Analysis of Lattice Size, Energy Density and Denaturation for a One-Dimensional DNA Model

There are several mechanical models to describe the DNA phenomenology. In this work the DNA denaturation is stu- died under thermodynamical and dynamical point of view using the well known Peyrard-Bishop model. The thermody-namics analysis using the transfer integral operator method is briefly reviewed. In particular, the lattice size is discussed and a conjecture about the minimum energy to denaturation is proposed. In terms of the dynamical aspects of the model, the equations of motion for the system are integrated and the results determine the energy density where the denatura- tion occurs. The behavior of the lattice near the phase transition is analyzed. The relation between the thermodynamical and dynamical results is discussed.

A Practical Micro Mechanical Model Based Local Approach Methodology for the Analysis of Ductile Fracture of Welded T-Joints

This thesis concentrates on developing a practical local approach methodology based on micro mechanical models for the analysis of ductile fracture of welded joints. Two major problems involved in the local approach, namely the dilational constitutive relation reflecting the softening behaviour of material, and the failure criterion associated with the constitutive equation, have been studied in detail. Firstly, considerable efforts were made on the numerical integration and computer implementation for the non trivial dilational Gurson Tvergaard model. Considering the weaknesses of the widely used Euler forward integration algorithms, a family of generalized mid point algorithms is proposed for the Gurson Tvergaard model. Correspondingly, based on the decomposition of stresses into hydrostatic and deviatoric parts, an explicit seven parameter expression for the consistent tangent moduli of the algorithms is presented. This explicit formula avoids any matrix inversion during numerical iteration and thus greatly facilitates the computer implementation of the algorithms and increase the efficiency of the code. The accuracy of the proposed algorithms and other conventional algorithms has been assessed in a systematic manner in order to highlight the best algorithm for this study. The accurate and efficient performance of present finite element implementation of the proposed algorithms has been demonstrated by various numerical examples. It has been found that the true mid point algorithm (a = 0.5) is the most accurate one when the deviatoric strain increment is radial to the yield surface and it is very important to use the consistent tangent moduli in the Newton iteration procedure. Secondly, an assessment of the consistency of current local failure criteria for ductile fracture, the critical void growth criterion, the constant critical void volume fraction criterion and Thomason's plastic limit load failure criterion, has been made. Significant differences in the predictions of ductility by the three criteria were found. By assuming the void grows spherically and using the void volume fraction from the Gurson Tvergaard model to calculate the current void matrix geometry, Thomason's failure criterion has been modified and a new failure criterion for the Gurson Tvergaard model is presented. Comparison with Koplik and Needleman's finite element results shows that the new failure criterion is fairly accurate indeed. A novel feature of the new failure criterion is that a mechanism for void coalescence is incorporated into the constitutive model. Hence the material failure is a natural result of the development of macroscopic plastic flow and the microscopic internal necking mechanism. By the new failure criterion, the critical void volume fraction is not a material constant and the initial void volume fraction and/or void nucleation parameters essentially control the material failure. This feature is very desirable and makes the numerical calibration of void nucleation parameters(s) possible and physically sound. Thirdly, a local approach methodology based on the above two major contributions has been built up in ABAQUS via the user material subroutine UMAT and applied to welded T joints. By using the void nucleation parameters calibrated from simple smooth and notched specimens, it was found that the fracture behaviour of the welded T joints can be well predicted using present methodology. This application has shown how the damage parameters of both base material and heat affected zone (HAZ) material can be obtained in a step by step manner and how useful and capable the local approach methodology is in the analysis of fracture behaviour and crack development as well as structural integrity assessment of practical problems where non homogeneous materials are involved. Finally, a procedure for the possible engineering application of the present methodology is suggested and discussed.

Non-linear analysis of laminated metal matrix composites by an integrated micro/macro-mechanical model

The present paper describes an integrated micro/macro mechanical study of the elastic-viscoplastic behavior of unidirectional metal matrix composites (MMC). The micromechanical analysis of the elastic moduli is based on the Composites Cylinder Assemblage model (CCA) with comparisons also draw with a Representative Unit Cell (RUC) technique. These "homogenization" techniques are later incorporated into the Vanishing Fiber Diameter (VFD) model and a new formulation is proposed. The concept of a smeared element procedure is employed in conjunction with two different versions of the Bodner and Partom elastic-viscoplastic constitutive model for the associated macroscopic analysis. The formulations developed are also compared against experimental and analytical results available in the literature.

On local analysis of oscillations of a non-ideal and non-linear mechanical model

It is of major importance to consider non-ideal energy sources in engineering problems. They act on an oscillating system and at the same time experience a reciprocal action from the system. Here, a non-ideal system is studied. In this system, the interaction between source energy and motion is accomplished through a special kind of friction. Results about the stability and instability of the equilibrium point of this system are obtained. Moreover, its bifurcation curves are determined. Hopf bifurcations are found in the set of parameters of the oscillating system.

Human temporal bones versus mechanical model to evaluate three middle ear transducers

A life-size mechanical middle ear model and human temporal bones were used to evaluate three different middle ear transducers for implantable hearing aids: the driving rod transducer (DRT), the floating mass transducer (FMT) or vibrant sound bridge, and the contactless transducer (CLT). Results of the experiments with the mechanical model were within the range of the results for human temporal bones. However, results with the mechanical model showed better reproducibility. The handling of the mechanical model was considerably simpler and less time-consuming. Systematic variations of mounting parameters showed that the angle of the rod has virtually no effect on the output of the DRT, the mass loading on the cable of the FMT has a larger impact on the output than does the tightness of crimping, and the output level of the CLT can be increased by 10 dB by optimizing the mounting parameters.

