Structural and elastic properties of DNA and chromatin

We investigate a chain consisting of two coupled worm-like chains withconstant distance between the strands. The effects due todouble-strandedness of the chain are studied. In a previous analyticalstudy of this system an intrinsic twist-stretch coupling and atendency of kinking is predicted. Even though a local twist structureis observed the predicted features are not recovered. A new model for DNA at the base-pair level is presented. Thebase-pairs are treated as flat rigid ellipsoids and thesugar-phosphate backbones are represented as stiff harmonic springs.The base-pair stacking interaction is modeled by a variant of theGay-Berne potential. It is shown by systematic coarse-graininghow the elastic constants of a worm-like chain are related to thelocal fluctuations of the base-pair step parameters. Even though a lotof microscopic details of the base-pair geometry is neglected themodel can be optimized to obtain a B-DNA conformation as ground stateand reasonable elastic properties. Moreover the model allows tosimulate much larger length scales than it is possible with atomisticsimulations due to the simplification of the force-field and inparticular due to the possibility of non-local Monte-Carlo moves. Asa first application the behavior under stretching is investigated. Inagreement with micromanipulation experiments on single DNA moleculesone observes a force-plateau in the force-extension curvescorresponding to an overstretching transition from B-DNA to aso-called S-DNA state. The model suggests a structure for S-DNA withhighly inclined base-pairs in order to enable at least partialbase-pair stacking. Finally a simple model for chromatin is introduced to study itsstructural and elastic properties. The underlying geometry of themodeled fiber is based on a crossed-linker model. The chromatosomesare treated as disk-like objects. Excluded volume and short rangenucleosomal interaction are taken into account by a variant of theGay-Berne potential. It is found that the bending rigidity and thestretching modulus of the fiber increase with more compact fibers. Fora reasonable parameterization of the fiber for physiologicalconditions and sufficiently high attraction between the nucleosomes aforce-extension curve is found similar to stretching experiments onsingle chromatin fibers. For very small stretching forces a kinkedfiber forming a loop is observed. If larger forces are applied theloop formation is stretched out and a decondensation of the fibertakes place.

Surface expression and functional characterization of alpha-granule factor V in human platelets: effects of ionophore A23187, thrombin, collagen, and convulxin

Factor V (FV) present in platelet alpha-granules has a significant but incompletely understood role in hemostasis. This report demonstrates that a fraction of platelets express very high levels of surface-bound, alpha-granule FV on simultaneous activation with 2 agonists, thrombin and convulxin, an activator of the collagen receptor glycoprotein VI. This subpopulation of activated platelets represents 30.7% +/- 4.7% of the total population and is referred to as convulxin and thrombin-induced-FV (COAT-FV) platelets. COAT-FV platelets are also observed on activation with thrombin plus collagen types I, V, or VI, but not with type III. No single agonist examined was able to produce COAT-FV platelets, although ionophore A23187 in conjunction with either thrombin or convulxin did generate this population. COAT-FV platelets bound annexin-V, indicating exposure of aminophospholipids and were enriched in young platelets as identified by the binding of thiazole orange. The functional significance of COAT-FV platelets was investigated by demonstrating that factor Xa preferentially bound to COAT-FV platelets, that COAT-FV platelets had more FV activity than either thrombin or A23187-activated platelets, and that COAT-FV platelets were capable of generating more prothrombinase activity than any other physiologic agonist examined. Microparticle production by dual stimulation with thrombin and convulxin was less than that observed with A23187, indicating that microparticles were not responsible for all the activities observed. These data demonstrate a new procoagulant component produced from dual stimulation of platelets with thrombin and collagen. COAT-FV platelets may explain the unique role of alpha-granule FV and the hemostatic effectiveness of young platelets. (Blood. 2000;95:1694-1702)

Role for ephrinB2 in postnatal lung alveolar development and elastic matrix integrity

