Unraveling the binding mechanisms of SARS-CoV-2 variants through molecular simulations.

The emergence of SARS-CoV-2 variants like Delta (AY.29) and Omicron (EG.5) poses continued challenges for vaccines and therapeutics. Mutations in the viral spike protein are key in altering infectivity and immune evasion. This study uses computational modeling to investigate the molecular binding mechanisms between spike protein variants and the ACE2 host receptor. Using the MARTNI force field, coarse-grained molecular dynamics (CGMD) simulations and nudged elastic band (NEB) calculations explore spike-ACE2 interactions for the wild type, Delta variant, and Omicron variant. The simulations reveal Omicron has the strongest binding affinity at -128.35 ± 10.91 kcal/mol, followed by Delta and wild type. Key mutations in Delta and Omicron, like Q493R and Q498R, optimize electrostatic contacts, enhancing ACE2 interactions. The wild-type spike has the highest transition state energy barrier at 17.87 kcal/mol, while Delta has the lowest barrier at 9.21 kcal/mol. Despite slightly higher dual barriers, Omicron's increased binding energy lowers its overall barrier to rapidly bind ACE2. These findings provide residue-level insights into mutation effects on SARS-CoV-2 infectivity. The computational modeling elucidates mechanisms underlying spike-ACE2 binding kinetics, aiding the development of vaccines and therapies targeting emerging viral strains.

AI-Driven Design System for Fabrication of Inhalable Nanocatchers for Virus Capture and Neutralization.

The global pandemic presents a critical threat to humanity, with no effective rapid-response solutions for early-stage virus dissemination. This study aims to create an AI-driven entry-blocker design system (AIEB) to fabricate inhalable virus-like nanocatchers (VLNCs) fused with entry-blocking peptides (EBPs) to counter pandemic viruses and explore therapeutic applications. This work focuses on developing angiotensin-converting enzyme 2 (ACE2)-mimic domain-fused VLNCs (ACE2@VLNCs) using AIEB and analyzing their interaction with the SARS-CoV-2 receptor binding domain (RBD), demonstrating their potential to hinder SARS-CoV-2 infection. Aerosol-based tests show ACE2@VLNCs persist over 70 min in the air and neutralize pseudoviruses within 30 min, indicating their utility in reducing airborne virus transmission. In vivo results reveal ACE2@VLNCs mitigate over 67% of SARS-CoV-2 infections. Biosafety studies confirm their safety, causing no damage to eyes, skin, lungs, or trachea, and not eliciting significant immune responses. These findings offer crucial insights into pandemic virus prevention and treatment, highlighting the potential of the ACE2@VLNCs system as a promising strategy against future pandemics.

Design single-stranded DNA aptamer of cluster of differentiation 47 protein by stochastic tunnelling-basin hopping-discrete molecular dynamics method.

The formation of the Cluster of Differentiation 47 (CD47, PDB code: 2JJT)/signal regulatory protein α (SIRPα) complex is very important as it protects healthy cells from immune clearance while promoting macrophage phagocytosis for tumour elimination. Although several antibodies have been developed for cancer therapy, new function-blocking aptamers are still under development. This study aims to design the aptamer AptCD47, which can block the formation of the CD47/SIRPα complex. This study employs the MARTINI coarse-grained (CG) force field and the stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method to identify the most stable AptCD47/CD47 complexes. Coarse-grained molecular dynamics (CGMD) simulations were used to obtain root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses. The results demonstrate that the formation of AptCD47/CD47 complexes renders the CD47 structure more stable than the single CD47 molecule in a water environment. The minimum energy pathway (MEP) obtained by the nudged elastic band (NEB) method indicates that the binding processes of 5'-ATTCAATTCC-3' and 5'-AGTGCAATCT-3' to CD47 are barrierless, which is much lower than the binding barrier of SIRPα to CD47 of about 14.23 kcal/mol. Therefore, these two AptCD47/CD47 complexes can create a high spatial binding barrier for SIRPα, preventing the formation of a stable CD47/SIRPα complex. The proposed numerical process with the MARTINI CG force field can be used to design CD47 aptamers that efficiently block SIRPα from binding to CD47.Communicated by Ramaswamy H. Sarma.

