvate-oxaloacetate node. This study aims to understand drug-like properties of the compounds derived from artemisinin, and to investigate their inhibitory roles against Mtb. Molecular docking was performed on a set of 56 artemisinin compounds to identify their binding efficacy to the Mtb protein target. Subsequently, the selected top three complexes were subjected to molecular dynamics simulations. By the trajectory analysis, root mean square deviation and radius of gyration indicated the compactness of the systems without much fluctuation. The principal component analysis revealed that the complexes were less dynamic and energetically more favourable, and Gibbs energy landscape revealed the favourable energetic transitions between conformations. The artemisinin dimer primary alcohol holding good bioavailability scores appears highly stable in complex with Pck (MM/GBSA of −37.67 kcal/mol) that stands as a potential inhibitor of the Mtb target. However, further preclinical experiments and investigations are necessary to evaluate the intrinsic properties and to confirm effectiveness of the drug candidate.

ABSTRACT It is known that the bonding strength of the aggregate/cement interface affects the overall durability of concrete. However, whether the modification of ethylene vinyl acetate (EVA) copolymer affects the interface interaction between aggregates and cementitious materials is unclear. This study analyzed the interface's static structure, dynamic characteristics, and binding energy. The interaction mechanisms between acid and alkali aggregates and hydrated calcium silicate and the modification effect of EVA were compared. The calculation results of relative density distribution and radial distribution function verified the difference in the structure of EVA-modified acidic or alkaline interfaces. EVA polymer chains significantly blocked the flow of Ca atoms in CaO at the CaO/C-S-H interface and weakened the van der Waals effect at the interface. The mean square displacement and time correlation function analysis indicate that all unmodified interfaces have stable interface structures. After EVA modification, the stability of CaCa-HW decreased significantly, hindered the generation of hydration products, and verified the weak Ca atom transport at the CaO/C-S-H interface. In addition, the adhesion energy of SiO2/C-S-H and CaO/C-S-H after EVA modification decreased by 6% and 14.8%, respectively, quantifying the modification effect of EVA.