Mean Square Displacement Research Articles

Extreme heterogeneity in the microrheology of lamellar surfactant gels analyzed with neural networks.

The heterogeneity of the viscoelasticity of a lamellar gel network based on cetyl-trimethylammonium chloride and cetostearyl alcohol was studied using particle-tracking microrheology. A recurrent neural network (RNN) architecture was used for estimating the Hurst exponent, H, on small sectionsof tracks of probe spheres moving with fractional Brownian motion. Thus, dynamic segmentation of tracks via neural networks was used in microrheology and it is significantly more accurate than using mean square displacements (MSDs). An ensemble of 414 particles produces a MSD that is subdiffusive in time, t, with a power law of the form t^{0.74±0.02}, indicating power law viscoelasticity. RNN analysis of the probability distributions of H, combined with detailed analysis of the time-averaged MSDs of individual tracks, revealed diverse diffusion processes belied by the simple scaling of the ensemble MSD, such as caging phenomena, which give rise to the complex viscoelasticity of lamellar gels.

Gaseous diffusion as a correlated random walk.

The mean-square displacement per collision of a molecule immersed in a gas at equilibrium is given by its mean-square displacement between two consecutive collisions (mean-square free path) corrected by a prefactor in the form of a series. The nth term of the series is proportional to the mean value of the scalar product r_{1}·r_{n}, where r_{i} is the displacement of the molecule between the (i-1)-th and ith collisions. Simple arguments are used to obtain approximate expressions for each term. The key finding is that the ratio of consecutive terms in the series closely approximates the so-called mean persistence ratio. Exact expressions for the terms in the series are considered and their ratios for several consecutive terms are calculated for the case of hard spheres, showing an excellent agreement with the mean persistence ratio. These theoretical results are confirmed by solving the Boltzmann equationby means of the direct simulation Monte Carlo method. By summing the series, the mean-square displacement and the diffusion coefficient can be determined using only two quantities: the mean-square free path and the mean persistence ratio. A simple and an improved expression for the diffusion coefficient D are considered and compared with the so-called first and second Sonine approximations to D as well as with computer simulations of the Boltzmann equation. It is found that the improved diffusion coefficient shows very good agreement with simulation results over all intruder and molecule mass ranges. When the intruder mass is smaller than that of the gas molecules, the improved formula even outperforms the first Sonine approximation.

Dynamic and phase transition studies of ionic surfactant-stabilized oil/water microemulsion: Effects of volume fraction, polymer grafting, and temperature

In this work, we study the dynamic/phase transition relationship of a system composed of spherical particles of oil/water microemulsion, stabilised by an ionic surfactant based on cetylpyridinium chloride (CpCl) and an octanol-based cosurfactant, and dispersed in salt water. We examine a large range of volume fractions Φ. To do this, we use molecular dynamics simulations with an appropriate interaction potential that accounts for Van der Waals and electrostatic interactions. We also graft different numbers of dodecyl-(polyethylene oxide)227-dodecyltriblock copolymers onto the microemulsion nanodroplets, which we denote (n(D−PEO227−D)), where n varies from 0 to 12. Specifically, we treat the dynamic properties, using the mean square displacement (MSD) and diffusion coefficients, and then use Arrhenius law to determine the activation energy. In our study, we vary three main parameters: the volume fraction, the number of polymer added to the n(D−PEO227−D) microemulsion, and the temperature. The result shows a transition from the sol to the gel state of the bare microemulsion as the volume fraction increases or as the temperature decreases. Also, it proves that when a D-PEO-D polymer is added to the microemulsion, the system rapidly changes its state either as the volume fraction Φ increases or as the temperature T decreases. We also calculate the activation energy of the bare particles in the microemulsion at different volume fractions (ϕ) using the Arrhenius equation.

