Relaxation Time, Diffusion, and Viscosity Analysis of Model Asphalt Systems Using Molecular Simulation

Molecular dynamics simulation was used to calculate rotational relaxation time, diffusion coefficient, and zero-shear viscosity for a pure aromatic compound naphthalene and for aromatic and aliphatic components in model asphalt systems over a temperature range of 298–443 K. The model asphalt systems were chosen previously to represent real asphalt. Green–Kubo and Einstein methods were used to estimate viscosity at high temperature 443.15 K. Rotational relaxation times were calculated by nonlinear regression of orientation correlation functions to a modified Kohlrausch–Williams–Watts function. The Vogel–Fulcher–Tammann equation was used to analyze the temperature dependences of relaxation time, viscosity, and diffusion coefficient. The temperature dependences of viscosity and relaxation time were related using the Debye–Stokes–Einstein equation, enabling viscosity at low temperatures of two model asphalt systems to be estimated from high temperature 443.15 K viscosity and temperature-dependent relaxation time results. Semiquantitative accuracy of such an equivalent temperature dependence was found for naphthalene. Diffusion coefficient showed a much smaller temperature dependence for all components in the model asphalt systems. Dimethylnaphthalene diffused the fastest while asphaltene molecules diffused the slowest. Neat naphthalene diffused faster than any component in model asphalts. © 2007 American Institute of Physics. DOI: 10.1063/1.279918

Rotational Relaxation Times of Individual Compounds With Simulations of Molecular Asphalt Models

The dynamical properties of a complex system incorporate contributions from the diverse components from which it is constituted. To study this relationship in a multicomponent system, relaxation times based on rotation autocorrelation functions in molecular dynamics simulations were analyzed for molecules in two sets of unmodified and polymer-modified model asphalt/bitumen systems over 298–473 K. The model asphalt systems were proposed previously to approximate the chemical and mechanical properties of real asphalts. Relaxations were modeled using a modified Kaulrausch–Williams–Watts function and were based on the third Legendre polynomial of normal vector time correlation functions for aromatic species asphaltene, polar aromatic, naphthene aromatic. Both the end-to-end vector and the longest axis eigenvector of the radius of gyration matrix were used for time correlation functions of chain molecules C22, polystyrene. Decreases in temperature induced large increases in relaxation time consistent with the Vogel–Fulcher–Tammann equation. The presence of a polymer slowed the decay of each correlation function to some extent. The product of relaxation time and diffusion coefficient revealed qualitative differences between larger and smaller molecules in the same system. These relaxation mechanisms remained coupled for small molecules, while the larger asphaltene and polymer molecules revealed significant slowdowns in rotation compared to translational diffusion at lower temperatures. Smaller values of the stretched exponential parameter for asphaltenes compared to smaller molecules suggested a broader range of relaxation times and were consistent with this distinction. Difficulties in converging polymer chain relaxation times are discussed in terms of fluctuations in the magnitude and orientation of the end-to-end vector and chain axis eigenvector. Viscosity results suggested by the Debye–Stokes–Einstein relationship are consistent with trends shown in the literature for true bitumen systems

Simulating Stress–Strain Behavior by Using Individual Chains: Uniaxial Deformation of Amorphous Cis- and Trans-1,4-Polybutadiene

This work develops a probability-based numerical method for quantifying mechanical properties of non-Gaussian chains subject to uniaxial deformation, with the intention of being able to incorporate polymer–polymer and polymer–filler interactions. The numerical method arises from a probabilistic approach for evaluating the elastic free energy change of chain end-to-end vectors under deformation. The elastic free energy change, force, and stress computed by applying the numerical method to uniaxial deformation of an ensemble of Gaussian chains were in excellent agreement with analytical solutions that were obtained with a Gaussian chain model. Next, the method was applied to configurations of cis- and trans-1,4-polybutadiene chains of various molecular weights that were generated under unperturbed conditions over a range of temperatures with a Rotational Isomeric State (RIS) approach in previous work (Polymer 2015, 62, 129–138). Forces and stresses increased with deformation, and further dependences on chain molecular weight and temperature were confirmed. Compression forces normal to the imposed deformation were much larger than tension forces on chains. Smaller molecular weight chains represent the equivalent of a much more tightly cross-linked network, resulting in greater moduli than larger chains. Young’s moduli computed from the coarse-grained numerical model were in good agreement with experimental results

Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling

Tryptophan and tyrosine are aromatic amino acids that play significant roles in the folding processes of proteins at water-membrane interfaces because of their amphipathic structures. Employing appropriate heteroaromatic molecular structures are essential for obtaining accurate dynamics and predictive capabilities in molecular simulations of these amino acids. In this study, molecular dynamics simulations that applied the most recent version of the CHARMM36 force field were conducted on aqueous solutions of tryptophan and of tyrosine. Geometric analysis and dynamics quantified how aromatic rings deviated from planar structures and exhibited out-of-plane fluctuations. Radial distribution functions showed possible biological significance because extent of ring planarity slightly affected local water concentrations near aromatic rings. Instantaneous all-atom normal mode analysis (NMA) and Fourier transformation of time autocorrelation functions of out-of-plane displacements were applied to study out-of-plane vibrations of atoms in those rings. NMA started with minimum energy configurations and then averaged over fluctuations in aqueous solution. The frequencies and frequency patterns that were obtained for tryptophan and tyrosine with CHARMM36 differed from literature reports of Raman spectra, infrared spectra, and frequencies calculated using quantum mechanics, with some out-of-plane modes found at higher frequencies. Effects of imposing improper torsion potentials and changing torsion angle force constants were investigated for all atoms in the rings of tryptophan and tyrosine. Results show that these coarse force fields variations only affect planarity and out-of-plane vibrations of atoms within the rings, not other vibrations. Although increasing improper torsion force constants reduced deviations from aromatic ring planarity significantly, it increased out-of-plane mode frequencies. Reducing torsion angle force constants (with and without improper torsions) shifted modes to lower frequencies. A combination of decreasing most torsion angle force constants for ring atoms in both amino acids and including improper torsion forces attained frequencies and frequency patterns for out-of-plane normal modes that were more similar to literature spectra. These force field variations decreased the extents of out-of-plane vibrations within the heteroaromatic rings of tryptophan, especially around the nitrogen atom in the ring, but not within the heteroaromatic ring of tyrosine. Conclusions were unaffected by peptide endgroup, water, or simulation ensemble

