Constant Pulling Velocity Research Articles

Pure elongation flow of an electrorheological fluid: insights on wall slip from electrorheology.

In this work we study the pure elongation flow behavior of an electrorheological (ER) fluid as a model soft-jammed system, wherein the extent of jamming is controlled by an externally applied electric-field. More specifically, a pure elongation flow has been achieved by facilitating significant slip at the contact between the material and rheometer-plate while pulling it with constant pulling velocity under a constant external electric-field. The normal force exerted by the top plate on the material was measured as a function of gap during the flow for various combinations of electric-field strength and pulling velocity. For any force-gap curve, at first force increases to the maximum (region-I), then it decreases with gap (region-II). In region-II, the normal force-gap curve shifts to higher gaps with increasing electric-field strength for any given pulling velocity. Interestingly, these curves (region-II) demonstrate gap-electric field-velocity superposition, manifesting the self-similar nature of the flow. Finally, we have modeled the flow curves using a slip-layer model, which rendered a remarkable prediction of flow curves and also led to estimation of slip-layer thickness. We observed that slip-layer thickness decreases with increasing magnitude of electric field for a given pulling velocity, which suggests that the extent of jamming plays a crucial role in slip dynamics.

Atomistic insight into the inhibition mechanisms of suppressors of cytokine signaling on Janus kinase.

Suppressors of cytokine signaling (SOCS) act as negative feedback regulators of the Janus kinase/signal transducer (JAK-STAT) signaling pathway by inhibiting the activity of JAK kinase. The kinase inhibitory region (KIR) of SOCS1 targets the substrate binding groove of JAK with high specificity, as demonstrated by significantly higher IC50 following the mutation of any of residue. To gain a greater understanding of the mechanisms of the inhibition of SOCS1 for JAK1, the binding mode, binding free energy decomposition, and desorption mechanism of JAK-SOCS1 complexes as well as a number of mutant systems were identified by extensive molecular dynamics (MD) simulations and the constant pulling velocity (PCV) method. Electrostatic interactions were identified for their contribution to protein-protein binding, which drove interactions between JAK1 and SOCS1. The polar residues Arg56, Arg59, and Asp105 of SOCS1 and Asp1042 and Asp1040 of JAK1 were key components in the binding, and electrostatic interactions of the side chains were prominent. The binding free energies of the six mutant proteins were lower when compared with those of the control proteins, and the side chain interactions were weakened. The residue Asp1040 played a crucial role in KIR close to the binding groove of JAK1. Moreover, salt bridges contributed significantly to JAK1 and SOCS1 binding and cleavage processes. The study presented herein provides a comprehensive understanding of the thermodynamic and dynamic processes of SOCS1 and JAK1 binding that will contribute meaningfully to the design of future studies related to peptide inhibitors based on SOCS1.

Delivery of nitric oxide to the interior of mammalian cell by carbon nanotube: MD simulation

Computer simulations have been performed to study the nanoindentation of phospholipid bilayer by the single-walled armchair carbon nanotube, filled with the nitric oxide molecules. The process has been simulated by means of molecular dynamics (MD) technique at physiological temperature T=310K with a constant pulling velocity of the nanotube. The force acting on the nanotube during membrane penetration has been calculated. We show that the indentation by carbon nanotube does not permanently destroy the membrane structure (self-sealing of the membrane occurs). The mobility of nitric oxide molecules during the membrane nanoindentation is discussed.

Nanoindentation of biomembrane by carbon nanotubes – MD simulation

A series of steered molecular dynamics simulations (SMD) has been performed to study the process of nanoindentation of phospholipid bilayer by single-walled carbon nanotubes. Two types of armchair nanotubes: open-ended and capped were taken into account. Simulations were performed at physiological temperature T=310K, with constant pulling velocity of carbon nanotube ranging from 2m/s to 20m/s. The force acting on nanotube during membrane penetration versus indentation depth and free energy changes (PMF) have been calculated. We show that carbon nanotube indentation does not permanently destroy the membrane structure and the capped nanotube is less invasive comparing to open-ended.

Phase field modeling the selection mechanism of primary dendritic spacing in directional solidification

Selection mechanisms of primary dendritic spacing in directional solidification are investigated by the phase field method. Results show that the lower and upper limits of primary spacing are determined by the interdendritic solutal interactions and the interdendritic undercooling respectively. The upper limit of primary spacing resulting from overgrowth of the tertiary arm could be about four times as large as the lower limit. The microstructural evolution from the onset of planar instability during directional solidification with a constant pulling velocity can be divided into three stages: an initial competition stage, a submerging stage and a lateral adjustment stage. Simulation results also demonstrate that the final primary spacing with a constant pulling velocity is very close to the lower limit due to the dendrite submerging mechanism.