In Silico Studies of a Novel Scaffold of Acetylsalicylic Acid Derivatives Against EGFR by Molecular Docking and Molecular Dynamics Simulations

In this study, a molecular docking study was performed to propose the acetylsalicylic acid derivative 2-[(4-Acetylphenyl)carbamoyl]phenyl acetate (AMPBS) as a potential cancer candidate targeting the Epidermal Growth Factor Receptor (EGFR). The native ligand erlotinib was used as a control compound. The calculated docking score of -7.4 kcal/mol compared to the native ligand erlotinib of -7.0 kcal/mol of AMPBS compound revealed a promising anticancer activity. The stability of the complex was interpreted by careful analysis of the root mean square deviation (RMSD), root mean square fluctuations (RMSF) and mean hydrogen bond number (Hb) plots obtained from the MD trajectories. The ADMET properties of AMPBS were evaluated using relevant online tools. Drug-likeness studies showed that AMPBS is suitable for use in living organisms. It was predicted that AMPBS in the active pocket could be a promising inhibitor due to its high binding energy, interaction mechanism and retention in the active pocket.

Molecular dynamics simulations of betaine-based deep eutectic solvents with varying iso-alcohols chain lengths

Betaine-based (BET) deep eutectic solvents (DESs) made with isoalcohols of varying hydrocarbon chain lengths, namely triethylene glycol (TEG), 1, 2-ethanediol (ETD), 1, 3-propanediol (PPD) and 1, 4-butanediol (BTD) were modelled. Their effects on the formation of aqueous biphasic system (ABS) with 2 M dipotassium phosphate salt solution (K2HPO4) as well as the extraction of common protein molecules, bovine serum albumin (BSA), were studied using molecular dynamics simulation with Gromacs. Qualitative and quantitative data were used to analyse the simulation results, which includes visualised systems in equilibrium, root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration, radial distribution function (RDF) and hydrogen bond analysis. The results and literature research validated the role of inorganic salt solute concentration on the phase forming ability as well as the possibility of protein denaturation. More investigations and experimental works are to be carried out regarding the type of inorganic salt and its concentration for aqueous biphasic systems (ABSs) with alcohol based DESs and salt solution for protein extraction purposes. This is essential to understand the salting-out effect and to isolate the effects of hydrocarbon chain length from other influencing factors. Additionally, inorganic salt concentrations, presence of ether linkage as well as hydrocarbon chain length is shown to play a role in the dynamics between molecules in the system as well as protein conformational changes. Overall, ABS incorporating PPD and BTD with hydrocarbon chain lengths not exceeding C4 demonstrated superior performance in terms of protein conformational stability and interaction, showcasing their efficacy in protein extraction process.

Wetting and aggregation mechanisms of coal molecules via XTG and SDBS based on molecular simulation

To study the interaction process of sodium dodecyl benzene sulfonate (SDBS) and xanthan gum (XTG) molecules in a composite dust suppressant and its influence mechanisms on the wettability and agglomeration characteristics of bituminous coal dust, Material Studio software was used to establish water–XTG binary system models, water–SDBS–XTG ternary system models, and water–SDBS–XTG–coal quaternary system models. Then, molecular dynamics simulations were performed through angular distribution, relative concentration distribution, mean squared displacement (MSD), and interaction energy to study the interaction mechanism between SDBS and XTG and the change in wettability of coal dust. Results showed that the configuration in the binary system changed after stabilization, and SDBS transformed from a disordered state into a directional arrangement with the head group oriented toward the liquid phase and the tail group oriented toward the gas phase. In the ternary system, the head group of SDBS interacted with the XTG molecules, and the XTG wound into a helical structure, reducing the viscosity of the solution. With an increase in the number of SDBS molecules, the angle of the head group of SDBS and the tail chain of SDBS increased to 113.95°. The number of H bonds in the system increased from 1676 to 1697. In the quaternary system, the rate of change of the diffusion coefficient continuously increases. The absolute value of the interaction energy increased from 5920.48 kJ/mol to 9295.35 kJ/mol. The higher the concentration of SDBS, the better the adsorption effect, and the more stable the molecular configuration. The number of H bonds and the distribution area of the overlapping region between water and coal gradually increased, indicating that the larger the area where water molecules could penetrate into the coal molecules, the better the wetting effect on coal. This study reveals the intermolecular interaction process and the mechanisms of coal dust wetting and agglomeration in a composite dust suppressant. It provides theoretical support for the application of this composite dust suppressant.

