Rex P. Hjelm

The Resolution of TOF Low-Q Diffractometers: Instrumental, Data Acquisition and Reduction Factors

The resolution of scattering vector, Q, in small-angle neutron scattering (SANS) measurements derives from uncertainties in scattered neutron wavelength and direction. The manner in which these are manifest on broad-band time-of-flight (TOF) spectrometers at pulsed sources is different from that for instruments using monochromated sources. In TOF instruments the uncertainties arise from the TOF measurement as well as the directional uncertainties due to collimation, finite sample and detector-element size that are present in any small-angle scattering instrument. Further, data from a TOF instrument must be mapped into Q space, and the strategy used to accomplish this affects the final resolution of the measurement. Thus for TOF-SANS instruments the question of resolution is more complicated than for instruments on monochromated sources. There is considerable flexibility in TOF data acquisition and Q mapping that can be utilized to optimize for intensity and Q resolution requirements of a particular measurement. In this work, present understanding of the effects of instrument geometry, TOF data acquisition and Q mapping strategies on the precision of the measurement is outlined. The goal is to establish guidelines on the best manner in which a particular measurement can be set up. Toward this end some new aspects are presented of optimal Q-mapping procedures, the effect of inelastic scattering on the measurement, and the calculation of instrument resolution functions. Some of these ideas are tested by comparison of simulations with measurement.

The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section of finite length

The theory of small-angle neutron or X-ray scattering from a solution consisting of rods that are uncorrelated in position and orientation and its use in determining the mass per unit length and cross-sectional radius of gyration is extended to rods of finite length and non-uniform cross-sectional structure. The case of a rod made up of identical motifs spaced in a regularly repeating axial structure is considered first. Analysis of the small-angle scatter by a modified Guinier plot gives the mean mass per unit length of the motifs. The apparent squared cross-sectional radius of gyration is the weight average. These results are then generalized to the case where variable randomly distributed structural elements are present including variable spacing between the motifs making up the rod. In this way expressions are obtained that describe the scatter from rods with structural contributions from random thermal fluctuations, bound ligands and intrinsic structural heterogeneity. It is shown that, in general, systematic errors are introduced in the analysis of rods of finite length having variable structural components. However, if all the motifs have the same mass, and if the variance in their spacing is small, such errors are not important provided that the rods are of sufficient length.

Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions

Significance The relationship between proteins unfolded under physiological conditions and those unfolded by chemical denaturation remains controversial. Specifically, although FRET studies suggest that unfolded proteins invariably contract with falling denaturant levels, scattering studies argue that they do not. Here, we explore the origins of this discrepancy using PEG as a negative control. Scattering indicates that, as expected, the polymer’s dimensions are denaturant-independent. The dye-labeled polymer, nevertheless, exhibits denaturant-dependent changes in measured transfer efficiency similar to those seen for unfolded proteins. This similarity raises questions regarding the interpretation of such changes as being indicative of hydrophobic or hydrogen bond-driven collapse. Small-angle scattering studies generally indicate that the dimensions of unfolded single-domain proteins are independent (to within experimental uncertainty of a few percent) of denaturant concentration. In contrast, single-molecule FRET (smFRET) studies invariably suggest that protein unfolded states contract significantly as the denaturant concentration falls from high (∼6 M) to low (∼1 M). Here, we explore this discrepancy by using PEG to perform a hitherto absent negative control. This uncharged, highly hydrophilic polymer has been shown by multiple independent techniques to behave as a random coil in water, suggesting that it is unlikely to expand further on the addition of denaturant. Consistent with this observation, small-angle neutron scattering indicates that the dimensions of PEG are not significantly altered by the presence of either guanidine hydrochloride or urea. smFRET measurements on a PEG construct modified with the most commonly used FRET dye pair, however, produce denaturant-dependent changes in transfer efficiency similar to those seen for a number of unfolded proteins. Given the vastly different chemistries of PEG and unfolded proteins and the significant evidence that dye-free PEG is well-described as a denaturant-independent random coil, this similarity raises questions regarding the interpretation of smFRET data in terms of the hydrogen bond- or hydrophobically driven contraction of the unfolded state at low denaturant.

A Theoretical Model for the Dynamic Structure of Hepatitis B Nucleocapsid

The genomic material of hepatitis B virus (HBV) is confined within a fenestrated nucleocapsid consisting of 240 identical copies of the capsid protein, which has a rigid core and a positively charged and highly flexible C-terminal domain (CTD). Although previous mutagenesis studies have demonstrated the importance of the CTD in viral RNA packaging and reverse transcription, the microscopic structure of the CTD and its interaction with encapsidated nucleic acids at various stages of viral maturation remain poorly understood. Here, we present a theoretical analysis of the radial distributions of the CTD chains and nucleic acids in the hepatitis B virus nucleocapsid at the beginning and final stages of viral reverse transcription based on classical density functional theory and a coarse-gained model for the pertinent biomolecules. We find that a significant portion of the CTD is exposed at the surface of the RNA-containing immature nucleocapsid and that the CTD is mostly confined within the DNA-containing mature nucleocapsid. Large accumulation of cations is predicted inside both immature and mature nucleocapsids. The theoretical results provide new insights into the molecular mechanism of CTD regulation of viral reverse transcription and nucleocapsid trafficking during various stages of the viral replication processes.

