Reorientation Angle Research Articles

Molecular dynamics simulation study of short time dynamics in polymer liquid and glass

Molecular dynamics simulation of a united-atom polyethylene model was performed to study the short time dynamics of polymer liquid and glass. Simulation runs lasting up to 5 ns were performed at ten temperatures above and below the estimated glass transition temperature. Both the segmental translational motion and the bond reorientational motion were investigated. Quantities evaluated for the study of the translational motion include: segmental mean square displacement, van Hove space-time correlation function, intermediate scattering function, and dynamic structure factor. For the reorientational motion, the quantities evaluated include: the rms reorientation angle and the time-correlation functions of various orders giving the decay in the correlation of the bond orientation with time. Many examples are cited to show that most of the features obtained from the simulation agree well with those observed experimentally, mainly by means of quasielastic neutron scattering with polymeric and non-polymeric liquids. In particular, the dynamics in the timescale between 0.01 and 10 3 ps clearly divide themselves into two regimes: the fast process, occurring below about 1.5 ps, is Debye-like, while the slower process that follows is fitted well with the Kohlrausch-Williams-Watts function. The former probably arises from motion of a segment within a cage, while the latter is the α-relaxation process involving structural rearrangement and cooperative motion of groups of segments. The hopping process, seen in the simulation of small molecule liquids, is not observed here at any temperature. Yet there is no indication that a non-ergodicity, or a state of complete structural arrest, sets in even at the lowest temperature studied. Rather, the temperature at which the ‘apparent’ glass transition sets in is seen to shift downward as the observation time is prolonged.

14N nuclear quadrupole resonance study of the structural phase transition in phenothiazine

14N nuclear quadrupole resonance frequencies have been measured in both the low-temperature and the high-temperature phase of phenothiazine by a 1H-14N nuclear quadrupole double-resonance technique. The proton spin-lattice relaxation time was measured in both crystallographic phases as well. The NQR data show the presence of large thermal librations of the phenothiazine molecules in both crystallographic phases. The NQR data are consistent with an order-disorder phase transition associated with the reorientations of the phenothiazine molecules around the orthorhombic b axis. The reorientation angle is at Tc equal to 9+or-2 degrees . The long proton spin-lattice relaxation times above and below Tc seem to rule out any large translation or butterfly motions associated with the phase transition.

Rapid pulsed field separation of DNA molecules up to 250 kb.

Pulsed field gel electrophoresis (PFGE) is capable of resolving a wide size range of DNA molecules which would all co-migrate in conventional agarose gels. We describe pulsed field gel conditions which permit DNA fragments of up to 250 kilobases (kb) to be separated in only 3.5 h. The separations, which employ commercially available gel boxes, are achieved using conditions which deviate significantly from traditional pulsed field conditions. PFGE separations have been thought to require reorientation angles greater than 90 degrees to be effective. However, reorientation angles of 90 degrees and even less will resolve DNA fragments a few hundred kb and smaller approximately 5 x faster than with standard pulsed field conditions. The mobility of DNA fragments separated with 90 degrees reorientation angles is switch time-dependent, as is seen for DNA run with the commonly used reorientation angle of 120 degrees. With DNA fragments of several hundred kb and smaller, higher field strengths may be used, resulting in still greater increases in separation speed. The conditions described allow DNA from large insert bacterial clones, such as those using cosmid, Fosmid, P1, bacterial artificial chromosome (BAC), or P1-derived artificial chromosome (PAC) vectors, to be prepared, digested and analyzed on gels within a single working day.

Static atomistic modelling of the structure and ring dynamics of bulk amorphous polystyrene

AbstractA detailed static atomistic model of dense, glassy polystyrene is simulated using a well established technique that previously proved successful for simple vinyl polymers. Initial chain conformations that are generated using a Monte Carlo technique including periodic continuation conditions are “relaxed” by potential energy minimization. In total 24 microstructures at densities of 1,07 g/cm3 were obtained with a cube‐edge length of 18,65 Å. Detailed analysis of the minimized structures indicates that intermolecular packing influences create a large variety of chain conformations different from the purely intramolecular ground states. The systems are amorphous, exhibiting random coil behavior. The described structures have been used for a quasistatic simulation of localized motions. These motions include stepwise rotation and oscillation of the phenyl groups. The frequency distribution for the simulated ring motions covers many orders of magnitude. It is very rare that an energy barrier with a reorientation angle indicating a ring “flip” is overcome. Motions with small reorientation of the phenyl rings, and therefore not leading to a ring “flip”, dominate with an average reorientation angle of 16° (±12°). The intermolecular effects of the analyzed processes were found very important and far‐reaching, widely influencing the cooperative motions of molecular groups.

