Molecular Dynamics of Lysozyme Amyloid Polymorphs Studied by Incoherent Neutron Scattering

Lysozyme amyloidosis is a hereditary disease, which is characterized by the deposition of lysozyme amyloid fibrils in various internal organs. It is known that lysozyme fibrils show polymorphism and that polymorphs formed at near-neutral pH have the ability to promote more monomer binding than those formed at acidic pH, indicating that only specific polymorphs become dominant species in a given environment. This is likely due to the polymorph-specific configurational diffusion. Understanding the possible differences in dynamical behavior between the polymorphs is thus crucial to deepen our knowledge of amyloid polymorphism and eventually elucidate the molecular mechanism of lysozyme amyloidosis. In this study, molecular dynamics at sub-nanosecond timescale of two kinds of polymorphic fibrils of hen egg white lysozyme, which has long been used as a model of human lysozyme, formed at pH 2.7 (LP27) and pH 6.0 (LP60) was investigated using elastic incoherent neutron scattering (EINS) and quasi-elastic neutron scattering (QENS). Analysis of the EINS data showed that whereas the mean square displacement of atomic motions is similar for both LP27 and LP60, LP60 contains a larger fraction of atoms moving with larger amplitudes than LP27, indicating that the dynamical difference between the two polymorphs lies not in the averaged amplitude, but in the distribution of the amplitudes. Furthermore, analysis of the QENS data showed that the jump diffusion coefficient of atoms is larger for LP60, suggesting that the atoms of LP60 undergo faster diffusive motions than those of LP27. This study thus characterizes the dynamics of the two lysozyme polymorphs and reveals that the molecular dynamics of LP60 is enhanced compared with that of LP27. The higher molecular flexibility of the polymorph would permit to adjust its conformation more quickly than its counterpart, facilitating monomer binding.

A molecular dynamics study on the diffusion and imprint ability of spectinomycin under different sizes of aniline oligomers

Molecularly imprinted polymers (MIP) are the polymers created by molecular imprinting techniques that leave cavities for the specific interactions with a template molecule, and have been applied in molecular selectivity tasks. In this study, the molecular dynamics (MD) simulation technique was used to demonstrate that aniline oligomer could be developed as a potential MIP for detection and separation of the spectinomycin drug molecule for gonorrhoea treatment. MD simulations were performed for the systems of a spectinomycin within aniline oligomers of different sizes. The mean square displacement (MSD) and the diffusivity calculated from MD simulations showed that the diffusion coefficient was significantly dropped when the length of aniline oligomer was greater than two. The diffusion coefficient of spectinomycin became the lowest within aniline trimers, corresponded to the highest atomic distribution of MIP around the template. Then, the specific cavity in MIP systems with and without spectinomycin were calculated to assess the stability of the cavity created by the template. The volume of a cavity created within the trimer system was closest to the spectinomycin volume, and therefore became the optimal oligomer size for further development of MIP.

Study on Strengthening Mechanism of Epoxy Resin/Rubber Concrete Interface by Molecular Dynamics Simulation

Rubber concrete has high environmental and economic benefits. However, the difference in the physical and chemical properties of the interface causes a weak interface between rubber and concrete, which limits the use of rubber concrete to a certain extent. Based on the macroexperiment of epoxy resin (EP) modified rubber concrete, from the nanoscale level, three interface models of Rh (natural rubber)/C-S-H, EP/C-S-H, and Rh/EP/C-S-H were constructed by molecular dynamics simulation to explore the interaction between epoxy resin and rubber cement-based interface and reveal its microreinforcement mechanism. The results of interaction energy, radial distribution function, and mean square displacement show that the addition of EP not only improves the interface interaction energy between Rh and C-S-H but also provides a large number of hydrogen bond donors and receptors, promotes the diffusion of Ca, and increases the adhesion between Rh and cement matrix. The results of the analysis of mechanical properties show that the elastic modulus of the rubber concrete interface model is improved and the interface properties are improved after adding EP.

Molecule Dynamics Simulation of the Effect of Oxidative Aging on Properties of Nitrile Rubber

The effects of oxidative aging on the static and dynamic properties of nitrile rubber at the molecular scale were investigated by molecular dynamics simulation. The aged nitrile rubber models were constructed by introducing hydroxyl groups and carbonyl groups into rubber molecular chains to mimic oxidative aging. The static and dynamic properties of the unaged and aged nitrile rubber under different conditions were evaluated by mean square displacement, self-diffusion coefficients, hydrogen bond, fractional free volume, radial distribution function, cohesive energy density and solubility parameter. The results show that the elevated temperature intensified significantly the mobility of rubber molecular chains and fractional free volume, while the compressive strain displayed the opposite effect resulting in packing and rearrangement of rubber chains. The introduction of hydroxyl groups and carbonyl groups enhanced the polarity, intermolecular interactions, the volume and rigidity of molecular chains, implying weaker mobility of molecular chains as compared to unaged models. The compressive strain and oxidative aging both decreased the fractional free volume, which inhibited gaseous and liquid diffusion into the rubber materials, and slowed down the oxidative aging rate. This study provides insights to better understand the effect of molecular changes due to oxidative aging on the structural and dynamic properties of rubber materials at the molecular level.

Neutron diffraction study of the Ti1-xMoxC alloy

In this work, the crystal structure and (RMSD) root-mean-square displacement of atoms in new cubic refractory interstitial alloys Ti0.74Mo0.26C and Ti0.70Mo0.30C were determined by neutron diffraction. These alloys are obtained by powder metallurgy by sintering fine powders of cubic titanium carbides TiC and molybdenum MoC. The values of the RMSD of atoms in these alloys, obtained by the methods of least squares and full-profile analysis from the neutron diffraction data, turned out to be identical. They turned out to be much larger than in the stoichiometric TiC alloy, which has a similar cubic structure and close geometric parameters of atoms with the Ti0.74Mo0.26C and Ti0.70Mo0.30C alloys. These alloys were explained by the occurrence of large static distortions in the lattice of the Ti0.70Mo0.30C alloy due to the differences in the masses and atomic radii of the titanium and molybdenum elements.