Application of small-angle neutron scattering to the study of porosity in energetic materials

Small-angle neutron scattering (SANS) and the method of contrast variation were used to measure porosity and crystallite surface area in the energetic system octahydro-1, 3, 5, 7- tetranitro-1, 3, 5, 7-tetrazocine (HMX) and to gauge the effects of mechanical deformation on the pore-size distribution and crystallite surface area. The crystallite surface area and the presence of voids (pores) in a high explosive system are known to affect its behavior and overall performance. Measures of these two quantities after an insult, resulting from various process and accident scenarios, can be used to predict the performance of an explosive system after process- and accident-related mechanical deformation. The contrast variation technique allows us to discriminate between internal pores and features that are on or contiguous with the crystallite surface. Measurements were conducted on loose powders of HMX (261 and 10 {mu}m, volume averaged mean particle diameters) and pellets made by uniaxial consolidation to 7 and 10 vol% porosity, respectively. Analysis of the SANS data indicates significant alteration of the intragranular pore structure and systematic shifts in the surface area that are dependent upon mechanical deformation. (c) 2000 Materials Research Society.

The Couette configuration of the Los Alamos Neutron Science Center Neutron Rheometer for the investigation of polymers in the bulk via small-angle neutron scattering

A neutron rheometer in the Couette geometry has been built at the Los Alamos Neutron Science Center to examine the molecular steady-state and dynamic responses of entangled polymeric materials in the bulk under the application of shear stress via small-angle neutron scattering. Although similar neutron rheometers have been fabricated elsewhere, this new design operates under the extreme conditions required for measuring the structure and behavior of high molecular weight polymer melts. Specifically, the rheometer achieves high torques (200 N m) and shear rates (865 s(-1)) simultaneously, never before attainable with other neutron rheometers at temperatures up to 240 degrees C under an inert gas environment. The design of the instrument is such that relatively small sample sizes are required. The testing of the Los Alamos Neutron Science Center Neutron Rheometer in the Couette design both as a rheometer and in the small-angle neutron optical configuration on highly viscous polystyrene is presented. The observed anisotropic neutron scattering pattern of the polystyrene melt at a molecular weight above entanglement provides evidence that the conformation of the polymer chains are elongated in the direction of the melt flow, in agreement with the current theories concerning linear polymers in the bulk.

Resolution of time-of-flight small-angle neutron diffractometers

A simple method of calculating the resolution of small-angle neutron data from diffractometers which use time-of-flight techniques has been derived in terms of the variances of the time and spatial channels of the measurement. The method is used to calculate the resolution in scattering-vector space of scattering intensity from a simulated isotropic scatterer on the small-angle neutron diffractometer at the Intense Pulsed Neutron Source at Argonne National Laboratory. The effects of the various instrumental geometries, time-of-flight measurement strategies and data reduction methods that can be chosen by the experimenter are considered. It is found that the best resolution is obtained with weighted constant At/t time-of-flight data acquisition schemes, with the detector placed in the beam in such a way that the highest possible angular range is accessed.

Structural characterization of energetic materials by small angle scattering

Microstructural aspects (particle size, defect structures, etc.) of energetic materials can affect their response to certain stimuli and are thus of great interest from both safety and performance perspectives. Small angle scattering (SAS) is well suited for microstructural characterization of energetic materials, allowing for quantitative measurement of particle/pore (open and closed) morphology and size distribution, as well as surface area. Here, we present small angle neutron (SANS) and x-ray (SAXS) scattering measurements of loose powders and pressed pellets of the energetic materials HMX, PBX 9501 and TATB. Analysis of the SANS and SAXS data reveals number averaged particle size distributions in good agreement with light scattering techniques and significant alteration of the intragranular pore structure and pressing-dependent shifts in the surface area.

Neutron instrument simulations in the next millennium

Abstract The Neutron Instrument Simulation Package (NISP) is available on the world-wide web at URL http://strider.lansce.lanl.gov/NISP/Welcome.html. With more than 20 years of development, there is a certain amount of maturity in the code, but also the potential for a great deal of growth. As requirements for more sophisticated simulations grow, NISP can be expanded or modified to meet those needs. This report describes features of the NISP structures that make it possible for users to contribute algorithms. Any interaction that can be coded as a Fortran-callable subroutine can be included as a region type in the simulations. New ideas are always solicited, and may be sent by e-mail to

Structure of a binary colloidal suspension under shear

Neutron scattering intensities from an aqueous mixture suspension of 91 nm polystyrene latex particles and 54 nm silica particles are reported in the range 0.02 < Q/nm–1 < 0.2, where Q is the momentum transfer. The suspension was dense at a mixture volume fraction of 0.15, and the polystyrene/silica particle ratio was ca. 1.7 : 1. Results are given for the suspension at rest and under shear. The sheared data were obtained with a concentric cylinder shearing apparatus constructed and tested at the SANS facility of the National Institute of Standards and Technology and the pulsed neutron facility, LANSCE, of the Los Alamos National Laboratory. The design and operation of the cell is described. The shear-influenced behaviour of the mixture is compared with and contrasted to that of a pure polystyrene suspension that can form a crystal lattice in equilibrium, but which melts to a liquid-like structure under shear.A method is proposed to measure, by contrast matching or variation, the polystyrene and silica partial scattered intensities from the mixture suspension in H2O–D2O solvents of different scattering-length densities. Estimates of the partial structure factors are given.