Enhancing Zn (II) recovery efficiency: Bi-divalent nickel–cobalt ferrite spinel NiXCo1-xFe2O4 as a Game-changing Adsorbent—an experimental and computational study

This study presents a comprehensive investigation into NiXCo1-xFe2O4 (x = 0.5) spinel nanoparticles synthesized through a one-pot hydrothermal method using Co(NO3)2.6H2O and Ni(NO3)2.6H2O salts. XRD, FTIR, FESEM, and VSM analyses confirmed a cubic structure of NiXCo1-xFe2O4 (x = 0.5) nanoparticles without impurities. These nanoparticles exhibit efficient Zn (II) adsorption characteristics, following Langmuir isotherm and pseudo-second-order kinetics. The maximum adsorption capacity was measured to be 666.67 mg g−1 at pH = 7, with mechanisms involving both electrostatic attraction and cation exchange. Desorption studies indicate more than 75% Zn (II) recovery in an acidic environment (pH = 2) after three cycles. Computational analysis was used to validate the experimental results through Molecular Dynamics simulations, initially focusing on NiXCo1-xFe2O4 (x = 0.5). Further exploration involved variations in x at 0.25 and 0.75 to identify the optimal Ni and Co ratio in this bivalent cation spinel ferrite. Computational analyses reveal the superior performance of NiXCo1-xFe2O4 (x = 0.75) in Zn (II) removal, supported by radial distribution analysis, VdW energy, Coulombic energy, mean square displacement (MSD), root mean square displacement (RMSD), and interaction energy. This comprehensive study provides valuable insights into the adsorption behavior and structural stability of NiXCo1-xFe2O4 nanoparticles, showcasing potential applications in Zn (II) removal.

Molecular dynamics study of cross‐linking degrees effect on the aging resistance of epoxy asphalt: Insights from oxygen diffusion

AbstractTo interpret the diffusion behavior of oxygen in epoxy asphalt with different cross‐linking degrees, epoxy asphalt‐oxygen diffusion layer models were constructed. The effect of temperature on oxygen diffusion and the number of oxygen molecules penetrating the epoxy asphalt was quantitatively analyzed. Fick's second law was used to determine the oxygen diffusion coefficient. The Mean square displacement (MSD) was extracted to analyze the effect of cross‐linking degree on the molecular motion of the base asphalt. The results show that as the cross‐linking degree increases, the number of oxygen in the epoxy asphalt decreases, accompanied by a reduction in the oxygen diffusion coefficient. Temperature significantly affects the rate of oxygen diffusion, with higher temperatures leading to greater diffusion depths over the same simulation time. The oxygen diffusion coefficient of epoxy asphalt ranges from 4.60 × 10−11 to 2.20 × 10−10 m2/s at temperatures of 298–373 K. The epoxy system markedly restricts the movement of base asphalt molecules, with saturate being most affected by cross‐linking degree and asphaltene the least. A high cross‐linking network impedes the asphalt‐oxygen contact oxidation, enhancing epoxy asphalt's anti‐aging capacity. These findings provide support for optimizing epoxy asphalt formulations and guiding the development of anti‐oxidant epoxy asphalt.

Unveiling the potential of Traditional Chinese Medicines in combating NorA-mediated S. aureus drug resistance. A molecular dynamic study

Drug resistance Staphylococcus aureus (S. aureus) is emerging as the most prevalent pathogen in surgical wounds and orthopedic surgeries. NorA is a major drug efflux involved in the drug resistance, reducing intracellular drug concentrations. The current study aimed to find some potential inhibitors derived from Traditional Chinese Medicines (TCM) against NorA using a 500 ns molecular dynamics (MD) simulation. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), free energy, dynamic cross correlation matrix (DCCM) was computed. Three TCM compound; piperine, demethoxycurcumin, and tectorigenin exhibited many hydrogen bonds and hydrophobic contacts in the binding pockets residues, especially with ionizable residues (Arg 98, Glu 222, Asp 307, and Arg 310), forming two different charged regions. RMSD of NorA-piperine complex shows some initial instability at 5.2 Å, followed by an increase to 5.8 Å at 222 ns, and a further rise to 6.1 Å by the end of the 500 ns simulation period. Similarly, the NorA-demethoxycurcumin and NorA-tectorigenin complexes display elevated terminal RMSD of 7.9 Å each. RMSF, Rg, free energy, and binding pockets interactions confirmed the potential activity of piperine, demethoxycurcumin, and tectorigenin against NorA inhibition. In apo state NorA exhibited dispersion within the ranges of −100 to 150 (PC1: 39.97 %) while in complexed with ligands it illustrated significant differences in the motion patterns on PC1 (46.04 % and 27.39 %). The NorA-ligands DCCM displayed predominantly negatively correlated motions, particularly at the terminal resides from 200 to 370 where the pocket binding residues are located. These compounds also demonstrated drug-likeness and fitting best in the binding pocket residues (Asn > 137, Phe > 140, Phe > 303 Asp > 307, Arg > 310, Glu > 222, and Thr > 223). In conclusion, the compounds piperine, demethoxycurcumin, and tectorigenin interact with NorA through hydrogen bonds and hydrophobic contacts, particularly with key ionizable residues, Arg 98, Glu 222, Asp 307, and Arg 310, indicating potential inhibitory activity.