Alveoli are formed in the lung by the insertion of secondary tissue folds, termed septa, which are subsequently remodeled to form the mature alveolar wall. Secondary septation requires interplay between three cell types: endothelial cells forming capillaries, contractile interstitial myofibroblasts, and epithelial cells. Here, we report that postnatal lung alveolization critically requires ephrinB2, a ligand for Eph receptor tyrosine kinases expressed by the microvasculature. Mice homozygous for the hypomorphic knockin allele ephrinB2DeltaV/DeltaV, encoding mutant ephrinB2 with a disrupted C-terminal PDZ interaction motif, show severe postnatal lung defects including an almost complete absence of lung alveoli and abnormal and disorganized elastic matrix. Lung alveolar formation is not sensitive to loss of ephrinB2 cytoplasmic tyrosine phosphorylation sites. Postnatal day 1 mutant lungs show extracellular matrix alterations without differences in proportions of major distal cell populations. We conclude that lung alveolar formation relies on endothelial ephrinB2 function.

Anelastic strain recovery and elastic properties of ODP Leg 123 oceanic basalt samples

A knowledge of rock stress is fundamental for improving our understanding of oceanic crustal mechanisms and lithospheric dynamic processes. However, direct measurements of stress in the deep oceans, and in particular stress magnitudes, have proved to be technically difficult. Anelastic strain recovery measurements were conducted on 15 basalt core samples from Sites 765 and 766 during Leg 123. Three sets of experiments were performed: anelastic strain recovery monitoring, dynamic elastic property measurements, and thermal azimuthal anisotropy observations. In addition, a range of other tests and observations were recorded to characterize each of the samples. One common feature of the experimental results and observations is that apparently no consistent orientation trend exists, either between the different measurements on each core sample or between the same sets of measurements on the various core samples. However, some evidence of correspondence between velocity anisotropy and anelastic strain recovery exists, but this is not consistent for all the core samples investigated. Thermal azimuthal anisotropy observations, although showing no conclusive correlations with the other results, were of significant interest in that they clearly exhibited anisotropic behavior. The apparent reproducibility of this behavior may point toward the possibility of rocks that retain a "memory" of their stress history, which could be exploited to derive stress orientations from archived core. Anelastic strain recovery is a relatively new technique. Because use of the method has extended to a wider range of rock types, the literature has begun to include examples of rocks that contracted with time. Strong circumstantial evidence exists to suggest that core-sample contractions result from the slow diffusion of pore fluids from a preexisting microcrack structure that permits the rock to deflate at a greater rate than the expansion caused by anelastic strain recovery. Both expansions and contractions of the Leg 123 cores were observed. The basalt cores have clearly been intersected by an abundance of preexisting fractures, some of which pass right through the samples, but many are intercepted or terminate within the rock matrix. Thus, the behavior of the core samples will be influenced not only by the properties of the rock matrix between the fractures, but also by how these macro- and micro-scale fractures mutually interact. The strain-recovery curves recorded during Leg 123 for each of the 15 basalt core samples may reflect the result of two competing time dependent processes: anelastic strain recovery and pore pressure recovery. Were these the only two processes to influence the gauge responses, then one might expect that given the additional information required, established theoretical models might be used to determine consistent stress orientations and reliable stress magnitudes. However, superimposed upon these competing processes is their respective interaction with the preexisting fractures that intersect each core. Evidence from our experiments and observations suggests that these fractures have a dominating influence on the characteristics of the recovery curves and that their effects are complex.

Velocities and elastic moduli of basalts from Pacific DSDP sites

Compressional (Vp) and shear (Vs) wave velocities have been measured to 10 kb in 32 cores of basalt from 14 Pacific sites of the Deep Sea Drilling Project. Both Vp and V s show wide ranges (3.70 to 6.38 km/sec for Vp and 1.77 to 3.40 km/sec for V s at 0.5 kb) which are linearly related to density and sea floor age, confirming earlier findings by Christensen and Salisbury of decreasing velocity with progressive submarine weathering based on studies of basalts from five sites in the Atlantic. Combined Pacific and Atlantic data give rates of decreasing velocity of -1.89 and -1.35 km/sec per 100 my for Vp and Vs respectively. New analyses of oceanic seismic refraction data indicate a decrease in layer 2 velocities with age similar to that observed in the laboratory, suggesting that weathering penetrates to several hundred meters in many regions and is largely responsible for the extreme range and variability of layer 2 refraction velocities.

