Intermediate scattering functions of a rigid body monoclonal antibody protein in solution studied by dissipative particle dynamic simulation.

In the past decade, there was increased research interest in studying internal motions of flexible proteins in solution using Neutron Spin Echo (NSE) as NSE can simultaneously probe the dynamics at the length and time scales comparable to protein domain motions. However, the collective intermediate scattering function (ISF) measured by NSE has the contributions from translational, rotational, and internal motions, which are rather complicated to be separated. Widely used NSE theories to interpret experimental data usually assume that the translational and rotational motions of a rigid particle are decoupled and independent to each other. To evaluate the accuracy of this approximation for monoclonal antibody (mAb) proteins in solution, dissipative particle dynamic computer simulation is used here to simulate a rigid-body mAb for up to about 200 ns. The total ISF together with the ISFs due to only the translational and rotational motions as well as their corresponding effective diffusion coefficients is calculated. The aforementioned approximation introduces appreciable errors to the calculated effective diffusion coefficients and the ISFs. For the effective diffusion coefficient, the error introduced by this approximation can be as large as about 10% even though the overall agreement is considered reasonable. Thus, we need to be cautious when interpreting the data with a small signal change. In addition, the accuracy of the calculated ISFs due to the finite computer simulation time is also discussed.

Contact and stress anisotropies in start-up flow of colloidal suspensions.

Spatiotemporal correlations in start-up flows of attractive colloids are explored by numerical simulations as a function of their volume fraction and shear rate. The suspension is first allowed to flocculate during a time tw, then the stress necessary to induce its flow is computed. We find that, at low volume fractions, the stress is a universal function of the strain. On the contrary, at high volume fractions, this scaling behavior is no longer observed and a supplementary stress becomes necessary to induce flow. To better understand the physical origin of the supplementary stress, we examine the creation, disruption, and orientation of contacts between the particles and the corresponding contribution to stress as a function of strain. Our simulations show that the onset of flow is dominated by the creation of contacts between the particles at low shear rates and by their disruption at high shear rates. However, neither the evolution of the number of contacts with strain nor their orientation can fully account for the nonscaling behavior of the stress at high volume fractions. At small strains, the relative importance of forcing in the compression quadrant increases with volume fraction and with flocculation time. This mechanism of stress transmission through the compression quadrant is not accounted for in the usual description of yield stress, which considers the breaking of bonds oriented in the extension quadrant.

A comparison of viscosity-concentration relationships for emulsions.

Differential effective medium theory (D-EMT) has been used by a number of investigators to derive expressions for the shear viscosity of a colloidal suspension or an emulsion as a function of the volume fraction of the dispersed phase. Pal and Rhodes [R. Pal, E. Rhodes, J. Rheol. 33 (7) (1989) 1021-1045] used D-EMT to derive a viscosity-concentration expression for non-Newtonian emulsions, in which variations among different oil-water emulsions were accommodated by fitting the value of an empirical solvation factor by matching the volume fraction at which the ratio of each emulsion was experimentally observed to have a viscosity 100 times greater than that of the pure solvent. When the particles in suspension have occluded volume due to solvation or flocculation, we show that the application of D-EMT to the problem becomes more ambiguous than these investigators have indicated. In addition, the resulting equations either do not account for the limiting behavior near the critical concentration, that is, the concentration at which the viscosity diverges, or they incorporate this critical behavior in an ad hoc way. We suggest an alternative viscosity-concentration equation for emulsions, based on work by Bicerano and coworkers [J. Bicerano, J.F. Douglas, D.A. Brune, J. Macromol. Sci., Rev. Macromol. Chem. Phys. C 39 (4) (1999) 561-642]. This alternative equation has the advantages that (1) its parameters are more closely related to physical properties of the suspension and (2) it recovers the correct limiting behavior both in the dilute limit and near the critical concentration for rigid particles. In addition, the equation can account for the deformability of flexible particles in the semidilute regime. The proposed equation is compared to the equation proposed by Pal and Rhodes.

Cross-property correlations and permeability estimation in sandstone.

We computationally investigate cross-property correlations linking fluid permeability to conductive properties in sedimentary rock for a number of pore size parameters based on three-dimensional digitized rock images. In particular, we focus on correlations based on the pore volume-to-surface-area ratio (V(p)/S), a critical channel diameter (c) associated with mercury porosimetry measurements, length scales associated with the nuclear magnetic resonance relaxation time T2, as well as the mean survival time (tau). Differences between the length scales are discussed. All these correlations yield good agreement with our simulations, but permeability estimates based on the critical diameter (c) are found to be most reliable.

Breakup of a fluid thread in a confined geometry: droplet-plug transition, perturbation sensitivity, and kinetic stabilization with confinement.

We investigate the influence of geometrical confinement on the breakup of long fluid threads in the absence of imposed flow using a lattice Boltzmann model. Our simulations primarily focus on the case of threads centered coaxially in a tube filled with another Newtonian fluid and subjected to both impulsive and random perturbations. We observe a significant slowing down of the rate of thread breakup ("kinetic stabilization") over a wide range of the confinement, Lambda= R(tube)/R(thread) < or =10 and find that the relative surface energies of the liquid components influence this effect. For Lambda<2.3, there is a transition in the late-stage morphology between spherical droplets and tube "plugs." Unstable distorted droplets ("capsules") form as transient structures for intermediate confinement (Lambda approximately equal 2.1-2.5). Surprisingly, the thread breakup process for more confined threads (Lambda< or =1.9 ) is found to be sensitive to the nature of the initial thread perturbation. Localized impulsive perturbations ("taps") cause a "bulging" of the fluid at the wall, followed by thread breakup through the propagation of a wave-like disturbance ("end-pinch instability") initiating from the thread rupture point. Random impulses along the thread, modeling thermal fluctuations, lead to a complex breakup process involving a competition between the Raleigh and end-pinch instabilities. We also briefly compare our tube simulations to threads confined between parallel plates and to multiple interacting threads under confinement.

Relating Fresh Concrete Viscosity Measurements from Different Rheometers.

Concrete rheological properties need to be properly measured and predicted in order to characterize the workability of fresh concrete, including special concretes such as self-consolidating concrete (SCC). It was shown by a round-robin test held in 2000 [1,2] that different rheometer designs gave different values of viscosity for the same concrete. While empirical correlation between different rheometers was possible, for a procedure that is supposed to "scientifically" improve on the empirical slump tests, this situation is unsatisfactory. To remedy this situation, a new interpretation of the data was developed. In this paper, it is shown that all instruments tested could be directly and quantitatively compared in terms of relative plastic viscosity instead of the plastic viscosity alone. This should eventually allow the measurements from various rheometer designs to be directly calibrated against known standards of plastic viscosity, putting concrete rheometry and concrete workability on a sounder materials science basis.

Accelerating Scientific Discovery Through Computation and Visualization II.

This is the second in a series of articles describing a wide variety of projects at NIST that synergistically combine physical science and information science. It describes, through examples, how the Scientific Applications and Visualization Group (SAVG) at NIST has utilized high performance parallel computing, visualization, and machine learning to accelerate research. The examples include scientific collaborations in the following areas: (1) High Precision Energies for few electron atomic systems, (2) Flows of suspensions, (3) X-ray absorption, (4) Molecular dynamics of fluids, (5) Nanostructures, (6) Dendritic growth in alloys, (7) Screen saver science, (8) genetic programming.