Fermionic and bosonic fluctuation-dissipation theorem from a deformed AdS holographic model at finite temperature and chemical potential

In this work we study fluctuations and dissipation of a string in a deformed anti-de Sitter (AdS) space at finite temperature and density. The deformed AdS space is a charged black hole solution of the Einstein–Maxwell–Dilaton action. In this background we take into account the backreaction on the horizon function from an exponential deformation of the AdS space. From this model we compute the admittance and study the influence of the temperature and the chemical potential on it. We calculate the two-point correlations functions, and the mean square displacement for bosonic and fermionic cases, from which we obtain the short and large time approximations. For the long time, we obtain a sub-diffusive regime $$\sim \log t$$ ∼ log t . Combining the results from the admittance and the correlations functions we check the fluctuation-dissipation theorem for bosonic and fermionic systems.

Mean square displacement for a discrete centroid model of cell motion

The mean square displacement (MSD) is an important statistical measure on a stochastic process or a trajectory. In this paper we find an approximation to the mean square displacement for a model of cell motion. The model is a discrete-time jump process which approximates a force-based model for cell motion. In cell motion, the mean square displacement not only gives a measure of overall drift, but it is also an indicator of mode of transport. The key to finding the approximation is to find the mean square displacement for a subset of the state space and use it as an approximation for the entire state space. We give some intuition as to why this is an unexpectedly good approximation. A lower bound and upper bound for the mean square displacement are also given. We show that, although the upper bound is far from the computed mean square displacement, in rare cases the large displacements are approached.

Study on Adsorption Behavior of a New Type Gemini Surfactant Onto Quartz Surface by a Molecular Dynamics Method

The adsorption mechanism of the branched quaternary ammonium salt Gemini surfactant (Gemini C3) at the water-surfactant-quartz interfaces for both neutral and negatively charged quartz surfaces was studied by a molecular dynamics (MD) method. Initial and final configurations, distributions of the surfactant and its interaction with surfaces, the radial distribution function (RDF) of water molecules, and the mean square displacement (MSD) of the surfactant in bulk phase have been elucidated at the molecular level. The results showed that the adsorption of Gemini surfactants onto the hydrophilic quartz surface was driven by electrostatic interaction, which increased the hydrophobicity of the solid surface when the surfactant concentration was lower than critical micelle concentration (CMC). However, the contact angle only slightly increased since the surface tension decreased simultaneously with growing concentration. Monolayers were formed during the adsorption process of Gemini C3 molecules on the quartz surface rather than a double layer when the concentration reached the CMC, indicating a gradual transformation of an extended monolayer adsorption configuration into a more compact one. The solid-liquid interfacial tension increased with the surfactant concentration and led to a significant increase of the contact angle. The simulation results were consistent with the experiments, which further revealed the microscopic adsorption mechanism of the Gemini C3 surfactant onto the quartz surface, and provided theoretical guidance for controlling the wetting properties and surface modification of the rock.

Structural and Dynamic Properties of Hydrophobic Eutectic Solvents Based on Menthol and Fatty Acids: a Molecular Dynamics Simulation Study

The structural and dynamical properties of the binary mixture of Menthol (MEN) and Fatty acids (FAs) were investigated using molecular dynamics simulations. We focused on the relationship between the structural and dynamical properties of the eutectic mixtures of MEN and FAs with different molar percentages of FAs. Structural properties of the eutectic mixtures were characterized by calculating the combined distribution functions(CDFs), the radial distribution functions (RDFs), and the angular distribution functions (ADFs), and the Hydrogen bonding network between species and Spatial distribution functions (SDF). Further interaction between menthol and Caprylic acid molecules was confirmed by the results of these analyzes. Also, the transport properties of the mixtures were investigated by using the mean square displacement (MSD) of the centers of mass of the species, self-diffusion coefficients and vector reorientation dynamics (VRD) of bonds. The simulation results indicated that intermolecular interactions have a significant effect on the dynamic properties of species.

The Role of Sulphonic and Phosphoric Pendant Groups on the Diffusion of Monovalent Ions in Polyelectrolyte Membranes: A Molecular Dynamics Study

Lithium-ion consumption has risen significantly in recent years due to its use in portable devices. Alternative sources of lithium, which include the recovery from brine using the sustainable and eco-friendly electrodialysis technology, has been explored. This technology, however, requires effective cation-exchange membranes that allow the selective permeation of lithium ions. In this study, we have investigated, via molecular dynamics simulations, the role of the two common charged groups, the sulfonic and the phosphoric groups, in promoting the adsorption of monovalent ions from brine comprising Li+, Na+, Mg2+, and Ca2+ ions. The analysis of the mean square displacement of the ions revealed that Li+ and Na+ ions exhibit superior diffusion behaviors within the polyelectrolyte system. The O-atoms of the charged groups bind strongly with the divalent ions (Mg2+ and Ca2+), which raises their diffusion energy barrier and consequently lowers their rate of permeation. In contrast, the monovalent ions exhibit weaker interactions, with Na+ being slightly above Li+, enabling the permeation of Li+ ions. The present study demonstrates the role of both charged groups in cation-exchange membranes in promoting the diffusion of Li+ and Na+ ions, and could serve as a guide for the design of effective membranes for the recovery of these ions from brine.