RNA-dependent genome processing during nuclear differentiation: the model systems of stichotrichous ciliates

We introduce ciliated protozoa, and more specifically the stichotrichous ciliates Oxytricha and Stylonychia, as biological model systems for the analysis of programmed DNA-reorganization processes during nuclear differentiation. These include DNA excision, DNA elimination, reordering of gene segments and specific gene amplification. We show that small nuclear RNAs specify DNA sequences to be excised or retained, but also discuss the need for a RNA template molecule derived from the parental nucleus for these processes. This RNA template guides reordering of gene segments to become functional genes and determines gene copy number in the differentiated nucleus. Since the template is derived from the parental macronucleus, gene reordering and DNA amplification are inherited in a non-Mendelian epigenetic manner.

Non-rigid Free-Form 2D-3D Registration Using Statistical Deformation Model

This paper presents a non-rigid free-from 2D-3D registration approach using statistical deformation model (SDM). In our approach the SDM is first constructed from a set of training data using a non-rigid registration algorithm based on b-spline free-form deformation to encode a priori information about the underlying anatomy. A novel intensity-based non-rigid 2D-3D registration algorithm is then presented to iteratively fit the 3D b-spline-based SDM to the 2D X-ray images of an unseen subject, which requires a computationally expensive inversion of the instantiated deformation in each iteration. In this paper, we propose to solve this challenge with a fast B-spline pseudo-inversion algorithm that is implemented on graphics processing unit (GPU). Experiments conducted on C-arm and X-ray images of cadaveric femurs demonstrate the efficacy of the present approach.

Finite deformation model of simple shear of fault with microrotations: apparent strain localisation and en-echelon fracture pattern

Strain localisation is a widespread phenomenon often observed in shear and compressive loading of geomaterials, for example, the fault gouge. It is believed that the main mechanisms of strain localisation are strain softening and mismatch between dilatancy and pressure sensitivity. Observations show that gouge deformation is accompanied by considerable rotations of grains. In our previous work as a model for gouge material, we proposed a continuum description for an assembly of particles of equal radius in which the particle rotation is treated as an independent degree of freedom. We showed that there exist critical values of the model parameters for which the displacement gradient exhibits a pronounced localisation at the mid-surface layers of the fault, even in the absence of inelasticity. Here, we generalise the model to the case of finite deformations characteristic for the gouge deformation. We derive objective constitutive relationships relating the Jaumann rates of stress and moment stress to the relative strain and curvature rates, respectively. The model suggests that the pattern of localisation remains the same as in the linear case. However, the presence of the Jaumann terms leads to the emergence of non-zero normal stresses acting along and perpendicular to the shear layer (with zero hydrostatic pressure), and localised along the mid-line of the gouge; these stress components are absent in the linear model of simple shear. These additional normal stresses, albeit small, cause a change in the direction in which the maximal normal stresses act and in which en-echelon fracturing is formed.

A deformation model of flexible, high area-to-mass ratio debris under perturbations and validation method

A new type of space debris was recently discovered by Schildknecht in near -geosynchronous orbit (GEO). These objects were later identified as exhibiting properties associated with High Area-to-Mass ratio (HAMR) objects. According to their brightness magnitudes (light curve), high rotation rates and composition properties (albedo, amount of specular and diffuse reflection, colour, etc), it is thought that these objects are multilayer insulation (MLI). Observations have shown that this debris type is very sensitive to environmental disturbances, particularly solar radiation pressure, due to the fact that their shapes are easily deformed leading to changes in the Area-to-Mass ratio (AMR) over time. This thesis proposes a simple effective flexible model of the thin, deformable membrane with two different methods. Firstly, this debris is modelled with Finite Element Analysis (FEA) by using Bernoulli-Euler theory called “Bernoulli model”. The Bernoulli model is constructed with beam elements consisting 2 nodes and each node has six degrees of freedom (DoF). The mass of membrane is distributed in beam elements. Secondly, the debris based on multibody dynamics theory call “Multibody model” is modelled as a series of lump masses, connected through flexible joints, representing the flexibility of the membrane itself. The mass of the membrane, albeit low, is taken into account with lump masses in the joints. The dynamic equations for the masses, including the constraints defined by the connecting rigid rod, are derived using fundamental Newtonian mechanics. The physical properties of both flexible models required by the models (membrane density, reflectivity, composition, etc.), are assumed to be those of multilayer insulation. Both flexible membrane models are then propagated together with classical orbital and attitude equations of motion near GEO region to predict the orbital evolution under the perturbations of solar radiation pressure, Earth’s gravity field, luni-solar gravitational fields and self-shadowing effect. These results are then compared to two rigid body models (cannonball and flat rigid plate). In this investigation, when comparing with a rigid model, the evolutions of orbital elements of the flexible models indicate the difference of inclination and secular eccentricity evolutions, rapid irregular attitude motion and unstable cross-section area due to a deformation over time. Then, the Monte Carlo simulations by varying initial attitude dynamics and deformed angle are investigated and compared with rigid models over 100 days. As the results of the simulations, the different initial conditions provide unique orbital motions, which is significantly different in term of orbital motions of both rigid models. Furthermore, this thesis presents a methodology to determine the material dynamic properties of thin membranes and validates the deformation of the multibody model with real MLI materials. Experiments are performed in a high vacuum chamber (10-4 mbar) replicating space environment. A thin membrane is hinged at one end but free at the other. The free motion experiment, the first experiment, is a free vibration test to determine the damping coefficient and natural frequency of the thin membrane. In this test, the membrane is allowed to fall freely in the chamber with the motion tracked and captured through high velocity video frames. A Kalman filter technique is implemented in the tracking algorithm to reduce noise and increase the tracking accuracy of the oscillating motion. The forced motion experiment, the last test, is performed to determine the deformation characteristics of the object. A high power spotlight (500-2000W) is used to illuminate the MLI and the displacements are measured by means of a high resolution laser sensor. Finite Element Analysis (FEA) and multibody dynamics of the experimental setups are used for the validation of the flexible model by comparing with the experimental results of displacements and natural frequencies.