Investigation of Debye temperature and temperature-dependent EXAFS cumulants of Zn, Zr, α-Ti, Ru and Hf metals

In this work, the anharmonic Einstein model is developed to determine the Debye temperature and investigate the temperature effects on the extended x-ray absorption fine structure (EXAFS) cumulants of hexagonal close-packed (hcp) metals. We have derived the analytical expressions of the anharmonic effective potential, the effective force constant, the Debye temperature and the first four EXAFS cumulants as a function of axial ratio e = c/a. Numerical calculations have been conducted for hcp Zn, Zr, α-Ti, Ru and Hf metals up to temperature 800 K. Our findings indicate that the anharmonicity of thermal lattice vibrations significantly influences the EXAFS cumulants, particularly at high temperatures. Ru atoms have the strongest coupling force causing a phenomenon that Ru lattice shows a smaller thermal disorder, and Zn has a greater thermal disorder. Additionally, we highlight the significant contributions of thermal disorder to the mean-square relative displacement at high temperatures due to thermal lattice vibrations. Moreover, our Debye temperatures derived from the developed model align reasonably well with those reported in previous studies.

The Effect of β-Sheet Secondary Structure on All-β Proteins by Molecular Dynamics Simulations.

The effect of β-sheet ratio and chain length on all-β proteins was investigated by MD simulations. Protein samples composed of different repeating units with various β-sheet ratios or a different number of repeating units were simulated under a broad temperature range. The simulation results show that the smaller radius of gyration was achieved by the protein with the higher proportion of β-sheet secondary structure, which had the lower nonbonded energy with more HBs within the protein. The root mean square deviation (RMSD) and the root mean square fluctuation (RMSF) both increased with temperature, especially in the case of a longer chain. The visible period was also shown according to the repeated secondary structure. Several minimum values of RMSF were located on the skeleton of Cα atoms participating in the β-sheet, indicating that it is a kind of stable secondary structure. We also concluded that proteins with a short chain or a lower ratio of β-sheet could easily transform their oriented and compact structures to other ones, such as random coils, turns, and even α-helices. These results clarified the relationship from the primary level to the 3D structure of proteins and potentially predicted protein folding.

Biocomputational screening of natural compounds targeting 15-hydroxyprostaglandin dehydrogenase to improve skeletal muscle during aging.

Skeletal muscle (SM) contains a diverse population of muscle stem (or satellite) cells, which are essential for the maintenance of muscle tissue and positively regulated by prostaglandin E2 (PGE2). However, in aged SM, PGE2 levels are reduced due to increased prostaglandin catabolism by 15-hydroxyprostaglandin dehydrogenase (15-PGDH), a negative regulator of SM tissue repair and regeneration. Screening of a library of 80,617 natural compounds in the ZINC database against 15-PGDH was conducted from PyRx. Further, drug-likeness rules, including those of Lipinski, Ghose, Veber, Egan, and Muegge were performed. The selected complex was forwarded for MD simulations up to 100ns. Based on free energy of binding obtained from docking revealed that ZINC14557836 and ZINC14638400 more potently inhibiting to 15-PGDH than SW033291 (the control and high-affinity inhibitor of 15-PGDH). The free energies of binding obtained from PyRx for 15-PGDH-ZINC14557836, 15-PGDH-ZINC14638400, and 15-PGDH-SW033291 complexes were - 10.30, -9.80, and - 8.0kcal/mol, respectively. Root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), radii of gyration (Rg), solvent-accessible surface areas (SASAs), and H-bond parameters obtained by 100 ns MD simulations predicted ZINC14557836 and ZINC14638400 more stably complexed with 15-PGDH than SW033291. The several parameters, including physicochemical properties and drug-likenesses, were within acceptable limits, and ZINC14557836 and ZINC14638400 also satisfied other drug-likeness rules, including those of Lipinski, Ghose, Veber, Egan, and Muegge. These findings suggest that ZINC14557836 and ZINC14638400 provide starting points for the development of medications that increase SM regeneration and muscle stem (or satellite) cell numbers by inhibiting 15-PGDH.

