Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches

Molecular dynamics simulations and experimental investigation of viscosity of CuO-oil nanolubricant at different temperatures and volume fractions of nanoparticles

Nanolubricant viscosity plays a crucial role in various industries due to its impact on pressure drop, pumping power, and heat transfer. The purpose of this research is to measure the viscosity of a (base oil) C30H62-CuO nano-lubricant experimentally using a viscometer and determine its viscosity using the equilibrium molecular dynamics (MD) simulation. In addition, the impacts of nano CuO particle volume fraction and temperature on the viscosity were investigated within different concentrations of nano CuO particles (0%, 0.25%, 0.5%, and 0.75%) and variable temperatures (300 K, 313 K, 323 K, and 373 K). The simulation results agreed with experimental results and depicted that the viscosity of base oil and nano lubricant of CuO-base oil decreased with increasing temperature. Additionally, increasing the concentration of nanoparticles increased the viscosity of the nano lubricant, but the effect of increasing the concentration of nanoparticles at high temperatures was not significant. For instance, the viscosity of the base oil increased by 1.2% and 1.5% after adding 0.5% and 0.75% copper oxide nanoparticles at 373 K. Based on our research; no study has been done to calculate the viscosity of nanolubricant (C30H62 (base oil) - CuO) and its influencing factors by molecular dynamics simulation and compare its results with experimental methods. The research findings have practical implications for using nano lubricants in various industries, such as the internal combustion engine industry or other industries that use lubricants, and it is a critical parameter in heat transfer.

Deciphering ACE2-RBD binding affinity through peptide scanning: A molecular dynamics simulation approach

Rapid discovery of target information for protein-protein interactions (PPIs) is significant in drug design, diagnostics, vaccine development, antibody therapy, etc. Peptide microarray is an ideal tool for revealing epitope information of PPIs. In this work, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike receptor-binding domain (RBD) and the host cell receptor angiotensin-converting enzyme 2 (ACE2) were introduced as a model to study the epitope information of RBD-specific binding to ACE2 via a combination of theoretical calculations and experimental validation. Through dock and molecular dynamics simulations, it was found that among the 22 peptide fragments that consist of RBD, #14 (YNYLYRLFRKSNLKP) has the highest binding strength. Subsequently, the experiments of peptide microarray constructed based on plasmonic materials chip also confirmed the theoretical calculation data. Compared to other methods, such as phage display technology and surface plasmon resonance (SPR), this method is rapid and cost-effective, providing insights into the investigation of pathogen invasion processes and the timely development of peptide drugs and other fields.

Design of High-Frequency Carbon Nanotube-Carbon Nanotorus Oscillators for Energy Harvesting: A Molecular Dynamics Study

The objective of this study is to examine the feasibility of using carbon-based nanostructures as nano-oscillators for future nanoelectromechanical applications such as energy harvesting devices and vibration sensing. The proposed nano-oscillator is comprised of a carbon nanotube (CNT) oscillating through a fixed carbon nanotorus molecule. For the first time in the literature, molecular dynamics (MD) simulations in conjunction with the Tersoff-Brenner (TB) and 6-12 Lennard-Jones (LJ) potential functions are adopted to determine the molecular interactions of the introduced nanodevice. To simulate the oscillatory behavior, two different schemes, namely, rigid and flexible, are considered. A detailed parametric study is performed to investigate the effects of rigidity, flexibility, and size of nanostructures as well as initial velocity on the force distribution and time histories of displacement and velocity of the core. Numerical results reveal that unlike the rigid oscillators, the flexible oscillators damp out within a few cycles. It is shown that the escape velocity of the flexible scheme is ∼6 times greater than that of the rigid scheme. The operating frequency and the generated power of rigid and flexible schemes under different system parameters are also calculated and compared. It is demonstrated that with increasing the ratio of nanotube-to-nanotorus diameter, the operating frequencies of both schemes decrease, while the generated powers do not behave monotonically. For a determined system parameter, it is observed that the flexible scheme provides higher operating frequencies compared to the rigid one. Moreover, considering that the initial velocity of the system is identical to the escape velocity, the generated power of the flexible scheme is calculated to be ∼14 times greater than that of the rigid scheme.