On the shear deformation theory for dynamic analysis of beams

Timoshenko's shear deformation theory is widely used for the dynamical analysis of shear-flexible beams. This paper presents a comparative study of the shear deformation theory with a higher order model, of which Timoshenko's shear deformation model is a special case. Results indicate that while Timoshenko's shear deformation theory gives reasonably accurate information regarding the set of bending natural frequencies, there are considerable discrepancies in the information it gives regarding the mode shapes and dynamic response, and so there is a need to consider higher order models for the dynamical analysis of flexure of beams.

Light-front quark-meson coupling model

We formulate a quark-meson coupling model for nuclear matter using light front variables. We present results for saturation properties of nuclear matter and in-medium nucleon properties. We also calculate the distribution function of the plus momentum carried by nucleons in nuclear matter. Our model predicts that vector mesons carry only 7% of the fraction per nucleon of the total plus momentum of the system.

Annealed Ising model on hierarchical structures: a transfer matrix approach.

Spin systems in the presence of disorder are described by two sets of degrees of freedom, associated with orientational (spin) and disorder variables, which may be characterized by two distinct relaxation times. Disordered spin models have been mostly investigated in the quenched regime, which is the usual situation in solid state physics, and in which the relaxation time of the disorder variables is much larger than the typical measurement times. In this quenched regime, disorder variables are fixed, and only the orientational variables are duly thermalized. Recent studies in the context of lattice statistical models for the phase diagrams of nematic liquid-crystalline systems have stimulated the interest of going beyond the quenched regime. The phase diagrams predicted by these calculations for a simple Maier-Saupe model turn out to be qualitative different from the quenched case if the two sets of degrees of freedom are allowed to reach thermal equilibrium during the experimental time, which is known as the fully annealed regime. In this work, we develop a transfer matrix formalism to investigate annealed disordered Ising models on two hierarchical structures, the diamond hierarchical lattice (DHL) and the Apollonian network (AN). The calculations follow the same steps used for the analysis of simple uniform systems, which amounts to deriving proper recurrence maps for the thermodynamic and magnetic variables in terms of the generations of the construction of the hierarchical structures. In this context, we may consider different kinds of disorder, and different types of ferromagnetic and anti-ferromagnetic interactions. In the present work, we analyze the effects of dilution, which are produced by the removal of some magnetic ions. The system is treated in a “grand canonical" ensemble. The introduction of two extra fields, related to the concentration of two different types of particles, leads to higher-rank transfer matrices as compared with the formalism for the usual uniform models. Preliminary calculations on a DHL indicate that there is a phase transition for a wide range of dilution concentrations. Ising spin systems on the AN are known to be ferromagnetically ordered at all temperatures; in the presence of dilution, however, there are indications of a disordered (paramagnetic) phase at low concentrations of magnetic ions.

Tidally compressed gas in centers of early-type and ultraluminous galaxies

In this paper we propose that the compressive tidal held in the centers of flat-core early-type galaxies and ultraluminous galaxies compresses molecular clouds producing dense gas observed in the centers of these galaxies. The effect of galactic tidal fields is usually considered disruptive in the literature. However, for some galaxies, the mass profile flattens toward the center and the resulting galactic tidal field is not disruptive, but instead it is compressive within the flat-core region. We have used the virial theorem to determine the minimum density of a molecular cloud to be stable and gravitationally bound within the tidally compressive region of a galaxy. We have applied the mechanism to determine the mean molecular cloud densities in the centers of a sample of flat-core, early-type galaxies and ultraluminous galaxies. For early-type galaxies with a core-type luminosity profile, the tidal held of the galaxy is compressive within half the core radius. We have calculated the mean gas densities for molecular gas in a sample of early-type galaxies which have already been detected in CO emission, and we obtain mean densities of [n] similar to 10(3)-10(6) cm(-3) within the central 100 pc radius. We also use our model to calculate the molecular cloud densities in the inner few hundred parsecs of a sample of ultraluminous galaxies. From the observed rotation curves of these galaxies we show that they have a compressive core within their nuclear region. Our model predicts minimum molecular gas densities in the range 10(2)-10(4) cm(-3) in the nuclear gas disks; the smaller values are applicable typically for galaxies with larger core radii. The resulting density values agree well with the observed range. Also, for large core radii, even fairly low-density gas (similar to 10(2) cm(-3)) can remain bound and stable close to the galactic center.