Aging and confinement in subordinated fractional Brownian motion.

We study the effects of aging properties of subordinated fractional Brownian motion (FBM) with drift and in harmonic confinement, when the measurement of the stochastic process starts a time t_{a}>0 after its original initiation at t=0. Specifically, we consider the aged versions of the ensemble mean-squared displacement (MSD) and the time-averaged MSD (TAMSD), along with the aging factor. Our results are favorably compared with simulations results. The aging subordinated FBM exhibits a disparity between MSD and TAMSD and is thus weakly nonergodic, while strong aging is shown to effect a convergence of the MSD and TAMSD. The information on the aging factor with respect to the lag time exhibits an identical form to the aging behavior of subdiffusive continuous-time random walks (CTRW). The statistical properties of the MSD and TAMSD for the confined subordinated FBM are also derived. At long times, the MSD in the harmonic potential has a stationary value, that depends on the Hurst index of the parental (nonequilibrium) FBM. The TAMSD of confined subordinated FBM does not relax to a stationary value but increases sublinearly with lag time, analogously to confined CTRW. Specifically, short aging times t_{a} in confined subordinated FBM do not affect the aged MSD, while for long aging times the aged MSD has a power-law increase and is identical to the aged TAMSD.

Comparison of Phosphogypsum-Steel Slag-Based cement and Portland cement for stabilization of heavy metals in oil-based drillings cuttings

This research compared Portland cement and Phosphogypsum-Steel Slag-Based (PSSB) cement in terms of their capabilities to stabilize heavy metals (specifically lead and nickel) in Oil-Based Drill Cuttings (OBDC). In the experimental section, the qualitative analysis of heavy metal constituents in OBDC was captured by X-ray Photoelectron Spectroscopy (XPS). Additionally, an acetic acid leaching test was implemented for the heavy metal leaching concentration to evaluate the ceramsite stabilization effect on OBDC. In the simulation phase, cement models, heavy metal ion models, and stabilization models were constructed to explore the stabilization mechanism of heavy metals. Results demonstrated that PSSB cement exhibits superior stabilization effects on OBDC compared to Portland cement. Flame Atomic Absorption Spectrophotometry (FAAS) tests showed that PSSB cement reduced Ni and Pb leaching by 21.87 % and 47.32 %, respectively, compared to Portland cement. In PSSB cement, the diffusion coefficients for Ni and Pb ions were observed to decrease by 42.92 % and 79.63 %, respectively, as revealed through Mean Square Displacement (MSD) analysis. The cohesive energy of PSSB cement was 76.73 % lower than that of Portland cement, and its interaction energies for stabilizing Ni and Pb ions were 59.43 % and 76.22 % lower, respectively, demonstrating greater stability and efficiency in metal stabilization. PSSB cement exhibited lower heavy metal concentration and better structural stability than Portland cement.

Computational Analysis of Albaflavenone Interaction with SlMAPK1 for Drought Resistance in Tomato.