Effect of interface layer on the enhancement of thermal conductivity of SiC-Water nanofluids: Molecular dynamics simulation

To investigate the impact of interfacial layer effects on the thermal conductivity of nanofluids and the microscopic mechanisms of enhanced thermal conductivity, this study employed non-equilibrium molecular dynamics to compute the thermal conductivity, number density, radial distribution function, and mean square displacement distribution of SiC nanofluids. The impact of nanoparticle volume fraction and particle size parameters on the thermal conductivity of nanofluids and the structure of interfacial adsorption layers was discussed. The simulation calculation results show that the coefficient of thermal conductivity of nanofluid is positively related to the volume fraction of nanoparticles, increasing from 0.6529 W/(m·K) to 0.8159 W/(m·K), and the enhancement of thermal conductivity by the volume fraction can be up to 33.97 %. The thermal conductivity is inversely correlated with the change in particle size, and the maximum improvement in thermal conductivity by particle size can reach up to 12.05 %. The simulated results of the thermal conductivity of nanofluid are almost consistent with the predicted results of the Yu&Choi model, and the error is controlled within 5 %. Simultaneously, the thickness of the interfacial adsorption layer decreases with an increase in particle size. This reduction arises due to larger particles having a smaller specific surface area, resulting in fewer particle surfaces covered by the interface layer. Moreover, the impact of particle size on the arrangement and affinity of molecules within the interface layer contributes to this decrease. Overall, interface layer effects exhibit a dual impact on the thermal conduction of nanofluids. The structured formation and high-density distribution of the adsorption layer contribute to enhanced heat transfer, while thermal resistance between nanoparticle surfaces and the fluid restricts heat transmission.

Weathered coal-based carbon dots modified by organic amine for enhanced crystallinity and toughness of poly(lactic acid) film

Poly(lactic acid) (PLA) has its own limitations in terms of slow crystallization rate and low crystallinity during processing, resulting in poor toughness and thermal stability, which seriously restricts the practical application of PLA. Blending nanoparticles into the PLA matrix is an effective way to improve PLA crystallization. In this study, carbon dots (CDs) were prepared by green oxidation using weathered coal as carbon source and then surface-modified with dodecylamine (DDA) and octadecylamine (ODA). Modified CDs (MCDs)/PLA composite films were prepared using MCDs as filler to improve the crystallinity and toughness of PLA films. The results showed that the improvement effect of ODA-modified CDs (ODACDs) was better than that of DDA-modified CDs (DDACDs). The crystallinity of PLA composite film (0.05 wt% ODACDs) was increased from 7.20% (pure PLA film) to 35.44%, and its elongation at break was increased by 5.01 times compared with that of the pure PLA film. Moreover, thermogravimetric analysis suggested that the thermal stability of MCDs/PLA films was also improved. The results of simultaneous rheology and in-situ FTIR analysis as well as molecular dynamics simulations confirmed that MCDs had a strong interaction with PLA molecules, which promoted the crystallization of PLA film, thereby improving its toughness and thermal stability.

Aggregation studies of alpha-lactalbumin induced by edible azo dyes with different sulfonyl group numbers: A comparative study

As an opaque and complex colloidal mixture, milk is usually present as a positively charged colloid under acidic conditions. Adding negatively charged colloids can lead to protein aggregation in milk. Alpha-lactalbumin (α-La) is an essential component of whey protein and has good physicochemical properties for functional food development. We combined spectroscopy, computer simulations, and other techniques to comparative analyze the mechanisms and characteristics of isolated α-La aggregation induced by CI Acid Red 27 (C27)/CI Acid Red 14 (FB) containing different sulfonyl groups in vitro. The results showed that C27/FB (5.25 × 10-5 mol·L-1 to 3.15 × 10-4 mol·L-1) induced the formation of fibril-like aggregates under acidic conditions (pH 2.0 and 4.0) mainly benefit from hydrophobic and electrostatic forces. Weakening and redshift of α-La's characteristics negative peak were observed (208 nm to 218 nm) on circular dichroism. β-Crosslinks self-assembly and reorganization of disulfide bonds occurred during protein fibrillation. Moreover, the different redshift intensity of Congo red binding to amyloid fibrils was observed to be induced by C27 (>551 nm) and FB (>536 nm), and the direct observation by TEM demonstrated the ability to induce protein fibrillation is C27 > FB. Edible azo dyes with more sulfonyl groups would possess a stronger ability to induce protein fibrillation.