Pull-in Instability Study of Carbon Nanotube Tweezers Under the Influence of Van der Waals Forces

The pull-in instability of two nanotubes under van der Waals force is studied. The cantilever beam with large deformation model is used. The influence of nanotube parameters such as the interior radius, the gap distance between the two nanotubes, etc, on the pull-in instability is studied. The critical nanotube length is determined for each specific set of nanotube parameters. The Galerkin method is applied to discretize the governing equations, and it shows good convergence.

砂砾岩储层流动单元四维模型研究

This article is an important part of "95" technological subject of SINOPEC. It has a large number of difficulties and workloads, and has significant theoretical meanings and practical value. The study area is composed of sandstone & conglomerate reservoir of alluvial fan & fan delta, which belong to Sha3 lower member and Sha4 upper member of lower tertiary of Yong'an Town Oilfield in Dongying Depression. The target stataum develops in the hanging wall of the synsedimentary fault in the scarp zone of Dongying Depression. The frequently intense movements result in the variation of sandstone and conglomerate reservoir and the evolution of the time and space of Sha3 lower member and Sha4 upper member in Yong'an Town Oilfield. As a result, it is difficult for the individual reservoir correlation at the root of fan, which bring about a tackle problem for the exploitation of oilfield. In this background, the research of fluid units will be more difficult. In this article, the new concepts, the new methods, and the new techniques of sedimentology, petroleum geology, reservoir geology, physics of crystal surface, dynamic & static state reservoir description and well logging geology are synthetically applied, and the computer technology are made full uses of, and the identifying, dividing and appraising of the two-formation-type sandstone & conglomerate reservoir fluid units of Sha3 lower member and Sha4 upper member systemically analyzed in Yong'an Town Oilfield, Dongying Depression. For the first time, the single-well model, the section model, the plane model, the nuclear magnetism log model, the microcosmic network model, the 4-D geology model and the simulation model of the two-formation-type reservoir fluid units of the of sandstone & conglomerate reservoir of Sha3 lower member and Sha4 upper member are established, and the formative mechanism and distributing & enrichment laws of oil-gas of the two type of sandstone and conglomerate reservoir fluid units are revealed. This article established the optimizing, identifying, classifying and appraising standard of the two-formation-type reservoir fluid units of the of sandstone and conglomerate reservoir of Sha3 lower member and Sha4 upper member, which settles the substantial foundations for static state model of the fluid units, reveals the macroscopic & microcosmic various laws of geometrical static state of the fluid units, and instructs the oil exploitation. This article established static state model of the two-formation-type sandstone and conglomerate reservoir fluid units by using the multi-subject theories, information and techniques, and reveals the geometrical configuration, special distribution and the oil-gas enrichment laws of the sandstone and conglomerate reservoir fluid units. For the first time, we established the nuclear magnetism log model of the two-formation-type sandstone and conglomerate reservoir of Sha3 lower member and Sha4 upper member, which reveals not only the character and distributing laws of the porosity and permeability, bat also the formation and distribution of the movable fluid. It established six type of microcosmic net model of the two-formation-type sandstone and conglomerate reservoir of Sha3 lower member and Sha4 upper member in the working area by using the advanced theories, such as rock thin section, SEM, image analysis, intrusive mercury, mold, rock C.T. measure & test image etc., which reveals the microcosmic characteristic of porosity & throat, filterate mode and microcosmic oil-gas enrichment laws of the sandstone and conglomerate reservoir. For the first time, it sets up the 4-D model and mathematic model of the sandstone and conglomerate reservoir, which reveals the distributing and evolving laws of macroscopic & microcosmic parameters of the two-formation-type sandstone and conglomerate reservoir and oil-gas in 4-D space. At the same time, it also forecasts the oil-gas distribution and instructs the oilfield exploitation. It established reservoir simulation model, which reveals the filterate character and distributing laws of oil-gas in different porosity & throat net models. This article established the assistant theories and techniques for researching, describing, indicating and forecasting the sandstone and conglomerate reservoir fluid units, and develops the theories and techniques of the land faces faulted basin exploitation geology. In instructing oilfield exploitation, it had won the notable economic & social benefits.