A finite population model of mlecular evolution: theory and computation

This article is concerned with the evolution of haploid organisms that reproduce asexually. In a seminal piece of work, Eigen and coauthors proposed the quasispecies model in an attempt to understand such an evolutionary process. Their work has impacted antiviral treatment and vaccine design strategies. Yet, predictions of the quasispecies model are at best viewed as a guideline, primarily because it assumes an infinite population size, whereas realistic population sizes can be quite small. In this paper we consider a population genetics-based model aimed at understanding the evolution of such organisms with finite population sizes and present a rigorous study of the convergence and computational issues that arise therein. Our first result is structural and shows that, at any time during the evolution, as the population size tends to infinity, the distribution of genomes predicted by our model converges to that predicted by the quasispecies model. This justifies the continued use of the quasispecies model to derive guidelines for intervention. While the stationary state in the quasispecies model is readily obtained, due to the explosion of the state space in our model, exact computations are prohibitive. Our second set of results are computational in nature and address this issue. We derive conditions on the parameters of evolution under which our stochastic model mixes rapidly. Further, for a class of widely used fitness landscapes we give a fast deterministic algorithm which computes the stationary distribution of our model. These computational tools are expected to serve as a framework for the modeling of strategies for the deployment of mutagenic drugs.

Application of a modified jogged-screw model for creep of titanium aluminides: evaluation of the key substructural parameters

A modification of the jogged-screw model has been adopted recently by the authors to explain observations of 1/2[110]-type jogged-screw dislocations in equiaxed Ti-48Al under creep conditions. The aim of this study has been to verify and validate the parameters and functional dependencies that have been assumed in this previous work. The original solution has been reformulated to take into account the finite length of the moving jog. This is a better approximation of the tall jog. The substructural model parameters have been further investigated in light of the Finite Length Moving Line (FLML) source approximation. The original model assumes that the critical jog height (beyond which the jog is not dragged) is inversely proportional to the applied stress. By accounting for the fact that there are three competing mechanisms (jog dragging, dipole dragging, dipole bypass) possible, we can arrive at a modified critical jog height. The critical jog height was found to be more strongly stress dependent than assumed previously. The original model assumes the jog spacing to be invariant over the stress range. However, dynamic simulation using a line tension model has shown that the jog spacing is inversely proportional to the applied stress. This has also been confirmed by TEM measurements of jog spacings over a range of stresses. Taylor's expression assumed previously to provide the dependence of dislocation density on the applied stress, has now been confirmed by actual dislocation density measurements. Combining all of these parameters and dependencies, derived both from experiment and theory, leads to an excellent prediction of creep rates and stress exponents. The further application of this model to other materials, and the important role of atomistic and dislocation dynamics simulations in its continued development is also discussed.

Reaction dynamics under confinement: an exact path integral treatment of a two-stage model of stochastic gene expression

Gene expression in living systems is inherently stochastic, and tends to produce varying numbers of proteins over repeated cycles of transcription and translation. In this paper, an expression is derived for the steady-state protein number distribution starting from a two-stage kinetic model of the gene expression process involving p proteins and r mRNAs. The derivation is based on an exact path integral evaluation of the joint distribution, P(p, r, t), of p and r at time t, which can be expressed in terms of the coupled Langevin equations for p and r that represent the two-stage model in continuum form. The steady-state distribution of p alone, P(p), is obtained from P(p, r, t) (a bivariate Gaussian) by integrating out the r degrees of freedom and taking the limit t -> infinity. P(p) is found to be proportional to the product of a Gaussian and a complementary error function. It provides a generally satisfactory fit to simulation data on the same two-stage process when the translational efficiency (a measure of intrinsic noise levels in the system) is relatively low; it is less successful as a model of the data when the translational efficiency (and noise levels) are high.

A micropolar peridynamic theory in linear elasticity

A state-based micropolar peridynamic theory for linear elastic solids is proposed. The main motivation is to introduce additional micro-rotational degrees of freedom to each material point and thus naturally bring in the physically relevant material length scale parameters into peridynamics. Non-ordinary type modeling via constitutive correspondence is adopted here to define the micropolar peridynamic material. Along with a general three dimensional model, homogenized one dimensional Timoshenko type beam models for both the proposed micropolar and the standard non-polar peridynamic variants are derived. The efficacy of the proposed models in analyzing continua with length scale effects is established via numerical simulations of a few beam and plane-stress problems. (C) 2015 Elsevier Ltd. All rights reserved.