Molecular Dynamics Study on the Mechanism of Gallium Nitride Radiation Damage by Alpha Particles

In special applications in nuclear reactors and deep space environments, gallium nitride detectors are subject to irradiation by α-particles. Therefore, this work aims to explore the mechanism of the property change of GaN material, which is closely related to the application of semiconductor materials in detectors. This study applied molecular dynamics methods to the displacement damage of GaN under α-particle irradiation. A single α-particle-induced cascade collision at two incident energies (0.1 and 0.5 MeV) and multiple α-particle injections (by five and ten incident α-particles with injection doses of 2 × 10¹² and 4 × 10¹² ions/cm², respectively) at room temperature (300 K) were simulated by LAMMPS code. The results show that the recombination efficiency of the material is about 32% under 0.1 MeV, and most of the defect clusters are located within 125 Å, while the recombination efficiency of 0.5 MeV is about 26%, and most of the defect clusters are outside 125 Å. However, under multiple α-particle injections, the material structure changes, the amorphous regions become larger and more numerous, the proportion of amorphous area is about 27.3% to 31.9%, while the material's self-repair ability is mostly exhausted.

Molecular dynamics simulation of thermal characteristics of globulin protein dissolved in dilute salt solutions using equilibrium and non-equilibrium methods

The aggregation of 7S globulin protein (7SGP) in mature soybean (Glycine max) seeds is an extracellular matrix protein. This atomic compound can be detected in various food products. So, this protein structure's thermal properties (TP) can be important for various food industry products. Molecular Dynamics (MD) simulations describe the atomic arrangement of this protein and forecast TP of them in various initial conditions. The present computational work estimates the 7SGP thermal behavior (TB) by equilibrium (E) and non-equilibrium (NE) methods. In these two methods, the 7SGP is represented using DREIDING interatomic potential. MD outputs predicted 0.59 and 0.58 W/mK values for thermal conductivity (TC) of 7SGP at T₀ = 300 K and P₀ = 1 bar using E and NE methods. Furthermore, computational results represented that the pressure (P) and temperature (T) are significant factors for the TB of 7SGP. Numerically, TC of 7SGP reaches 0.68 W/mK, 0.52 W/mK by T/P increasing. MD results predicted the interaction energy (IE) between 7SGP and aqueous media could fluctuate between -110.64 and 161.53 kcal/mol by the change in T/P after t = 10 ns?These results should be supposed to design new methods for various food industry purposes, such as producing and processing edible oils.

The numerical study of pressure and temperature effects on mechanical properties of baghdadite-based nanostructure: molecular dynamics simulation

Bioceramics have been commonly implemented to replace and restore hard tissues such as teeth and bones in recent years. Among different bioceramics, Baghdadite (BAG) has high bioactivity due to its ability to form apatite and stimulate cell proliferation. So, this structure is used widely for medical applications to treat bone-based diseases. Physically, we expect changes in temperature and pressure to affect the Baghdadite-based nanostructure's mechanical behaviour. So, in this computational study, we report the pressure/temperature effect on Baghdadite matrix with nanoscale size by using Molecular Dynamics (MD) approach. To this end, physical values like the total energy, temperature, final strength (FS), stress-strain curve, potential energy, and Young's modulus (YM) are reported. Simulation results indicated the mechanical properties of Baghdadite (BAG) nanostructure weakened by temperature and pressure increase. Numerically, the FS and YM of the defined structure reach 131.40 MPa/159.43 MPa, and 115.15 MPa/139.72 MPa with temperature/pressure increasing. Therefore, the increase in initial pressure and temperature leads to a decrease in the mechanical properties of nanostructures. These results indicate the importance of the initial condition in the Baghdadite-based nanostructures' mechanical behaviour that must be considered in clinical applications.

The investigation of energy management and atomic interaction between coronavirus structure in the vicinity of aqueous environment of H2O molecules via molecular dynamics approach

The coronavirus pandemic is caused by intense acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Identifying the atomic structure of this virus can lead to the treatment of related diseases in medical cases. In the current computational study, the atomic evolution of the coronavirus in an aqueous environment using the Molecular Dynamics (MD) approach is explained. The virus behaviors by reporting the physical attributes such as total energy, temperature, potential energy, interaction energy, volume, entropy, and radius of gyration of the modeled virus are reported. The MD results indicated the atomic stability of the simulated virus significantly reduced after 25.33 ns. Furthermore, the volume of simulated virus changes from 182397 Å³ to 372589 Å³ after t = 30 ns. This result shows the atomic interaction between various atoms in coronavirus structure decreases in the vicinity of H₂O molecules. Numerically, the interaction energy between virus and aqueous environment converges to −12387 eV and −251 eV values in the initial and final time steps of the MD study procedure, respectively.