Physical properties and elastic constants of ODP Holes 137-504B and 140-504B upper crustal rocks

Seismic velocities have been measured at confining pressures of 100 MPa and 600 MPa for sheeted dike samples recovered during Ocean Drilling Program Legs 137 and 140. The compressional- and shear-wave velocities show an increase with depth at Hole 504B, which is in sharp contrast to the atmospheric pressure velocity measurements performed as part of the shipboard analyses. Rocks exposed to different types of alteration and fracture patterns show distinct changes in their physical properties. The seismic reflectors observed on the vertical seismic profile (VSP) experiment performed during Leg 111 may have been caused by low velocity zones resulting from alteration. The amount of fracturing and hydrothermal alteration in several zones also may have contributed to the acoustic impedance contrast necessary to produce the E5 reflector. Poisson's ratios calculated from laboratory velocity measurements show several low values at depths ranging from 1600 mbsf to 2000 mbsf, which tends to follow similar trends obtained from previous oceanic refraction experiments. A comparison of physical properties between samples recovered from Hole 504B and ophiolite studies in the Bay of Islands and Oman shows a good correlation with the Bay of Islands but significant differences from the measurements performed in the Oman complex.

Compressional and shear wave velocities and elastic constants at DSDP Leg 59 Holes

Prior to the Deep Sea Drilling Project the composition of the oceanic crust could only be inferred from seismic-refraction and gravity data and the recovery of a wide variety of dredged rocks. Through the success of the Deep Sea Drilling Project, it is now clear that the top of oceanic Layer 2 usually consists of basalt. Several laboratory studies (e.g., Fox et al., 1972; Christensen and Shaw, 1970; Hyndman and Drury, 1976) have demonstrated that the seismic velocities of oceanic basalt are similar to velocities reported from refraction studies of Layer 2 and that the variability in Layer 2 velocities has many causes, the most important being fracturing and sea-floor alteration produced by the interaction of basalt and sea water (Christensen and Salisbury, 1973). To date, most reported measurements of velocities in oceanic basalts are from samples obtained from the main ocean basins. With the exception of an earlier study of velocities and related elastic properties of a suite of rocks from DSDP Sites 292, 293, 294, and 296 located in the Philippine Sea (Christensen et al., 1975; Fountain et al., 1975), elastic properties have not been determined for oceanic rocks from marginal basins. In this chapter compressional- and shear-wave velocities and elastic constants are reported at elevated confining pressures for basalt and volcanic breccias from Holes 447A, 448, and 448A.

(Table 1) Compressional-wave and shear-wave velocities and elastic constants from DSDP Legs 69 and 70

Shear-wave and compressional-wave velocities of 26 basalt samples collected at Site 504 during Deep Sea Drilling Project Legs 69 and 70 were measured at elevated confining pressures. The young basalts have higher velocities than average DSDP basalts, because of their lack of alteration. Measurements of sample porosity are combined with laboratory and in situ velocity measurements to yield estimates of total crustal porosity: 13% at the top of Layer 2, and very low porosity below a depth of 2.0 km.