Cyclin A activates the DNA polymerase δ-dependent elongation machinery in vitro: A parvovirus DNA replication model

Replication of the single-stranded linear DNA genome of parvovirus minute virus of mice (MVM) starts with complementary strand synthesis from the 3′-terminal snap-back telomere, which serves as a primer for the formation of double-stranded replicative form (RF) DNA. This DNA elongation reaction, designated conversion, is exclusively dependent on cellular factors. In cell extracts, we found that complementary strand synthesis was inhibited by the cyclin-dependent kinase inhibitor p21WAF1/CIP1 and rescued by the addition of proliferating cell nuclear antigen, arguing for the involvement of DNA polymerase (Pol) δ in the conversion reaction. In vivo time course analyses using synchronized MVM-infected A9 cells allowed initial detection of MVM RF DNA at the G1/S phase transition, coinciding with the onset of cyclin A expression and cyclin A-associated kinase activity. Under in vitro conditions, formation of RF DNA was efficiently supported by A9 S cell extracts, but only marginally by G1 cell extracts. Addition of recombinant cyclin A stimulated DNA conversion in G1 cell extracts, and correlated with a concomitant increase in cyclin A-associated kinase activity. Conversely, a specific antibody neutralizing cyclin A-dependent kinase activity, abolished the capacity of S cell extracts for DNA conversion. We found no evidence for the involvement of cyclin E in the regulation of the conversion reaction. We conclude that cyclin A is necessary for activation of complementary strand synthesis, which we propose as a model reaction to study the cell cycle regulation of the Pol δ-dependent elongation machinery.

A statistical mechanical model for β-hairpin kinetics

Understanding the mechanism of protein secondary structure formation is an essential part of the protein-folding puzzle. Here, we describe a simple statistical mechanical model for the formation of a β-hairpin, the minimal structural element of the antiparallel β-pleated sheet. The model accurately describes the thermodynamic and kinetic behavior of a 16-residue, β-hairpin-forming peptide, successfully explaining its two-state behavior and apparent negative activation energy for folding. The model classifies structures according to their backbone conformation, defined by 15 pairs of dihedral angles, and is further simplified by considering only the 120 structures with contiguous stretches of native pairs of backbone dihedral angles. This single sequence approximation is tested by comparison with a more complete model that includes the 215 possible conformations and 15 × 215 possible kinetic transitions. Finally, we use the model to predict the equilibrium unfolding curves and kinetics for several variants of the β-hairpin peptide.

Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation

Modification of damaged replication forks is emerging as a crucial factor for efficient chromosomal duplication and the avoidance of genetic instability. The RecG helicase of Escherichia coli, which is involved in recombination and DNA repair, has been postulated to act on stalled replication forks to promote replication restart via the formation of a four-stranded (Holliday) junction. Here we show that RecG can actively unwind the leading and lagging strand arms of model replication fork structures in vitro. Unwinding is achieved in each case by simultaneous interaction with and translocation along both the leading and lagging strand templates at a fork. Disruption of either of these interactions dramatically inhibits unwinding of the opposing duplex arm. Thus, RecG translocates simultaneously along two DNA strands, one with 5′-3′ and the other with 3′-5′ polarity. The unwinding of both nascent strands at a damaged fork, and their subsequent annealing to form a Holliday junction, may explain the ability of RecG to promote replication restart. Moreover, the preferential binding of partial forks lacking a leading strand suggests that RecG may have the ability to target stalled replication intermediates in vivo in which lagging strand synthesis has continued beyond the leading strand.

A neuro-mechanical model for interpersonal coordination

The present study investigates the coordination between two people oscillating handheld pendulums, with a special emphasis on the influence of the mechanical properties of the effector systems involved. The first part of the study is an experiment in which eight pairs of participants are asked to coordinate the oscillation of their pendulum with the other participant's in an in-phase or antiphase fashion. Two types of pendulums, A and B, having different resonance frequencies (Freq A=0.98 Hz and Freq B=0.64 Hz), were used in different experimental combinations. Results confirm that the preferred frequencies produced by participants while manipulating each pendulum individually were close to the resonance frequencies of the pendulums. In their attempt to synchronize with one another, participants met at common frequencies that were influenced by the mechanical properties of the two pendulums involved. In agreement with previous studies, both the variability of the behavior and the shift in the intended relative phase were found to depend on the task-effector asymmetry, i.e., the difference between the mechanical properties of the effector systems involved. In the second part of the study, we propose a model to account for these results. The model consists of two cross-coupled neuro-mechanical units, each composed of a neural oscillator driving a wrist-pendulum system. Taken individually, each unit reproduced the natural tendency of the participants to freely oscillate a pendulum close to its resonance frequency. When cross-coupled through the vision of the pendulum of the other unit, the two units entrain each other and meet at a common frequency influenced by the mechanical properties of the two pendulums involved. The ability of the proposed model to address the other effects observed as a function of the different conditions of the pendulum and intended mode of coordination is discussed.

A Model Coupling Vibrational and Rotational Motion for the DNA Molecule

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Statistical Model to DNA Melting

We explore a DNA statistical model to obtain information about the behavior of the thermodynamics quantities. Special attention is given to the thermal denaturation of this macromolecule.

Statistical Model to DNA Melting

Um modelo estatístico para o DNA é estudado a fim de se obter informações sobre o comportamento de variáveis termodinâmicas. Atenção especial é dada à desnaturação térmica desta macromolécula.

Modelo vibro-rotacional para a molécula de DNA

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)