Understanding the Structure and Apo Dynamics of the Functionally Active JIP1 Fragment.

Recent experiments indicate that the C-Jun amino-terminal kinase-interacting protein 1 (JIP1) binds to and activates the c-Jun N-terminal kinase (JNK) protein. JNK is an integral part of cell apoptosis, and misregulation of this process is a causative factor in diseases such as Alzheimer's disease (AD), obesity, and cancer. It has also been shown that JIP1 may increase the phosphorylation of tau by facilitating the interaction between the tau protein and JNK, which could also be a causative factor in AD. Very little is known about the structure and dynamics of JIP1; however, the amino acid composition of the first 350 residues suggests that it contains an intrinsically disordered region. Molecular dynamics (MD) simulations using AMBER 14 were used to study the structure and dynamics of a functionally active JIP1 10mer fragment to better understand the solution behavior of the fragment. Two microseconds of unbiased MD was performed on the JIP1 10mer fragment in 10 different seeds for a total of 20 µs of simulation time, and from this, seven structurally stable conformations of the 10mer fragment were identified via classical clustering. The 10mer ensemble was also used to build a Markov state model (MSM) that identified four metastable states that encompassed six of the seven conformational families identified by classical dimensional reduction. Based on this MSM, conformational interconversions between the four states occur via two dominant pathways with probability fluxes of 55 and 44% for each individual pathway. Transitions between the initial and final states occur with mean first passage times of 31 (forward) and 16 (reverse) µs.

Dynamical insights into the mechanism of a droplet detachment from a fiber.

Quantifying the detachment behavior of a droplet from a fiber is important in many applications such as fog harvesting, oil-water separation, or water management in fuel cells. When the droplets are forcibly removed from hydrophilic fibers, the ease of detachment strongly depends on droplet volume and the rate of the process controlled by the applied force. Experiments, conducted on a ferrofluid under magnetic force, as well as continuum level calculations from fluid mechanics have so far been unable to resolve the time-dependent dynamics of droplet detachment and, most importantly, to assess the role of the applied force as the key determinant of the volume of the droplet residue remaining on the fiber after detachment. In the present work, we study the mechanism of water droplet detachment and retention of residual water on smooth hydrophilic fibers using nonequilibrium molecular dynamics simulations. We investigate how the applied force affects the breakup of a droplet and how the minimal detaching force per unit mass decreases with droplet size. We extract scaling relations that allow extrapolation of our findings to larger length scales that are not directly accessible by molecular models. We find that the volume of the residue on a fiber varies nonmonotonically with the detaching force, reaching the maximal size at an intermediate force and associated detachment time. The strength of this force decreases with the size of the drop, while the maximal residue increases with the droplet volume, V, sub-linearly, in proportion to the V2/3.

Solvent-Solvent Correlations across Graphene: The Effect of Image Charges.

Wetting experiments show pure graphene to be weakly hydrophilic, but its contact angle (CA) also reflects the character of the supporting material. Measurements and molecular dynamics simulations on suspended and supported graphene often reveal a CA reduction due to the presence of the supporting substrate. A similar reduction is consistently observed when graphene is wetted from both sides. The effect has been attributed to transparency to molecular interactions across the graphene sheet; however, the possibility of substrate-induced graphene polarization has also been considered. Computer simulations of CA on graphene have so far been determined by ignoring the material's conducting properties. We improve the graphene model by incorporating its conductivity according to the constant applied potential molecular dynamics. Using this method, we compare the wettabilities of suspended graphene and graphene supported by water by measuring the CA of cylindrical water drops on the sheets. The inclusion of graphene conductivity and concomitant polarization effects leads to a lower CA on suspended graphene, but the CA reduction is significantly bigger when the sheets are also wetted from the opposite side. The stronger adhesion is accompanied by a profound change in the correlations among water molecules across the sheet. While partial charges on water molecules interacting across an insulator sheet attract charges of the opposite sign, apparent attraction among like charges is manifested across the conducting graphene. The change is associated with graphene polarization, as the image charges inside the conductor attract equally signed partial charges of water molecules on both sides of the sheet. Additionally, using a nonpolar liquid (diiodomethane), we affirm a detectable wetting translucency when liquid-liquid forces are dominated by dispersive interactions. Our findings are important for predictive modeling toward a variety of applications including sensors, fuel cell membranes, water filtration, and graphene-based electrode materials in high-performance supercapacitors.

Structural and elastic properties of a confined two-dimensional colloidal solid: a molecular dynamics study.

We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a two-dimensional crystal of point particles interacting with an inverse power law potential proportional to r^{-12} in a narrow channel. This system can describe colloidal particles at the air-water interface. It is shown that the system characteristics depend sensitively on the boundary conditions at the two walls providing the confinement. The walls exert perpendicular forces on their adjacent particles. The potential between walls and particles varies as the inverse power of ten. Structural quantities such as density profile, structure factor, and orientational order parameter are computed. It is shown that orientational order persists near the walls even at temperatures where the system in the bulk is in fluid state. The dependence of elastic constants, stress tensor elements, shear, and bulk moduli on density as well as the channel width is discussed. Moreover, the effect of channel incommensurability with the triangular lattice structure is discussed. It is shown that incommensurability notably affects the system properties. We compare our findings to those obtained by Monte Carlo simulations in Rici et al. [Phys. Rev. E 75, 011405 (2007)] and to the case with the periodic boundary condition along the channel width.