Seismic velocities and elastic properties of gabbroic rocks from ODP Hole 118-735B

The nearly continuous recovery of 0.5 km of generally fresh, layer 3 gabbroic rocks at Hole 735B, especially near the bottom of the section, presents scientists an unusual opportunity to study the detailed elastic properties of the lower oceanic crust. Extending compressional-wave and density shipboard measurements at room pressure, Vp and Vs were measured at pressures from 20 to 200 MPa using the pulse transmission method. All of the rocks exhibit significant increases in velocity with increasing pressure up to about 150 MPa, a feature attributed to the closing of microcrack porosity. Measured velocities reflect the mineralogical makeup and microstructures acquired during the tectonic history of Hole 735B. Most of the undeformed and unaltered gabbros are approximately 65:35 plagioclase/clinopyroxene rocks plus olivine or oxide minerals, and the observed densities and velocities are fully consistent with the Voigt-Reuss-Hill (VRH) averages of the component minerals and their proportions. Depending on their olivine content, the predominant olivine gabbros at 200 MPa have average Vp = 7.1 ± 0.2 km/s, Vs = 3.9 ± 0.1 km/s, and grain densities of 2.95 ± 0.5 g/cm3. The less abundant iron-titanium (Fe-Ti) oxide gabbros average Vp = 6.75 ± 0.15 km/s, Vs = 3.70 ± 0.1 km/s, and grain densities of 3.22 ± 0.05 g/cm3, reflecting the higher densities and lower velocities of oxide minerals compared to olivine. About 30% of the core is plastically deformed, and the densities and directionally averaged velocities of these shear-zone tectonites are generally consistent with those of the gabbros, their protoliths. Three sets of observations indicate that the shear-zone metagabbros are elastically anisotropic: (1) directional variations in Vp, both vertical and horizontal and with respect to foliation and lineation; (2) discrepancies among Vp values for the horizontal cores and the VRH averages of the component minerals and their mineral proportions, suggesting preferred crystallographic orientations of anisotropic minerals; and (3) variations of Vs of up to 7%, with polarization directions parallel and perpendicular to foliation. Optical inspection of thin sections of the same samples indicates that plagioclase feldspar, clinopyroxene, and amphibole typically display crystallographic-preferred orientations, and this, plus the elastic anisotropy of these minerals, suggests that preferred orientations are responsible for much of the observed anisotropy, particularly at high pressure. Alteration tends to be localized to brittle faults and brecciated zones, and typical alteration minerals are amphibole and secondary plagioclase, which do not significantly change the velocity-density relationships.

(Table 1) Compressional and shear wave velocities and elastic constants of DSDP Hole 83-504B basalts

Compressional and shear wave velocities at confining pressures to 6 kb, densities, and porosities were measured for 32 samples obtained from 836 to 1350 m below seafloor (BSF) in Hole 504B, the section drilled on Leg 83 of the Deep Sea Drilling Project. These data in combination with similar measurements on 28 basalt samples from the section from 274.5 to 836 m, drilled on Legs 69 and 70, provide a comprehensive set of physical property data for over 1000 m of oceanic crust. The velocities, densities, and porosities measured in the laboratory exhibit greater variability in the upper portion of the hole. In general, compressional and shear wave velocities and densities increase with depth, reaching average values at 1 kbar of Vp = 6.45 km/s, Ks = 3.45 km/s and p = 2.94 g/cm3 within the sheeted dike section. Porosities decrease with depth to values generally less than 1% near the bottom of the hole

Railway Rapid Transit timetables with variable and elastic demand.

This paper focuses on the design of railway timetables considering a variable elastic demand profile along a whole design day. Timetabling is the third stage in the classical hierarchical railway planning process. Most of previous works on this topic consider a uniform demand behavior for short planning intervals. In this paper, we propose a MINLP model for designing non-periodic timetables on a railway corridor where demand is dependent on waiting times. In the elastic demand case, long waiting times lead to a loss of passengers, who may select an alternative transportation mode. The mode choice is modeled using two alternative methods. The first one is based on a sigmoid function and can be used in case of absence of information for competitor modes. In the second one, the mode choice probability is obtained using a Logit model that explicitly considers the existence of a main alternative mode. With the purpose of obtaining optimal departure times, in both cases, a minimization of the loss of passengers is used as objective function. Finally, as illustration, the timetabling MINLP model with both mode choice methods is applied to a real case and computational results are shown.