Synergistic Functionality of Dopants and Defects in Co-Phthalocyanine/B-CN Z-Scheme Photocatalysts for Promoting Photocatalytic CO2 Reduction Reactions.

The realization of solar-light-driven CO2  reduction reactions (CO2 RR) is essential for the commercial development of renewable energy modules and the reduction of global CO2 emissions. Combining experimental measurements and theoretical calculations, to introduce boron dopants and nitrogen defects in graphitic carbon nitride (g-C3 N4 ), sodium borohydride is simply calcined with the mixture of g-C3 N4 (CN), followed by the introduction of ultrathin Co phthalocyanine through phosphate groups. By strengthening H-bonding interactions, the resultant CoPc/P-BNDCN nanocomposite showed excellent photocatalytic CO2 reduction activity, releasing 197.76 and 130.32 µmol h-1  g-1 CO and CH4 , respectively, and conveying an unprecedented 10-26-time improvement under visible-light irradiation. The substantial tuning is performed towards the conduction and valance band locations by B-dopants and N-defects to modulate the band structure for significantly accelerated CO2 RR. Through the use of ultrathin metal phthalocyanine assemblies that have a lot of single-atom sites, this work demonstrates a sustainable approach for achieving effective photocatalytic CO2 activation. More importantly, the excellent photoactivity is attributed to the fast charge separation via Z-scheme transfer mechanism formed by the universally facile strategy of dimension-matched ultrathin (≈4 nm) metal phthalocyanine-assisted nanocomposites.

How atoms of polycrystalline Nb20.6Mo21.7Ta15.6W21.1V21.0 refractory high-entropy alloys rearrange during the melting process.

The melting mechanism of single crystal and polycrystalline Nb20.6Mo21.7Ta15.6W21.1V21.0 refractory high entropy alloys (RHEAs) were investigated by the molecular dynamics (MD) simulation using the second-nearest neighbor modified embedded-atom method (2NN MEAM) potential. For the single crystal RHEA, the density profile displays an abrupt drop from 11.25 to 11.00 g/cm3 at temperatures from 2910 to 2940 K, indicating all atoms begin significant local structural rearrangement. For polycrystalline RHEAs, a two-stage melting process is found. In the first melting stage, the melting of the grain boundary (GB) regions firstly occurs at the pre-melting temperature, which is relatively lower than the corresponding system-melting point. At the pre-melting temperature, most GB atoms have enough kinetic energies to leave their equilibrium positions, and then gradually induce the rearrangement of grain atoms close to GB. In the second melting stage at the melting point, most grain atoms have enough kinetic energies to rearrange, resulting in the chemical short-ranged order changes of all pairs.

Design the RNA aptamer of PCA3 long non-coding ribonucleic acid by the coarse-grained molecular mechanics.

The stochastic tunneling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to predict the tertiary structure of the prostate cancer marker PCA3 using two respective secondary structures predicted by the Vienna RNA package and Mathews lab package. The RNA CG force field with the geometrical restraints for maintaining PCA3 secondary structures is used. For each secondary structure, 5000 PCA3 structures were predicted by using 5000 independent initial structures. These structures were then evaluated by a scoring function, considering the contributions from the radius of gyration, contact energy, and surface fraction of complementary nucleotides to ASO683 and ASO735 used in the related experiment. For each secondary structure, the PCA3 structures with the highest three scores were selected for aptamer design and further adsorption simulation. The ASOs complementary to PCA3 surface segments possessing relatively higher RMSF values are selected to be the potential PCA3 aptamers. After the adsorption simulation, the adsorption energies of ASO961, ASO3181, ASO3533, and ASO3595 are higher than or comparable to those of ASO683 and ASO735 used in the experiment. The NEB method was used to obtain MEPs for the adsorption process of all predicted ASOs onto PCA3. The adsorption barriers range between 29 ∼ 39 kcal/mol, while the desorption barriers range between 112 ∼ 352 kcal/mol, indicating these aptamer/PCA3 complexes are very stable. Using PCA3 surface segments with relatively higher RMSF values, longer ASOs can be also obtained and most longer ASOs possess lower binding energy, ranging between -486.1 and -618.2 kcal/mol.Communicated by Ramaswamy H. Sarma.

Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method.

The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (AptEpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the AptEpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the AptEpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For AptEpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each AptEpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable AptEpA/EpCAM complex in water.

Improvement of Model Predictive Current Control Sensing Strategy for a Developed Small Flux-Switching Permanent Magnet Motor.

This paper presents an improved control system for a small flux-switching permanent magnet motor (FSPM) to enhance its performance and torque sensing. The analytical magnetic circuit design was used to determine the related motor parameters, such as the air gap flux density, permeance coefficient (Pc), torque, winding turns, pole number, width, length, magnet geometry, and the current density of FSPM. The electromagnetic analysis of this motor was performed by software (ANSYS Maxwell) to optimize the motor performance. In this study, the performance of FSPM was investigated by the uniform design experimentation (UDE). For the control system, the model predictive current control (MPCC) is currently recognized as a high-performance control strategy, due to its quick response and simple principle. This model contained the nonlinear part of the system, to improve the torque ripple of FSPM. A modified MPCC strategy was proposed to improve the distortion of the current waveform and decrease the computational burden. The new modified control architecture was mainly composed of three parts, such as the estimation of electromotive force (EMF), current prediction, and optimal vector selection/vector duration. When the reference voltage vector was obtained, the three-phase duties were easily determined by the principle of space vector modulation (SVM). The results show the different strategy methods between the newly proposed modified MPCC and traditional proportional integral (PI) controller. In the control of FSPM, a modified MPCC strategy was able to achieve a better performance response and decrease the computational burden. At a low speed of 350 rpm, the proposed modified MPCC can achieve a better dynamic response. The nonlinear problem of the startup speed was also effectively resolved. The torque sensing performance of the simulation and the experimental test value were compared. The torque sensing performance of the simulation and the actual test value were also examined. In this study, the optimization focused not only on the motor design and fabrication, but also on an improved motor control strategy and torque sensing, in order to achieve the integrity of the FSPM system.

The Mechanical Behaviors of Polyethylene/Silver Nanoparticle Composites: an Insight from Molecular Dynamics study.

This research uses molecular dynamics simulation (MD) to study the mechanical properties of pristine polyethylene (PE) and its composites which include silver nanoparticles (PE/AgNPs) at two AgNP weight fractions of 1.05 wt% and 3.10 wt%. The stress-strain distribution of the tensile process shows that the embedded AgNPs can significantly improve the Young's modulus and tensile strength of the pristine PE, due to improvements in the local density and strength of the PE near the AgNP surface in the range of 12 Å. Regarding the effect of temperature on the mechanical properties of pristine PE and PE/AgNP composites, the Young's modulus and the strength of the pristine PE and PE/AgNP composites decreased significantly at 350 K and 450 K, respectively, consistent with predicted melting temperature of pristine PE, which lies at around 360 K. At such temperatures as these, PE material has stronger ductility and a higher mobility of AgNPs in the PE matrix than those at 300 K. With the increase of tensile strain, AgNPs tend to be close, and the fracture of PE leads to a similarity between both the Young's modulus and ultimate strength found for the pristine PE and those found for the PE/AgNP composites at 350 K and 450 K, respectively.

Effects of Strontium incorporation to Mg-Zn-Ca biodegradable bulk metallic glass investigated by molecular dynamics simulation and density functional theory calculation.