Time-optimal three-axis reorientation of a rigid spacecraft

New results are presented for the minimum-time rest-to-rest reorientation control problem of a rigid spacecraft with independent three-axis control. It is shown that in general the eigenaxis rotation maneuver is not time optimal. An inertially symmetric (e.g., spherical or cubical) rigid body is examined to demonstrate that an eigenaxis rotation about a control axis of even such a simple body is not time optimal. The computed optimal solution is bang-bang in all three control components and has a significant nutational component of motion. The total number of switches is found to be a function of the specified reorientation angle.

Phonon-induced site relaxation of tetracene guests in p-terphenyl single crystals

Site relaxation processes of tetracene-h12 and tetracene-d12 guests in p-terphenyl crystals are examined using high-resolution fluorescence and fluorescence excitation spectroscopy. Two of the four sites, the so-called O3 and O4 sites, undergo this process and their phonon sidebands observed in the excitation spectra are characterized by an exceptionally long and well resolved progression of a low-frequency (pseudo-) local phonon mode superimposed on a broad background. Perdeuteration of tetracene results in a frequency reduction of the progression forming mode which identifies this local phonon as a guest librational mode. The latter is suggested to induce the site relaxation via guest reorientation processes. The intensity distribution in the phonon sideband of the O3 site indicates a reorientational angle of ∼21° about the L-axis for the tetracene guest in the excited singlet state.

Magnetic correlations in ferromagnets undergoing spin reorientation transitions

The longitudinal (parallel to the c axis) and transverse (to the c axis) spin correlation functions are calculated for ferromagnetic systems with crystalline axial symmetries, and undergoing spin reorientation (SR) transitions under the effects of competing crystal electric field (CEF) anisotropies of axial and planar character. The structure factor is a combination of a long-range ferromagnetic one, F( theta ) delta (k), with amplitude dependent on the SR angle theta , plus a finite contribution at finite wavevectors k. This small-angle neutron scattering (SANS) structure factor is contributed by a Lorentzian (L) term, due to the magnon scattering, plus a squared Lorentzian (L2) term produced by zero-point uniform quantum spin fluctuations. This SANS scattering in the canted magnetization phase is produced within the magnetic domain walls, and therefore has a correlation length of the order of the domain wall width. The prefactors of the L and L2 SANS factors are complex functions of the spin reorientation angle and of the CEF strength parameters and spin-wave stiffness constant. These results are briefly discussed in connection with recent SANS experiments performed in the tetragonal (ErxNd1-x)2Fe14B hard intermetallic pseudoternary compounds.

The determination of the reorientational angle distribution in two-dimensional exchange nuclear magnetic resonance spectroscopy on powder samples

The Tikhonov regularization method is applied to two-dimensional nuclear magnetic resonance (NMR) data directly in the time domain in order to estimate the reorientational angle distribution. This method is an appropriate and reliable tool to treat such ill-posed inverse problems formulated as integral equations of the first kind. The parameters needed for a complete specification of the kernel function will also be estimated from the time domain data. Results for simulated and for real data are presented.

A determination of the crystal electric field and exchange parameters of Pr 3+ and Nd 3+ ions in RCo 5 intermetallics

A non-collinear three-sublattice mean field crystal electric field (CEF) model has been introduced in order to explain the observed complex magnetic behaviour in the pseudobinary Pr x Nd 1− x Co 5. A comparison with the experimental data of the spin reorientation temperature and also with the thermal evolution of the spontaneous spin reorientation angle, have allowed a determination of a reliable set of CEF and exchange parameters for the Pr 3+ and Nd +3 ions.

LASER-INDUCED OPTICAL SWITCHING OF A FERROELECTRIC LIQUID CRYSTAL

Optically induced rotation of the optical axis in a chiral smectic-C* liquid crystal has been investigated in a two-wavelength pump-probe arrangement. It is shown that optical axis reorientation is a result of opto-thermal tilt-angle changes in the SmC*-phase, which are excited by an argon-ion laser and probed by a weak He-Ne laser. The maximum induced reorientation angle has been 23 deg in these experiments. The switching times are governed by thermal-relaxation processes, and are in the range of milliseconds or less in the present arrangement. The experimental results are described by a Landau-theory of the SmC*-SmA phase transition in addition to a relaxation-time approximation of the heat-flow equation.