A meso elastoplastic constitutive model for polycrystalline metals based on equivalent slip systems with latent hardening

A meso material model for polycrystalline metals is proposed, in which the tiny slip systems distributing randomly between crystal slices in micro-grains or on grain boundaries are replaced by macro equivalent slip systems determined by the work-conjugate principle. The elastoplastic constitutive equation of this model is formulated for the active hardening, latent hardening and Bauschinger effect to predict macro elastoplastic stress-strain responses of polycrystalline metals under complex loading conditions. The influence of the material property parameters on size and shape of the subsequent yield surfaces is numerically investigated to demonstrate the fundamental features of the proposed material model. The derived constitutive equation is proved accurate and efficient in numerical analysis. Compared with the self-consistent theories with crystal grains as their basic components, the present theory is much simpler in mathematical treatment.

Peierls-Nabarro model of interfacial misfit dislocation: An analytic solution

We propose a method to treat the interfacial misfit dislocation array following the original Peierls-Nabarro's ideas. A simple and exact analytic solution is derived in the extended Peierls-Nabarro's model, and this solution reflects the core structure and the energy of misfit dislocation, which depend on misfit and bond strength. We also find that only with beta < 0.2 the structure of interface can be represented by an array of singular Volterra dislocations, which conforms to those of atomic simulation. Interfacial energy and adhesive work can be estimated by inputting ab initio calculation data into the model, and this shows the method can provide a correlation between the ab initio calculations and elastic continuum theory.

The Displacement and Strain Field of Three-Dimensional Rheologic Model of Earthquake Preparation

Based on the three-dimensional elastic inclusion model proposed by Dobrovolskii, we developed a rheological inclusion model to study earthquake preparation processes. By using the Corresponding Principle in the theory of rheologic mechanics, we derived the analytic expressions of viscoelastic displacement U(r, t) , V(r, t) and W(r, t), normal strains epsilon(xx) (r, t), epsilon(yy) (r, t) and epsilon(zz) (r, t) and the bulk strain theta (r, t) at an arbitrary point (x, y, z) in three directions of X axis, Y axis and Z axis produced by a three-dimensional inclusion in the semi-infinite rheologic medium defined by the standard linear rheologic model. Subsequent to the spatial-temporal variation of bulk strain being computed on the ground produced by such a spherical rheologic inclusion, interesting results are obtained, suggesting that the bulk strain produced by a hard inclusion change with time according to three stages (alpha, beta, gamma) with different characteristics, similar to that of geodetic deformation observations, but different with the results of a soft inclusion. These theoretical results can be used to explain the characteristics of spatial-temporal evolution, patterns, quadrant-distribution of earthquake precursors, the changeability, spontaneity and complexity of short-term and imminent-term precursors. It offers a theoretical base to build physical models for earthquake precursors and to predict the earthquakes.

The development of an inhomogeneous damage field in an elastic-plastic model

By making use of the evolution equation of the damage field as derived from the statistical mesoscopic damage theory, we have preliminarily examined the inhomogeneous damage field in an elastic-plastic model under constant-velocity tension. Three types of deformation and damage field evolution are presented. The influence of the plastic matrix is examined. It seems that matrix plasticity may defer the failure due to damage evolution. A criterion for damage localization is consistent with the numerical results.

Energy Conversion in Shape Memory Alloy Heat Engine Part I: Theory

Shape Memory Alloy (SMA) can be easily deformed to a new shape by applying a small external load at low temperature, and then recovers its original configuration upon heating. This unique shape memory phenomenon has inspired many novel designs. SMA based heat engine is one among them. SMA heat engine is an environment-friendly alternative to extract mechanical energy from low-grade energies, for instance, warm wastewater, geothermal energy, solar thermal energy, etc. The aim of this paper is to present an applicable theoretical model for simulation of SMA-based heat engines. First, a micro-mechanical constitutive model is derived for SMAs. The volume fractions of austenite and martensite variants are chosen as internal variables to describe the evolution of microstructure in SMA upon phase transition. Subsequently, the energy equation is derived based on the first thermodynamic law and the previous SMA model. From Fourier’s law of heat conduction and Newton’s law of cooling, both differential and integral forms of energy conversion equation are obtained.