Molecular dynamics (MD) simulation and density functional theory (DFT) calculations were used to predict the material properties and explore the improvement on the surface corrosion resistance for the Mg66Zn30Ca3Sr1 bulk metallic glass (BMG). The Mg66Zn30Ca4 BMG was also investigated to realize the influence of the addition of Sr element on the material behaviors of Mg66Zn30Ca4. The Mg-Zn-Ca-Sr parameters of the next nearest-neighbor modified embedded atom method (2NN MEAM) potential were first determined by the guaranteed convergence particle swarm optimization (GCPSO) method based on the reference data from the density functional theory (DFT) calculation. Besides, using the 2NN MEAM parameters of the Mg-Zn-Ca-Sr system, the structures of Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1 were predicted by the simulated-annealing basin-hopping (SABH) method. The local atomic arrangements of the predicted BMG structures are almost the same as those measured in some related experiments from a comparison with the calculated and experimental X-ray diffraction (XRD) profiles. Furthermore, the HA index analysis shows that the fractions of icosahedra-like local structures are about 72.20% and 72.73% for Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1, respectively, indicating that these two BMG structures are entirely amorphous. The uniaxial tensile MD simulation was conducted to obtain the stress-strain relationship as well as the related mechanical properties of Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1. Consequently, the predicted Young's moduli of both BMGs are about 46.4 GPa, which are very close to the experimental values of 48.8 ± 0.2 and 49.1 ± 0.1 GPa for Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1, respectively. However, the predicted strengths of Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1 are about 850 and 900 MPa, both are slightly higher than the measured experimental values about 747 ± 22 and 848 ± 21 MPa for Mg66Zn30Ca4 and Mg66Zn30Ca3Sr1. Regarding the thermal properties, the predicted melting temperature of Mg66Zn30Ca3Sr1 by the square displacement (SD) profile is about 620 K, which is very close to the experimental melting temperature of about 613 K. The self-diffusion coefficients of Mg, Zn, Ca, and Sr elements were also calculated for temperatures near their melting points by means of the Einstein equation. The methodology can determine the diffusion barriers for different elements by utilizing these diffusion coefficients resulting in a fact that the diffusion barriers of Ca and Sr elements of Mg66Zn30Ca3Sr1 are relatively high. For the electronic properties predicted by the DFT calculation, the projected density of states (PDOS) profiles of surface Mg, Zn, Ca, and Sr elements clearly show that the addition of Sr into Mg66Zn30Ca4 effectively reduces the s and p orbital states of surface Mg and Zn elements near the Fermi level, particularly the p orbits, which suppresses the electron transfer as well as increases the surface corrosion resistance of Mg66Zn30Ca4. Consequently, this study has provided excellent 2NN MEAM parameters for the Mg, Zn, Ca, and Sr system by the GCPSO method to predict real BMG structures as well as by means of the DFT calculation to explore the electronic properties. Eventually, through our developed numerical processes the material properties of BMGs with different compositions can be predicted accurately for the new BMG design.

Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches.

The stochastic tunneling-basin hopping method (STUN-BH) was utilized to obtain the most stable peptide S7 configuration (Ac-Ser-Ser-Phe-Pro-Gln-Pro-Asn-CONH2) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigate the thermal stability between S7 and Au facet at 300 K in both vacuum and water environment. Moreover, further design sets of peptide sequences on Au(111) facet were used to compare with S7. All molecular simulations were carried out by the large-scale atomic/molecular massively parallel simulator (LAMMPS). The Amber99sb-ILDN force field was employed for modeling the interatomic interaction of peptides, and the TIP3P water was used for the water environment. The CHARMM-METAL force field was introduced to model the S7, PF8 (Ac-Pro-Phe-Ser-Pro-Phe-Ser-Pro-Phe-CONH2) and FS8 (Ac-Phe-Ser-Phe-Ser-Phe-Ser-Phe-Ser-CONH2) interactions with Au(111). The MD simulation results demonstrate that the morphology of Pro affects the adsorption stability of Phe. Therefore, we designed two sequences, PF8 and FS8, to confirm our simulation result through experiment. The present study also develops a novel low-temperature plasma synthesis method to evaluate the facet selecting performance of the designed peptide sequences of S7, PF8, and FS8. The experimental results suggest that the reduced Au atom seed is captured with the designed peptide sequences and slowing growing under room temperature for 72 hours. The experimental results are in the excellent agreement with the simulation finding that the Pro in the designed peptide sequences plays a critical role in the facet selection for Au atom stacking.

Observing the three-dimensional terephthalic acid supramolecular growth mechanism on a stearic acid buffer layer by molecular simulation methods.

