A Drosophila XPD model links cell cycle coordination with neuro-development and suggests links to cancer

XPD functions in transcription, DNA repair and in cell cycle control. Mutations in human XPD (also known as ERCC2) mainly cause three clinical phenotypes: xeroderma pigmentosum (XP), Cockayne syndrome (XP/CS) and trichothiodystrophy (TTD), and only XP patients have a high predisposition to developing cancer. Hence, we developed a fly model to obtain novel insights into the defects caused by individual hypomorphic alleles identified in human XP-D patients. This model revealed that the mutations that displayed the greatest in vivo UV sensitivity in Drosophila did not correlate with those that led to tumor formation in humans. Immunoprecipitations followed by targeted quantitative MS/MS analysis showed how different xpd mutations affected the formation or stability of different transcription factor IIH (TFIIH) subcomplexes. The XP mutants most clearly linked to high cancer risk, Xpd R683W and R601L, showed a reduced interaction with the core TFIIH and also an abnormal interaction with the Cdk-activating kinase (CAK) complex. Interestingly, these two XP alleles additionally displayed high levels of chromatin loss and free centrosomes during the rapid nuclear division phase of the Drosophila embryo. Finally, the xpd mutations showing defects in the coordination of cell cycle timing during the Drosophila embryonic divisions correlated with those human mutations that cause the neurodevelopmental abnormalities and developmental growth defects observed in XP/CS and TTD patients.

Multi-vehicles interaction graph model for cooperative collision warning system

Cooperative collision warning system for road vehicles, enabled by recent advances in positioning systems and wireless communication technologies, can potentially reduce traffic accident significantly. To improve the system, we propose a graph model to represent interactions between multiple road vehicles in a specific region and at a specific time. Given a list of vehicles in vicinity, we can generate the interaction graph using several rules that consider vehicle's properties such as position, speed, heading, etc. Safety applications can use the model to improve emergency warning accuracy and optimize wireless channel usage. The model allows us to develop some congestion control strategies for an efficient multi-hop broadcast protocol.

Fluid-structure interaction analysis by coupled FE-SPH model based on a novel searching algorithm

Fluid–Structure Interaction (FSI) problem is significant in science and engineering, which leads to challenges for computational mechanics. The coupled model of Finite Element and Smoothed Particle Hydrodynamics (FE-SPH) is a robust technique for simulation of FSI problems. However, two important steps of neighbor searching and contact searching in the coupled FE-SPH model are extremely time-consuming. Point-In-Box (PIB) searching algorithm has been developed by Swegle to improve the efficiency of searching. However, it has a shortcoming that efficiency of searching can be significantly affected by the distribution of points (nodes in FEM and particles in SPH). In this paper, in order to improve the efficiency of searching, a novel Striped-PIB (S-PIB) searching algorithm is proposed to overcome the shortcoming of PIB algorithm that caused by points distribution, and the two time-consuming steps of neighbor searching and contact searching are integrated into one searching step. The accuracy and efficiency of the newly developed searching algorithm is studied on by efficiency test and FSI problems. It has been found that the newly developed model can significantly improve the computational efficiency and it is believed to be a powerful tool for the FSI analysis.

A model for the interaction of trifluoroethanol with peptides and proteins

The structural stabilizing property of 2,2,2-trifluoroethanol (TFE) in peptides has been widely demonstrated, More recently, TFE has been shown to enhance secondary structure content in globular proteins, and to influence quaternary interactions in protein multimers. The molecular mechanisms by which TFE exerts its Influence on peptide and protein structures remain poorly understood. The present analysis integrates the known physical properties of TFE with a variety of experimental observations on the interaction of TFE with peptides and proteins and on the properties of fluorocarbons. Two features of TFE, namely the hydrophobicity of the trifluoromethyl group and the hydrogen bonding character (strong donor and poor acceptor), emerge as the most important factors for rationalising the observed effects of TFE. A model is proposed for TFE interaction with peptides which involves an initial replacement of the hydration shell by fluoroalcohol molecules, a process driven by apolar interactions and favourable entropy of dehydration. Subsequent bifurcated hydrogen-bond formation with peptide carbonyl groups, which leave intramolecular interactions unaffected, promotes secondary structure formation.