As global agricultural challenges intensify, particularly drought stress, the exploration of innovative strategies for crop resilience has become crucial. This study focuses on the role of the microbial endophyte metabolite Albaflavenone in enhancing drought resistance in tomato (Solanum lycopersicum L.) through the activation of the SlMAPK1 protein in the MAPK pathway. To computationally analyze the interaction between Albaflavenone and SlMAPK1 and to elucidate the potential enhancement of drought tolerance in tomato plants through this interaction. We utilized molecular docking, homology modeling, and molecular dynamics simulations to investigate the binding affinities and interaction dynamics between SlMAPK1 and Albaflavenone. Functional network analysis was employed to examine protein-protein interactions within the MAPK pathway, while the MM-GBSA method was used to calculate binding free energies. Our computational analyses revealed that Albaflavenone exhibited a high binding affinity to SlMAPK1 with a binding energy of - 8.9kcal/mol. Molecular dynamics simulations showed this interaction significantly stabilized SlMAPK1, suggesting enhanced activity. Specifically, the root mean square deviation (RMSD) of the Albaflavenone-SlMAPK1 complex stabilized at around 3.1Å, while the root mean square fluctuations (RMSF) indicated consistent amino acid conformations. Additionally, the radius of gyration (Rg) analysis demonstrated minimal variance, suggesting a compact and stable protein-ligand complex. The significant binding affinity between Albaflavenone and SlMAPK1 highlights the potential of leveraging plant-microbe interactions in developing sustainable agricultural practices. These findings also demonstrate the effectiveness of computational methods in dissecting complex biological interactions, contributing to a deeper understanding of plant resilience strategies against environmental stresses.

Distinct Sub- to Superdiffuse Insulin Granule Transport Behaviors in β-Cells Are Strongly Affected by Granule Age.

Intracellular transport is a complex process that is difficult to describe by a single general model for motion. Here, we study the transport of insulin containing vesicles, termed granules, in live MIN6 cells. We characterize how the observed heterogeneity is affected by different intracellular factors by constructing a MIN6 cell line by CRISPR-CAS9 that constitutively expresses mCherry fused to insulin and is thus packaged in granules. Confocal microscopy imaging and single particle tracking of the granule transport provide long trajectories of thousands of single granule trajectories for statistical analysis. Mean squared displacement (MSD), angle correlation distribution, and step size distribution analysis allowed identifying five distinct granule transport subpopulations, from nearly immobile and subdiffusive to run-pause and superdiffusive. The subdiffusive subpopulation recapitulates the subordinated random walk we reported earlier (Tabei, 2013; ref 18). We show that the transport characteristics of the five subpopulations have a strong dependence on the age of insulin granules. The five subpopulations also reflect the effect of local microtubule and actin networks on transport in different cellular regions. Our results provide robust metrics to clarify the heterogeneity of granule transport and demonstrate the roles of microtubule versus actin networks with granule age since initial packaging in the Golgi.

Molecular dynamic simulation on comprehensive performance of ferrocene-based burning rate catalysts in a solid propellent

To determine the compatibility and interaction between ferrocene (Fc) and other components in AP/HTPB/Fc-based BRCs propellant, molecular dynamics simulation (MD simulation) method was used to study the binding energy, cohesive energy density (CED), mean square displacement (MSD) and mechanical properties of mononuclear ferrocenyl compounds (ethyl ferrocene, butyl ferrocene and octyl ferrocene), dinuclear ferrocenyl compounds (2,2′-(ethylferrocene)propane, 2,2′-(butylferrocene)propane) propane and hydroxymethyl bis-ferrocenyl propane), ionic ferrocenyl compounds (three ionic ferrocenes with ferrocene methyl dimethyl ammonium as cation, perchlorate, nitrate and picrate as anions respectively) and cyclic ferrocenyl compounds (1-ferrocenylmethyl-2-ferrocenyl-3-methylbenzimidazolium, binuclear ferrocene bridged by bridged biphenylferrocene and dihydropyrazole).The binding energy results show that alkyl groups, polar groups (such as hydroxyl groups) and cyclic substituents can improve the interaction between Fc and AP/HTPB. Moreover, the electrostatic interaction between ionic ferrocene and AP is strong, but the van der Waals interaction between ionic ferrocene and HTPB is weak. The CED data show that the mixed models based on alkyl mononuclear ferrocene, catocene, cyclic ferrocene and ionic ferrocene all have high cohesive energy with good safety performance. The MSD results show that the order of anti-migration ability is cyclic ferrocene > binuclear alkyl ferrocene > mononuclear alkyl ferrocene > binuclear hydroxyl ferrocene > ionic ferrocene. Regarding to the value of mechanical parameters (K, G, E and K/G), the mixed model of AP/HTPB/ dihydropyrazole bridged binuclear ferrocene possess the best mechanical properties among the 12 models. Based on the comprehensive data, we conclude that dihydropyrazole bridged binuclear ferrocene is the most ideal ferrocene-based burning rate catalyst among 12 ferrocenes.