The terephthalic acid (TPA) supramolecular growth mechanisms on the stearic acid (STA) buffer layer, such as the phase separation and layer-by-layer (LBL) mechanisms, were considered by molecular simulations. The electrostatic surface potential (ESP) charges obtained by the semi-empirical ab initio package VAMP with PM6 were used with the Dreiding force field. The stochastic tunneling-basin hopping-discrete molecular dynamics method (STUN-BH-DMD) was first used to construct the most stable STA buffer layers (STA100, STA120, and STA140) on graphene. At STA100 and STA120, the STA molecule stacking along their long axis is the major mechanism to obtain the stable STA buffer layer. At STA140, the hydrogen bond network between the terminal COOH groups of STA molecules makes the STA buffer layer the most stable, leading to a higher disintegration temperature among all STA coverages. In the early growth of the TPA supramolecule, TPA molecules were first adsorbed by the holes between STA piles. At STA100 and STA120, the subsequent TPA molecules were adsorbed by the TPA molecules within the holes, leading to the phase separation growth. At STA140, the TPA supramolecule tends to grow by the LBL mechanism.

Predicting the Most Stable Aptamer/Target Molecule Complex Configuration Using a Stochastic-Tunnelling Basin-Hopping Discrete Molecular Dynamics Method: A Novel Global Minimum Search Method for a Biomolecule Complex.

This study proposed a novel global minimum search method for predicting the most stable biomolecule complex, which combines the strengths of three global minimum search methods (stochastic tunnelling, basin hopping, and discrete molecular dynamics) to efficiently improve the spatial domain search ability of the stochastic tunnelling-basin hopping (STUN-BH) method from our previous study. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as a benchmark target molecule for the EpCAM aptamer EpA (AptEpA). For the most stable AptEpA/EpCAM complex predicted by our new method, the AptEpA was attached to the entangling loop fragments of the two EpCAM molecules with the most AptEpA residues. After the AptEpA/EpCAM complex had equilibrated with the water environment through a molecular dynamics simulation at 300 K for 10 ns, stable hydrogen bonds formed between the bases of AptEpA and EpCAM residues of the secondary structures, which included the alpha helix and beta sheet becoming less stable in the water environment. Those hydrogen bonds formed between the bases of AptEpA and EpCAM loop fragment residues remained stable in the water environment.

Bio-Inspired NanoVilli Chips for Enhanced Capture of Tumor-Derived Extracellular Vesicles: Toward Non-Invasive Detection of Gene Alterations in Non-Small Cell Lung Cancer.

Tumor-derived extracellular vesicles (EVs) present in bodily fluids are emerging liquid biopsy markers for non-invasive cancer diagnosis and treatment monitoring. Because the majority of EVs in circulation are not of tumor origin, it is critical to develop new platforms capable of enriching tumor-derived EVs from the blood. Herein, we introduce a biostructure-inspired NanoVilli Chip, capable of highly efficient and reproducible immunoaffinity capture of tumor-derived EVs from blood plasma samples. Anti-EpCAM-grafted silicon nanowire arrays were engineered to mimic the distinctive structures of intestinal microvilli, dramatically increasing surface area and enhancing tumor-derived EV capture. RNA in the captured EVs can be recovered for downstream molecular analyses by reverse transcription Droplet Digital PCR. We demonstrate that this assay can be applied to monitor the dynamic changes of ROS1 rearrangements and epidermal growth factor receptor T790M mutations that predict treatment responses and disease progression in non-small cell lung cancer patients.

Temperature dependent Young's modulus of ZnO nanowires.

A thermal resonant method was developed to accurately determine the temperature-dependent Young's moduli of nanowires. In this method, the frequency spectra of a [0001]-oriented ZnO nanowire cantilever at elevated temperatures were measured using scanning laser Doppler vibrometry. The temperature-dependent Young's moduli were derived from the resonant frequencies using Euler-Bernoulli beam theory. It was found that the modulus of ZnO nanowires decreased linearly with the increase of temperature from 300 to 650 K, independent of the nanowire diameter ranged from 101 to 350 nm. The temperature coefficient that defines the linear relationship between the dimensionless modulus and temperature is [Formula: see text] which agrees with that of [Formula: see text] being calculated using molecular dynamics with a partially charged rigid ion model.