A deuteron NMR study of axial motion and side chain conformation in the mesophase of discotic liquid crystal main-chain polymers

Pulsed deuteron NMR spectroscopy has been used to examine the axial motion and the side-chain conformation in both oriented and unoriented mesophases of discotic liquid crystal main-chain polymers based on pentyloxy or heptyloxy substituted triphenylenes. Lineshape simulations show that the rotational motion of the triphenylene rings about the column axes can be described by an inhomogeneous distribution of reorientation angles around 45°. However, only about 60% of the discs are involved in such large amplitude motions; the remaining 40% have reorientation angles below 10°. This illustrates the severe restrictions imposed on the rotation of the discs by the interlinkage of the columns via the alkylene spacers. Furthermore, the simulations demonstrate that, at the α-carbon, the side chains show very little fast internal motion, but have a relatively complex conformation involving a disorder which does not change on the microsecond timescale. Since such a disorder is not present in the corresponding monomeric samples it is ascribed to the presence of the spacers. These results are also consistent with the presence of large sterical hindrances between the first side chains segments of adjacent discs, and they indicate a correlated reorientation of the discotic units within a column.

Molecular dynamics simulation of local chain motion in bulk amorphous polymers. II. Dynamics at glass transition

The local chain dynamics of bulk amorphous polymers has been studied by means of molecular dynamics simulation in the vicinity of the glass transition temperature Tg. Two models of polymers are used, one mimicking a polyethylene chain and the other a hypothetical freely-rotating chain, both of infinite chain length. The structural relaxations are examined by means of the time-correlation function of vectors embedded in the polymer backbone and of the distribution of the angles by which these vectors reorient after a time interval t. Some degree of chain mobility is seen to persist even as the temperature is lowered to Tg and below. In addition to the rotational diffusion process that takes place as a result of a series of small step motions, some large-angle jump motions are also seen to occur in both models. The jump motions, which are obscured by prevalent faster modes of motions at high temperatures, become clearly revealed in the reorientation angle distributions as the temperature is lowered. In the polyethylene model, the large-angle jump is directly associated with conformational transitions, while in the freely-rotating chain model, in which no torsional barrier exists, the jump probably arises because of the local potential minima created by the surrounding chains. The conformational transitions in the polyethylene model are highly cooperative among the segments neighboring along the chain, especially so as the temperature is lowered through Tg.

Rotational Brownian dynamics of semiflexible broken rods

Using the Brownian dynamics simulation technique, we study the rotational dynamics of a semiflexible broken rod. We employ a suitable bead model with stiff springs between beads and strong forces opposing to bending, except at the joint where flexibility is variable. We consider mostly broken rods with equal arms. From the simulated Brownian trajectories we obtain the correlation function for the second order Legendre polynomial of the reorientational angle of the end-to-end vector and of the arm vector. These correlation functions are closely related to fluorescence anisotropy decay and electric birefringence decay, respectively. In the first case, the relaxation time for a completely flexible rod agrees with the Harvey-Wegener theory, and in the second, the longest relaxation time agrees well with that obtained from the rigid-body treatment over the whole range of flexibility. Furthermore, we discuss the relative importance of flexibility in both types of decay. Finally, we present results for a case with unequal arms, confirming the validity of the Harvey-Wegener theory and the rigid-body treatment.

2D-solid state NMR studies of ultraslow motions: phenylflips and chain motions in the glassy state

The deuteron 2D exchange NMR experiment was applied to study ultraslow molecular reorientations in polymers below the glass transition. Experimental spectra are presented for phenyldeuterated polycarbonate (PC-d 4) and an ionene polyelectrolyte ([poly-( N, N-dimethylimino)decamethylenetetrafluoroborate] (I-10-Me-BF 4), deuterated in the α-position of the alkylene chain. In PC the phenylflip motion in the glassy state does not involve rotations by exactly 180°. Instead the reorientational angle distribution (RAD) of this local process is rather ill-defined and changes when mechanical stress is applied to the sample. The chain dynamics in the solid polyelectrolyte can be considered as a motion between fixed ends, due to the strong Coulomb interaction of the ionic centres. No evidence is found for trans-gauche isomerization; instead the spectra exhibit the characteristics of a restricted diffusive motion.

Separation of large DNA by a variable-angle contour-clamped homogeneous electric field apparatus

A device for separating large DNA molecules by pulsed field electrophoresis is described. Based on the principles of contour-clamped homogeneous electric fields (CHEF), it uses feedback to clamp voltages in a square electrode array, which is compact and inexpensive to construct, adaptable to computer control, and reorients the electric field by arbitrary angles. To illustrate its capabilities, pulsed fields with reorientation angles ranging from 90 to 140° were used to separate DNAs of 4.7 and 5.7 megabases by up to four bandwidths in 20 h. The combination of accessible technology and complete control of the electric field should facilitate the search for ways to resolve even larger DNA.