Computing Individual Area per Head Group Reveals Lipid Bilayer Dynamics

Lipid bilayers express a range of phases from solid-like to gel-like to liquid-like as a function of temperature and lipid surface concentration. The area occupied per lipid head group serves as one useful indicator of the bilayer phase, in conjunction with the two-dimensional radial distribution function (i.e., structure factor) within the bilayer. Typically, the area per head group is determined by dividing the bilayer area equally among all head groups. Such an approach is less satisfactory for a multicomponent set of diverse lipids. In this work, area determination is performed on a lipid-by-lipid basis by attributing to a lipid the volume that surrounds each atom. Voronoi tessellation provides this division of the interfacial region on a per-atom basis. The method is applied to a multicomponent system of water, NaCl, and 19 phospholipid types that was devised recently [Langmuir 2022, 38, 9481–9499] as a computational representation of the Gram-positive Staphylococcus aureus phospholipid bilayer. Results demonstrate that lipids and water molecules occupy similar extents of area within the interfacial region; ascribing area only to head groups implicitly incorporates assumptions about head group hydration. Results further show that lipid tails provide non-negligible contributions to area on the membrane side of the bilayer–water interface. Results for minimum and maximum area of individual lipids reveal that spontaneous fluctuations displace head groups more than 10 Å from the interfacial region during an NPT simulation at 310 K, leading to a zero contribution to total area at some times. Total area fluctuations and fluctuations per individual lipid relax with a correlation time of ∼10 ns. The method complements density profile as an approach to quantify the structure and dynamics of computational lipid bilayers

Effect of pressure profile of shock waves on lipid membrane deformation

Use of shock waves to temporarily increase the permeability of the cell membrane is a promising approach in drug delivery and gene therapy to allow the translocation of macromolecules and small polar molecules into the cytoplasm. Our understanding of how the characteristics of the pressure profile of shock waves, such as peak pressure and pulse duration, influences membrane properties is limited. Here we study the response of lipid bilayer membranes to shock pulses with different pressure profiles using atomistic molecular dynamics simulations. From our simulation results, we find that the transient deformation/disordering of the membrane depends on both the magnitude and the pulse duration of the pressure profile of the shock pulse. For a low pressure impulse, peak pressure has a dominant effect on membrane structural changes, while for the high pressure impulse, we find that there exists an optimal pulse duration at which membrane deformation/disordering is maximized

Intrathecal B-cell activation in LGI1 antibody encephalitis.

ObjectiveTo study intrathecal B-cell activity in leucine-rich, glioma-inactivated 1 (LGI1) antibody encephalitis. In patients with LGI1 antibodies, the lack of CSF lymphocytosis or oligoclonal bands and serum-predominant LGI1 antibodies suggests a peripherally initiated immune response. However, it is unknown whether B cells within the CNS contribute to the ongoing pathogenesis of LGI1 antibody encephalitis.MethodsPaired CSF and peripheral blood (PB) mononuclear cells were collected from 6 patients with LGI1 antibody encephalitis and 2 patients with other neurologic diseases. Deep B-cell immune repertoire sequencing was performed on immunoglobulin heavy chain transcripts from CSF B cells and sorted PB B-cell subsets. In addition, LGI1 antibody levels were determined in CSF and PB.ResultsSerum LGI1 antibody titers were on average 127-fold higher than CSF LGI1 antibody titers. Yet, deep B-cell repertoire analysis demonstrated a restricted CSF repertoire with frequent extensive clusters of clonally related B cells connected to mature PB B cells. These clusters showed intensive mutational activity of CSF B cells, providing strong evidence for an independent CNS-based antigen-driven response in patients with LGI1 antibody encephalitis but not in controls.ConclusionsOur results demonstrate that intrathecal immunoglobulin repertoire expansion is a feature of LGI1 antibody encephalitis and suggests a need for CNS-penetrant therapies

Water diffusion mechanisms in bitumen studied through molecular dynamics simulations

Water transport is one of the major factors responsible for moisture damage in asphalt pavements. To study the thermodynamics and kinetics of water transport in bitumen and to uncover microscale mechanisms of moisture-induced damage, molecular dynamics simulations were performed for up to 600 ns for water–bitumen systems with realistic water contents that varied from 0 to 1.76 wt%. Hydrogen bonding interactions and clustering of water molecules at various combinations of temperature and water content were investigated, and their effects on the self-diffusion coefficient of water and bitumen properties are computed and discussed. It is shown that the saturated water concentration in bitumen is small, especially at low temperatures, and additional water molecules tend to form large water clusters via hydrogen bonding, indicating micro-phase separation of the water and bitumen phases inside the simulation box. Hydrogen bonding and water clustering play a crucial role on the magnitude of the self-diffusion coefficient of water. Physical properties of bitumen that include viscosity and cohesive energy are affected by water. The presence of large water clusters is indicative of how degradation in cohesion is observed on the microscale