Ovalbumin-Loaded Gelation Microneedles Made of Predictive Formulation by Molecular Dynamics Simulation for Enhancement of Skin Immunization.

Gelation microneedle (GMNs) based vaccinations with tumor antigens have been considered to be an attractive method for transcutaneous immunization because of their superior ability to deliver vaccines through the stratum corneum (SC) in a minimally invasive manner, which subsequently induces adaptive antitumor immunity. In this study, molecular dynamics (MD) uniaxial tension simulations were conducted to predict the formulation of poly(vinyl alcohol) (PVA; possesses high water solubility) and poly(methyl vinyl ether-altmaleic anhydride) (PMVEMA; possesses high mechanical strength) blend that has the strongest mechanical properties. To validate the accuracy of the Dreiding potential for these two polymers, their densities and Hildebrand solubility parameters were first predicted using MD simulations. These values exhibited good agreement with the corresponding experimental results, indicating the accuracy of the Dreiding potential for the polymers. Regarding the simulation results, the number density of H-bonds between PVA and PMVEMA was the highest at 50% PMVEMA, which can significantly enhance the mechanical strength of pristine PVA for enhanced skin immunization. In terms of further experimental validation, evidence from mechanical strength, solubility, in vitro porcine skin penetration tests, and in vivo immunization were consistent with our simulation predictions. In addition, our results indicated that delivery of ovalbumin (OVA) using GMN patches fabricated using PVA/PMVEMA (50%/50%) provided even stronger immune responses. Using this molecular simulation procedure, the optimal fraction of PVA/PMVEMA composite for the strongest mechanical properties can be rapidly predicted to reduce research time and costs in related experiments.

Catalytic polymerization of naphthalene by HF/BF3 super acid: an ab initio density functional theory study.

Mesophase pitch fabricated through polymerization of polycyclic aromatic hydrocarbons (PAHs) is highly aromatic and of high quality, and it can be used as a raw material to produce other carbon-based materials. Hydrofluoride/boron trifluoride (HF/BF3) is currently an efficient reagent to catalyze the PAH polymerization to produce mesophase pitch. In this study, density functional theory (DFT) calculations are performed to propose a mechanism for naphthalene catalytic polymerization using HF/BF3. The overall reaction mechanism can be conceptualized as having two stages: activation, followed by polymerization. During activation, HF/BF3 acts a proton donor to activate naphthalene, whose then-protonated form can promote the formation of a C-C bond with another naphthalene molecule via electrophilic addition. We also propose a catalyst recovery pathway, which can stabilize the intermediate products. In the polymerization stage, two types of pathways are proposed, those of chain elongation and intramolecular cyclization. According to the proposed catalytic mechanism in this study, the predicted mesophase product shows highly aliphatic hydrogens, which is consistent with the experimental results. We propose the full catalytic mechanism using DFT calculations. Our results provide a better understanding of how to develop novel and green catalysts, which can replace the HF/BF3 reagent in future applications.

Aptasensor designed via the stochastic tunneling-basin hopping method for biosensing of vascular endothelial growth factor.