Theory Of Phase Transformation And Reorientation In Single Crystalline Shape Memory Alloys

A constitutive model, based on an (n + 1)-phase mixture of the Mori-Tanaka average theory, has been developed for stress-induced martensitic transformation and reorientation in single crystalline shape memory alloys. Volume fractions of different martensite lattice correspondence variants are chosen as internal variables to describe microstructural evolution. Macroscopic Gibbs free energy for the phase transformation is derived with thermodynamics principles and the ensemble average method of micro-mechanics. The critical condition and the evolution equation are proposed for both the phase transition and reorientation. This model can also simulate interior hysteresis loops during loading/unloading by switching the critical driving forces when an opposite transition takes place.

On the interaction of water waves and seabed by the porous medium model

The interaction of water waves and seabed is studied by using Yamamoto's model, which takes into account the deformation of soil skeletal frame, compressibility of pore fluid flow as well as the Coulumb friction. When analyzing the propagation of three kinds of stress waves in seabed, a simplified dispersion relation and a specific damping formula are derived. The problem of seabed stability is further treated analytically based on the Mohr-Coulomb theory. The theory is finally applied to the coastal problems in the Lian-Yun Harbour and compared with observations and measurements in soil-wave tank with satisfactory results.

On the strategic equivalence of multiple-choice test scoring rules

A disadvantage of multiple-choice tests is that students have incentives to guess. To discourage guessing, it is common to use scoring rules that either penalize wrong answers or reward omissions. These scoring rules are considered equivalent in psychometrics, although experimental evidence has not always been consistent with this claim. We model students' decisions and show, first, that equivalence holds only under risk neutrality and, second, that the two rules can be modified so that they become equivalent even under risk aversion. This paper presents the results of a field experiment in which we analyze the decisions of subjects taking multiple-choice exams. The evidence suggests that differences between scoring rules are due to risk aversion as theory predicts. We also find that the number of omitted items depends on the scoring rule, knowledge, gender and other covariates.

The Displacement and Strain Field of Three-Dimensional Rheologic Model of Earthquake Preparation

Based on the three-dimensional elastic inclusion model proposed by Dobrovolskii, we developed a rheological inclusion model to study earthquake preparation processes. By using the Corresponding Principle in the theory of rheologic mechanics, we derived the analytic expressions of viscoelastic displacement U(r, t) , V(r, t) and W(r, t), normal strains epsilon(xx) (r, t), epsilon(yy) (r, t) and epsilon(zz) (r, t) and the bulk strain theta (r, t) at an arbitrary point (x, y, z) in three directions of X axis, Y axis and Z axis produced by a three-dimensional inclusion in the semi-infinite rheologic medium defined by the standard linear rheologic model. Subsequent to the spatial-temporal variation of bulk strain being computed on the ground produced by such a spherical rheologic inclusion, interesting results are obtained, suggesting that the bulk strain produced by a hard inclusion change with time according to three stages (alpha, beta, gamma) with different characteristics, similar to that of geodetic deformation observations, but different with the results of a soft inclusion. These theoretical results can be used to explain the characteristics of spatial-temporal evolution, patterns, quadrant-distribution of earthquake precursors, the changeability, spontaneity and complexity of short-term and imminent-term precursors. It offers a theoretical base to build physical models for earthquake precursors and to predict the earthquakes.

New Strain Gradient Theory And Analysis

A new strain gradient theory which is based on energy nonlocal model is proposed in this paper, and the theory is applied to investigate the size effects in thin metallic wire torsion, ultra-thin beam bending and micro-indentation of polycrystalline copper. First, an energy nonlocal model is suggested. Second, based on the model, a new strain gradient theory is derived. Third, the new theory is applied to analyze three representative experiments.