Structured model-following neuro-adaptive design for attitude maneuver of rigid bodies

A new structured model-following adaptive approach is presented in this paper to achieve large attitude maneuvers of rigid bodies. First, a nominal controller is designed using the dynamic inversion philosophy. Next, a neuro- adaptive design is proposed to augment the nominal design in order to assure robust performance in the presence of parameter inaccuracies as well as unknown constant external disturbances. The structured approach proposed in this paper (where kinematic and dynamic equations are handled separately), reduces the complexity of the controller structure. From simulation studies, this adaptive controller is found to be very effective in assuring robust performance.

Resolution of racemic gossypol and interaction of individual enantiomers with serum albumins and model peptides

Racemic gossypol has been resolved by HPLC separation of diastereomeric (−) norepinephrine adducts on a reverse-phase column. The binding constants for the interaction of the three gossypol forms (+, − and −) with human and bovine serum albumins have been determined by fluoresence quenching studies. The KD values demonstrate that all three forms bind equally effectively to the two proteins, suggesting an absence of chiral discrimination in albumin-gossypol interactions. Circular dichroism studies of (+)-gossypol binding to the model dibasic peptides, Boc-Lys-Pro-Aib-Lys-NHMe and gramicidin S, suggesting that distortions of binaphthyl geometry may occur only for specific orientations of interacting residues at the receptor site.

On a generalized dynamic model of bi-state social interaction processes

A non-linear model, construed as a generalized version of the models put forth earlier for the study of bi-state social interaction processes, is proposed in this study. The feasibility of deriving the dynamics of such processes is demonstrated by establishing equivalence between the non-linear model and a higher order linear model.

Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Frame Soil Interaction And Winkler Model

The Winkler spring model is the most convenient representation of soil support in the domain of linear elasticity for framed structure-soil interaction analyses. The closeness of the analytical results obtained using this model with those corresponding to the elastic half-space continuum has been investigated in the past for foundation beams. The findings, however, are not applicable to framed structures founded on beam or strip footings. Moreover, the past investigations employ the concept of characteristic length which does not adequately account for the stiffness contribution of the superstructure. A framed structure on beam foundation can be described parametrically by the ratios of stiffnesses of superstructure and foundation beams to that of soil. For a practical range of soil allowable pressures, the ranges of these relative stiffness ratios have been established. The present study examines the variation between interactive analyses based on Winkler springs with those using the half-space continuum over these ranges of relative stiffness ratios. The findings enable the analyst to undertake a Winkler spring-based-interaction analysis with knowledge of the likely variation of values with those derived for the more computation-intensive half-space continuum.

Model-following Neuro-adaptive approach for robust control of high performance aircrafts

Based on dynamic inversion, a relatively straightforward approach is presented in this paper for nonlinear flight control design of high performance aircrafts, which does not require the normal and lateral acceleration commands to be first transferred to body rates before computing the required control inputs. This leads to substantial improvement of the tracking response. Promising results are obtained from six degree-offreedom simulation studies of F-16 aircraft, which are found to be superior as compared to an existing approach (which is also based on dynamic inversion). The new approach has two potential benefits, namely reduced oscillatory response (including elimination of non-minimum phase behavior) and reduced control magnitude. Next, a model-following neuron-adaptive design is augmented the nominal design in order to assure robust performance in the presence of parameter inaccuracies in the model. Note that in the approach the model update takes place adaptively online and hence it is philosophically similar to indirect adaptive control. However, unlike a typical indirect adaptive control approach, there is no need to update the individual parameters explicitly. Instead the inaccuracy in the system output dynamics is captured directly and then used in modifying the control. This leads to faster adaptation, which helps in stabilizing the unstable plant quicker. The robustness study from a large number of simulations shows that the adaptive design has good amount of robustness with respect to the expected parameter inaccuracies in the model.

Effect of Super-exchange Interaction on Ground state Magnetic Properties of Spin-dependent Falicov-Kimball Model on a Triangular Lattice

Ground state magnetic properties are studied by incorporating the super-exchange interaction (J(se)) in the spin-dependent Falicov-Kimball model (FKM) between localized (f-) electrons on a triangular lattice for half filled case. Numerical diagonalization and Monte-Carlo simulation are used to study the ground state magnetic properties. We have found that the magnetic moment of (d-) and (f-) electrons strongly depend on the value of Hund's exchange (J), super-exchange interaction (J(se)) and also depends on the number of (d-) electrons (N-d). The ground state changes from antiferromagnetic (AFM) to ferromagnetic (FM) state as we decrease (N-d). Also the density of d electrons at each site depends on the value of J and J(se).