Changing the Mechanical Unfolding Pathway of FnIII10 by Tuning the Pulling Strength

We investigate the mechanical unfolding of the tenth type III domain from fibronectin (FnIII10) both at constant force and at constant pulling velocity, by all-atom Monte Carlo simulations. We observe both apparent two-state unfolding and several unfolding pathways involving one of three major, mutually exclusive intermediate states. All three major intermediates lack two of seven native β-strands, and share a quite similar extension. The unfolding behavior is found to depend strongly on the pulling conditions. In particular, we observe large variations in the relative frequencies of occurrence for the intermediates. At low constant force or low constant velocity, all three major intermediates occur with a significant frequency. At high constant force or high constant velocity, one of them, with the N- and C-terminal β-strands detached, dominates over the other two. Using the extended Jarzynski equality, we also estimate the equilibrium free-energy landscape, calculated as a function of chain extension. The application of a constant pulling force leads to a free-energy profile with three major local minima. Two of these correspond to the native and fully unfolded states, respectively, whereas the third one can be associated with the major unfolding intermediates.

Steered unfolding of ricin A and B chains

Highly toxic, heterodimeric protein ricin binds itself to the cell surface glycolipids or glycoproteins via its B-chain. The toxic A-chain halts protein synthesis by inactivating the ribosomes, leading to cell death. The translocation step requires partial unfolding of the protein. In this work mechanical unfolding of intact ricin as well as the individual A- and B-chains has been studied. A total of 110 ns simulation run has been performed to observe the unfolding of ricin dimer using steered molecular dynamics simulation. A gradual unfolding against a constant pulling velocity is observed for the ricin A-chain leaving the B-chain in its native-like structure. The breakage of the disulfide linkage connecting the two chains and reversal of the pulling ends of B-chain surprisingly reversed the picture as the B-chain starts to unfold from its N-terminal end. Due to the unfolding of B-chain from N-terminal end, the A-chain appears structurally rigid, which comes from the strong interfacial interactions (hydrophobic, hydrogen bonding, salt bridge). Mechanical unfolding of the individual monomers has also been performed to compare their stabilities in the monomeric and dimeric forms.

Numerical simulation of bubble growth in Newtonian and viscoelastic filaments undergoing stretching

Numerical results are presented concerning bubble growth in Newtonian and viscoelastic filaments undergoing stretching. In practice, such bubbles or cavities develop in materials (either in their bulk or at their interface with a substrate) such as the pressure sensitive adhesives. The problem we address here is how such an initially spherical bubble deforms inside a filament (which at the beginning has the shape of a cylinder with uniform radius) undergoing stretching with a constant pulling velocity. The lower end of the liquid filament is fixed at the substrate; stretching along the filament axis is achieved by means of an imposed force on the upper end. The governing equations consist of the momentum, continuity and constitutive equations and the free surface boundary conditions at the two interfaces (the bubble–liquid and the liquid–air interfaces). These are solved by a finite element/Galerkin method coupled with a first-order implicit Euler scheme for time integration. In the case of a viscoelastic medium (here the Phan-Thien/Tanner constitutive model is chosen), the elastic viscous stress splitting-G (EVSS-G) technique is used to separate the elastic and viscous contributions to the stress tensor together with a streamline upwind Petrov-Galerkin (SUPG) discretization of the constitutive equation. Our numerical calculations provide information on the effect of a number of important parameters on bubble and filament growth rate and deformation. These include mainly the capillary and Deborah numbers. The effect of other variables such as the relative size of the bubble, the proximity of the bubble to and liquid slippage on the substrate are also studied and discussed in detail.

Initial front transients in directional solidification of thin samples of dilute alloys

We study the dynamics of recoil of a planar front in a directional solidification process, following a sudden jump from rest to a constant pulling velocity V. To this end, we solve numerically the full integral equation describing the front dynamics in the one-sided model. We find, in particular, that the asymptotic (respectively initial) regimes, for which we derive analytical expressions for the front position, are restricted to such long (respectively short) times that they are in practice irrelevant for the analysis of experiments. We show that the results obtained from the heuristic approximation recently proposed by Warren and Langer are in remarkably good agreement with the exact ones in the regimes relevant to planar recoil experiments. Equally good agreement is found for the velocity threshold and the critical wavelength of the cellular instability after a large velocity jump, as calculated in the adiabatic approximation.