Molecular dynamics simulation for membrane separation and porous materials: A current state of art review

Computational frameworks have been under specific attention within the last two decades. Molecular Dynamics (MD) simulations, identical to the other computational approaches, try to address the unknown question, lighten the dark areas of unanswered questions, to achieve probable explanations and solutions. Owing to their complex microporous structure on one side and the intricate biochemical nature of various materials used in the structure, separative membrane materials possess peculiar degrees of complications. More notably, as nanocomposite materials are often integrated into separative membranes, thin-film nanocomposites and porous separative nanocomposite materials could possess an additional level of complexity with regard to the nanoscale interactions brought to the structure. This critical review intends to cover the recent methods used to assess membranes and membrane materials. Incorporation of MD in membrane technology-related fields such as desalination, fuel cell-based energy production, blood purification through hemodialysis, etc., were briefly covered. Accordingly, this review could be used to understand the current extent of MD applications for separative membranes. The review could also be used as a guideline to use the proper MD implementation within the related fields.

Thermal Conductivity of B-DNA

The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical molecular dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D model or a coarse-grained model of DNA to reduce simulation times, full atomistic simulations are employed to understand the thermal conduction in B-DNA. Thermal conductivities at different temperatures from 100 to 400 K are investigated using the Einstein-Green-Kubo equilibrium and Müller-Plathe non-equilibrium formalisms. The thermal conductivity of B-DNA at room temperature is found to be 1.5 W/m·K in equilibrium and 1.225 W/m·K in the non-equilibrium approach. In addition, the denaturation regime of B-DNA is obtained from the variation of thermal conductivity with temperature. It is in agreement with previous studies using the Peyrard-Bishop-Dauxois model at a temperature of around 350 K. The quantum heat capacity (C_vq) has given additional clues regarding the Debye and denaturation temperature of 12-bp B-DNA.

Thermal and hydrodynamic properties of coronavirus at various temperature and pressure via molecular dynamics approach

COVID-19 is an epidemic virus arising from a freshly discovered coronavirus. Most people involved with the coronavirus will experience slight to moderate respiratory disease and recover without needing particular therapy. In this work, the atomic stability of the coronavirus at different thermodynamic properties such as temperature and pressure, was studied. For this purpose, the manner of this virus by atomic precession was described with a molecular dynamics approach. For the atomic stability of coronavirus description, physical properties such as temperature, total energy, volume variation, and atomic force of this structure were reported. In molecular dynamics approach, coronavirus is precisely simulated via S, O, N, and C atoms and performed Dreiding force field to describe these atoms interaction in the virus. Simulation results show that coronavirus stability has reciprocal relation with atomic temperature and pressure. Numerically, after 2.5 ns simulation, the potential energy varies from - 31,163 to - 26,041 eV by temperature changes from 300 to 400 K. Furthermore, this physical parameter decreases to - 28,045 eV rate at 300 K and 2 bar pressure. The volume of coronavirus is another crucial parameter to the stability description of this structure. The simulation shows that coronavirus volume 92% and 14% increases by 100 K and 2 bar variation of simulation temperature and pressure, respectively.

Molecular dynamics performance for coronavirus simulation by C, N, O, and S atoms implementation dreiding force field: drug delivery atomic interaction in contact with metallic Fe, Al, and steel

Coronavirus causes some illnesses to include cold, COVID-19, MERS, and SARS. This virus can be transmitted through contact with different atomic matrix between humans. So, this atomic is essential in medical cases. In this work, we describe the atomic manner of this virus in contact with various metallic matrix such as Fe, Al, and steel with equilibrium molecular dynamic method. For this purpose, we reported physical properties such as temperature, total energy, distance and angle of structures, mutual energy, and volume variation of coronavirus. In this approach, coronavirus is precisely simulated by O, C, S, and N atoms and they are implemented dreiding force field. Our simulation shows that virus interaction with steel matrix causes the maximum removing of the virus from the surfaces. After 1 ns, the atomic distance between these two structures increases from 45 to 75 Å. Furthermore, the volume of coronavirus 14.62% increases after interaction with steel matrix. This atomic manner shows that coronavirus removes and destroyed with steel surface, and this metallic structure can be a promising material for use in medical applications.