Theoretical and experimental investigations of the reorientation of liquid crystal molecules induced by laser beams

Theoretical investigations, relying mainly on numerical solutions of the non-linear differential equations of the reorientation angle, are conducted for a wide range of parameters and for a number of physical configurations which include self-diffraction and fast transients. The experiments are performed using homeotropically aligned 5CD liquid crystalscells. In particular, the temporal evolution of a ring structure in the far field pattern and response to short pulses are investigated involving time scales from nanosecond to tens of seconds regions. Comparisons between experimental results and theoretical predictions show that excellent match can be achieved for any one experiment by the choice of parameters like optical anisotropy, elastic constant and viscosity, but when parameter values derived from different experiments are compared, these parameters turn out to depend on the experimental conditions.

Velocity changes, long runs, and reversals in the Chromatium minus swimming response

The velocity, run time, path curvature, and reorientation angle of Chromatium minus were measured as a function of light intensity, temperature, viscosity, osmotic pressure, and hydrogen sulfide concentration. C. minus changed both velocity and run time. Velocity decreased with increasing light intensity in sulfide-depleted cultures and increased in sulfide-replete cultures. The addition of sulfide to cultures grown at low light intensity (10 microeinsteins m-2 s-1) caused mean run times to increase from 10.5 to 20.6 s. The addition of sulfide to cultures grown at high light intensity (100 microeinsteins m-2 s-1) caused mean run times to decrease from 15.3 to 7.7 s. These changes were maintained for up to an hour and indicate that at least some members of the family Chromatiaceae simultaneously modulate velocity and turning frequency for extended periods as part of normal taxis.

Apparatus for contour-clamped homogeneous electric fields

These notes and diagrams describe the construction of a simple hexagonal electrode array contour-clamped homogeneous electric field (CHEF) apparatus (1, 2). Included are a number of improvements on the original design. The circuit is shown in modules so that the investigator can upgrade an existing device as desired. The modules represent modifications of a second-generation device with vertical electrodes (2). One module replaces the original mechanical relay with an electronic switching circuit, which is (blissfully) silent and more reliable and permits faster switch times. The other module inserts transistor circuits to provide more accurate voltage clamping. However, it should be noted that the clamping is still not as precise as it is in commercial devices available from Bio-Rad or BRL. We have also developed a new system with electrodes in a square array that produces precise voltage clamping with operational amplifiers and is capable of arbitrary reorientation angles. That device is described elsewhere (3). Nevertheless, the circuits shown here are inexpensive, are easy to construct, are adaptable to older generation devices, and give good results for most applications. The circuits can be followed by anyone with a rudimentary training in electronics.

A new accurate technique for determination of crystallographic orientation of surfaces of single crystal wafers

A technique based on high resolution X-ray diffractometry employing multicrystal X-ray diffractometers is described. The wafer is mounted against the flat surface of a device and is aligned for diffraction of X-rays from lattice planes that are nearly parallel to its surface. The device is rotated azimuthally around an axis perpendicular to the wafer surface in a stepwise manner. The specimen has to be reoriented after each step to be on the peak of the diffraction curve due to finite angle alpha between the visible surface and the lattice planes. A plot of the reorientation angle as a function of the azimuthal position gives a sinusoidal curve. From three such plots at different known azimuthal orientations of the wafer with respect to the device, the value of angle alpha can be determined. The spatial orientation of the normal to the lattice planes is obtained. A general mathematical formulation has been given for the first time. The finite angle between the axis of rotation of the device and its flat surface against which the specimen is held, is determined. Once a device has been characterised only two azimuthal positions of the wafer are sufficient to determine its crystallographic orientation. Illustrative results of characterisation of a device and determination of orientation of a (111) silicon wafer are described. An overall uncertainty of +or-6 arc sec in the determination of alpha is achieved.

The Value of Oblique Angle Reorientation in SPECT Bone Scintigraphy of the Hips

SPECT bone scintigraphy has been shown useful for detecting avascular necrosis (AVN) of the femoral heads. Because the femoral necks project in a 15-20 degree posterior angulation from the coronal plane, the femoral head is partially superimposed upon the acetabulum in standard coronal SPECT images. To avoid this problem, the authors now perform oblique angle reorientation of all hip SPECT studies. This new technique, which allows display of the hip in a more anatomic fashion and better definition of hip abnormalities, is described. No new data acquisition is needed, and only a small amount of extra time is required for reconstruction.