Robust Quantification of Live-Cell Single-Molecule Tracking Data for Fluorophores with Different Photophysical Properties.

High-speed single-molecule tracking in live cells is becoming an increasingly popular method for quantifying the spatiotemporal behavior of proteins in vivo. The method provides a wealth of quantitative information, but users need to be aware of biases that can skew estimates of molecular mobilities. The range of suitable fluorophores for live-cell single-molecule imaging has grown substantially over the past few years, but it remains unclear to what extent differences in photophysical properties introduce biases. Here, we tested two fluorophores with entirely different photophysical properties, one that photoswitches frequently between bright and dark states (TMR) and one that shows exceptional photostability without photoswitching (JFX650). We used a fusion of the Escherichia coli DNA repair enzyme MutS to the HaloTag and optimized sample preparation and imaging conditions for both types of fluorophore. We then assessed the reliability of two common data analysis algorithms, mean-square displacement (MSD) analysis and Hidden Markov Modeling (HMM), to estimate the diffusion coefficients and fractions of MutS molecules in different states of motion. We introduce a simple approach that removes discrepancies in the data analyses and show that both algorithms yield consistent results, regardless of the fluorophore used. Nevertheless, each dye has its own strengths and weaknesses, with TMR being more suitable for sampling the diffusive behavior of many molecules, while JFX650 enables prolonged observation of only a few molecules per cell. These characterizations and recommendations should help to standardize measurements for increased reproducibility and comparability across studies.

Adsorption behaviors and mechanisms of bilirubin onto charged amorphous carbon surface with and without water by a molecular dynamics simulation

The adsorption of bilirubin onto a carbon surface holds pivotal significance in enhancing bilirubin clearance efficiency within artificial liver devices. We performed molecular dynamics simulations to reveal the adsorption behaviors and mechanisms of bilirubin onto a charged amorphous carbon surface. The hydrogen atoms are used as binding sites facilitating the adsorption of bilirubin molecules onto the uncharged amorphous carbon surface. Conversely, the oxygen atoms are used as binding sites, enhancing bilirubin adsorption on charged amorphous carbon surfaces due to their higher electronegativity. The bilirubin adsorption rate, the mean-squared displacements of bilirubin, and the interaction energy between bilirubin and amorphous carbon increase as the surface charge increases, and the adsorption amount reaches an asymptotic value as the surface charge approaches a certain threshold. In the presence of water, the competitive adsorption between bilirubin and water would occur. The hydration layer formed on charged amorphous carbon surface and the electrostatic and near-wall hydrogen-bond interactions emerge as two pivotal factors influencing bilirubin adsorption. The structured arrangement of hydration water can hinder the bilirubin adsorption, whereas the electrostatic interaction and near-wall hydrogen-bond interaction promote it. The whole competitive adsorption process unfolded in distinct stages of bilirubin adsorption and desorption, and a critical value of surface charge exists for the complete desorption of bilirubin.

Anisotropic remixing of a phase separated binary colloidal system with particles of different sizes in an external modulation.

We explore the phase behavior of a binary colloidal system under external spatially periodic modulation. We perform Monte Carlo simulations on a binary mixture of big and small repulsive Lennard-Jones particles with a diameter ratio of 2:1. We characterize structure by isotropic and anisotropic pair correlation functions, cluster size distribution, bond angle distribution, order parameter, and specific heat. We observe the demixing of the species in the absence of external modulation. However, the mixing of the species gets enhanced with increasing potential strength along with the alignment of the particles transverse to the modulation. The de-mixing order parameter shows discontinuity with increasing modulation strength, characterizing a first order phase transition. The peak in specific heat increases linearly with the size of the system. We also look into the dynamical behavior of the system via computing Mean Square Displacement (MSD) along both parallel and perpendicular directions to the modulation. We observe a decrease in the diffusion coefficient for both types of particles as we increase the strength of the modulation.