Computer modeling of pulsatile blood flow in elastic artery using a software program for application in biomedical engineering

BACKGROUND AND OBJECTIVE

Atherosclerosis-a condition in which an artery is constricted-alters blood flow in the artery, that can exacerbate the condition. Focusing on previous studies, it can be seen that the k-ε model has been used in the simulation. Therefore, the reverse flow on the back of stenosis is not well represented. In this study, the simulated results are much closer to clinical results, relying on the use of physiological pulses, and considering elasticity of the vessel wall, and the applying k-ω model. It can therefore be claimed that a much more accurate prediction will be made regarding the formation, development and progression of the disease.

METHODS

Modeling biological systems usually contain many parameters, which cannot be calculated experimentally, or are too costly and time consuming. In addition, it is occasionally required to examine the influence of different physical variables, which, given the complexity of the governing equations, make analytical methods feasible (or very limited). The present study is an attempt to investigate the turbulent pulsatile blood flow in an elastic artery with single and double stenoses using a finite element software program, ADINA 8.8.

RESULTS

According to the results, the k - ω turbulence model predicted a larger reverse flow in the post-stenotic region and between the two stenoses in comparison with the k - ε model. In other words, the k - ω model results suggest that a larger region is prone to atherosclerosis. In addition, that the k - ε model predicted a greater maximum shear stress at the throat and a shorter reverse flow region (Mean WSS < 0) in both stenosis scenarios. In other words, relative to the k - ε model, the k - ω model underestimated the damage to the plaque and the risk of its rupture though it predicted new stenosis developing behind the previous one. It was observed that the presence of a double stenosis causes the upstream pressure to reach the critical value in less time. Velocity profiles revealed that in the stenosis throat, the maximum velocity exceeds the normal biological state, which may cause disorders in the blood circulation.

CONCLUSIONS

The artery wall displacement results are suggestive of the greater difference between the two turbulence models in the case with double stenosis compared with single stenosis. Moreover, the difference between the two turbulence models in double stenosis is minimized in both post-stenotic and pre-stenotic regions.

pH-sensitive loading/releasing of doxorubicin using single-walled carbon nanotube and multi-walled carbon nanotube: A molecular dynamics study

BACKGROUND AND OBJECTIVE

Doxorubicin is one of the drugs used to treat cancer, and many studies have been conducted to control its release. In this study, carbon nanotubes have been proposed as a doxorubicin carrier, and the effect of carboxyl functional group on the controlled release of doxorubicin has been studied.

METHODS

This study has been done by molecular dynamics simulation and was based on changing the pH as a mechanism controller.

RESULTS

This work is intended to test the efficacy of this drug carrier for the release of doxorubicin. A comparison was also made between single-walled and double-walled carbon nanotubes to answer the question of which one can be a better carrier for doxorubicin. The study of DOXORUBICIN adsorption and release showed that the DOXORUBICIN adsorption on single-walled carbon nanotube and multi-walled carbon nanotube in neutral pH was stronger than it was in acidic pH, which could be due to the electrostatic interactions between the carboxyl group of nanotubes and DOXORUBICIN. Based on this and according to the investigation of hydrogen bonds, diffusion coefficients, and other results it was clear that the drug release in acidic pH was appropriate for body conditions. Since cancer tissues pH is acidic, this shows the suitability of carbon nanotube in drug delivery and DOXORUBICIN release in cancer tissues. In addition, it was shown that the blood pH (pH = 7) is suitable for DOXORUBICIN loading on the carbon nanotube and carbon nanotube-DOXORUBICIN linkage remained stable at this pH; accordingly, the carbon nanotube could deliver DOXORUBICIN in blood quite well and release it in cancerous tissues. This suggests the carbon nanotubes as a promising drug carrier in the cancer therapy which can be also investigated in experiments.

CONCLUSION

It was revealed that the bonds between multi-walled carbon nanotube and DOXORUBICIN was stronger and this complex had a slower release in the cancer tissues compared to the single-walled carbon nanotube; this can be regarded as an advantage over the single-walled carbon nanotube in the DOXORUBICIN delivery and release.