The Systematic Evolution Ligands by Exponential Enrichment (SELEX) is common used for selection of high affinity single-stranded DNA (ssDNA) aptamer with target protein. However, we do not know what the most stable configuration of the selected aptamer bound with target protein is. Therefore, a systematic search process using the stochastic tunneling-basin hopping (STUN-BH) method is proposed to find the most stable configuration of the ssDNA aptamer specific for vascular endothelial growth factor (VEGF) capture (AptVEGF; 5'-TGTGGGGGTGGACGGGCCGGGTAGA-3'). After the most stable configuration was obtained by the STUN-BH method, molecular dynamics (MD) simulation was carried out to investigate the thermal stability of AptVEGF/VEGF at 300 K in both vacuum and water. All molecular simulations were conducted with the large-scale atomic/molecular massively parallel simulator (LAMMPS), and the AMBER99SB force field was used to describe the atomic interactions for the current AptVEGF/VEGF system. The three most stable AptVEGF/VEGF configurations obtained by the STUN-BH method indicated that AptVEGF residues exhibit greater affinity for VEGF surface loop fragments as compared with surface alpha helix and beta sheet fragments. Results indicated that after the first AptVEGF (AptVEGF I) occupies most of the VEGF loop fragment, the second AptVEGF (AptVEGF II) is adsorbed by the rest of the VEGF loop fragment and the VEGF Chain B beta sheet fragment, resulting in a 24.8% reduction in binding strength as compared to that of AptVEGF I. Furthermore, when AptVEGF I and AptVEGF II chains were stably adsorbed by VEGF, the third AptVEGF (AptVEGF III) chain can only partially attach to VEGF, as confirmed by real AptVEGF-VEGF binding experiments. Lastly, we demonstrated that the aptasensor constructed according to MD simulation is highly sensitive for VEGF with a linear detection range of 10 pg/mL-10 ng/mL.

Diagnosis by simplicity: an aptachip for dopamine capture and accurate detection with a dual colorimetric and fluorometric system.

In this study, we aim to rapidly fabricate an aptachip with a dual colorimetric and fluorometric sensing strategy for easy dopamine (DA) detection with high sensitivity and selectivity. To construct an aptachip with high DA capture efficiency, molecular dynamics (MD) simulations were utilitized to predict the most stable configuration of the DA-binding aptamer (DBA) for DA recognition. The DA in the specimen would be specifically captured on the DBA-aptachip, then released from the DBA in alkaline solution to form DA-quinone (DAQ), thus leading to a color change (from colorless to brown) and inducing a dramatic decrease in the fluorescence intensity as a result of the photoinduced electron transfer (PET) for bovine serum albumin (BSA)-stabilized Au nanoclusters (BSA-Au NCs). The detection limit of DA is as low as 0.1 µg mL-1 for the colorimetric system and 0.5 ng mL-1 for the fluorometric system. In addition, this biosensing of DA is easy to implement for visual detection owing to the DA oxidation and fluorescence quenching by BSA-AuNCs in the presence of the alkaline solution. Both the colorimetric and fluorometric systems showed excellent selectivity toward DA over interfering substances. Furthermore, we demonstrated the application of the present approach to analysis of artificial cerebrospinal fluid (ACSF) and serum samples, suggesting that this system holds promise for diagnostics.

Investigation of the self-assembly of CS and PCL copolymers with different molecular weights in water solution by coarse-grained molecular dynamics simulation.

Coarse-grained molecular dynamics (CGMD) simulation was employed to investigate how stable chondroitin sulfate-graft-polycaprolactone (CS-PCL, CP) copolymers self-assemble into micelles in an aqueous environment. Three types of CP containing low (2.4%), medium (6.3%), and high (18.7%) PCL contents (denoted L-CP, M-CP, and H-CP, respectively) in which PCL molecules consisting of 63 monomers were grafted onto each CS molecule consisting of 120 monomers were considered. L-CP and M-CP were found to display spheroidal micellar structures, while H-CP presented a rod-like structure, in agreement with previous experimental observations. In addition, the entanglement of the PCL segment increased as its molecular weight was increased. The number density distribution profiles of PCL, CS, and water molecules indicated that there were a few water molecules between the PCL core of the micelle and the water solution surrounding the micelle (in the micelle layer immediately above the core), and the number density of water in the CP micelle increased as the PCL content decreased. Using the radius of gyration, the three-dimensional conformations of the micelles were explored. When the number of CP chains was 3, H-CP adopted a long nanorod form, whereas L-CP and M-CP were roughly nanospherical. When the number of CP chains was increased beyond 3, however, the structure of L-CP changed from a nanosphere to a nanodisk. Finally, the slope of the mean square displacement profile was greatest when the molecular weight of the PCL segment was lowest, indicating that the mobilities of the CS and PCL segments are highest in L-CP. The self-diffusion coefficients of the CS and PCL segments decreased as the number of PCL segments grafted increased. Graphical abstract Morphologies of H-CP micelle.