Mechanical modeling of viral capsids

As revealed by techniques of structural biology and single-molecule experimentation, the protein shells of viruses (capsids) are some of nature’s best examples of highly symmetric multiscale self-assembled structures, with impressive mechanical properties of strength and elasticity. Mechanical models of viral capsids built “from the bottom up,” i.e., from all-atom models in the context of molecular dynamics and normal mode analysis, have chiefly focused on unforced vibrational capsid dynamics. Due to the size of viral capsids, which can contain several hundred thousand atoms, the computer power needed for these types of methods has only recently reached the level required for all-atom simulations of entire viral capsids. Coarse-grained normal mode analysis has provided a simplified means of studying the unforced vibrational dynamics of viral capsids. Recent focus on “top-down” mechanical models of viral capsids based on two- and three-dimensional continuum elasticity have provided a theoretical complement to single molecule experiments such as atomic force microscopy, and have advanced the fundamental understanding of the forced mechanics. This review serves to assess the current state of modeling techniques for the study of the mechanics of viral capsids, and to highlight some of the key insights gained from such modeling. In particular, a theme is established of a link between shape—or geometry—and the global mechanical properties of these hierarchical multiscale biological structures.     

Mathematical modeling of the heat treatment and combustion of a coal particle. V. Burn-up stage

The present material is a sequel of the previous publications of the authors in this journal under a common title in which by means of mathematical modeling the sequential stages of the process of combustion of coal fuels have been obtained: heating, drying, escape of volatiles, and ignition. Mathematical models of the final stage of combustion of an individual particle — the burn-up stage — have been formulated. On the basis of the solution methods for nonlinear boundary-value problems developed by us, approximate-analytic formulas for two characteristic regimes, burn-up simultaneously with the evaporation of the remaining moisture and burn-up of the completely dried coke residue, have been obtained. The previous history of the physical and chemical phenomena in the general burning pattern is taken into account. The influence of the ash shell on the duration of combustion has been extimated. Comparison of calculations by the obtained dependences with the results of other authors has been made. It showed an accuracy sufficient for engineering applications.     

Fast pyrolysis of an ensemble of biomass particles in a fluidized bed

A combined approach to the modeling of fast pyrolysis of biomass particles in a fluidized bed has been used. We used models of different levels: two models of pyrolysis of a single particle — with lumped and distributed parameters — and a model of pyrolysis of an ensemble of biomass particles based on the continuum equations for the gas blown through the bed and the equations of motion for individual particles. We have determined optimal (in terms of the biofuel yield) temperatures of the process for various particle sizes of wood biomass and various values of its moisture.     

Asymptotic analysis of the small-scale structure of the laminar boundary layer with suction

The features of the gas flow in the working section of a transonic wind tunnel have been considered. On the basis of the method of joining asymptotic expansions and the theory of detached zones mathematical models of the flow are proposed. The flow over a perforation and transverse and longitudinal slots has been investigated. In the latter case, a nonstationary and a stationary analogy with a two-dimensional flow are stated. A deflector — a new device for reflecting shocks — is proposed. The problems are discussed.     

An assessment of five modeling approaches for thermo-mechanical stress analysis of laminated composite panels

 A study is made of the effects of variation in the lamination and geometric parameters, and boundary conditions of multi-layered composite panels on the accuracy of the detailed response characteristics obtained by five different modeling approaches. The modeling approaches considered include four two-dimensional models, each with five parameters to characterize the deformation in the thickness direction, and a predictor-corrector approach with twelve displacement parameters. The two-dimensional models are first-order shear deformation theory, third-order theory; a theory based on trigonometric variation of the transverse shear stresses through the thickness, and a discrete layer theory. The combination of the following four key elements distinguishes the present study from previous studies reported in the literature: (1) the standard of comparison is taken to be the solutions obtained by using three-dimensional continuum models for each of the individual layers; (2) both mechanical and thermal loadings are considered; (3) boundary conditions other than simply supported edges are considered; and (4) quantities compared include detailed through-the-thickness distributions of transverse shear and transverse normal stresses. Based on the numerical studies conducted, the predictor-corrector approach appears to be the most effective technique for obtaining accurate transverse stresses, and for thermal loading, none of the two-dimensional models is adequate for calculating transverse normal stresses, even when used in conjunction with three-dimensional equilibrium equations. Received 14 September 1999     

Coupled modeling of steady-state creep rate and creep rupture strength for metals

New methods of coupled mathematical modeling of steady-state creep rate and creep rupture strength of metals in tension have been devised. Two nonlinear fractional power functions with four material constants are used as basic dependences of the steady-state creep and creep rupture life on stress. Computation of the functions is based on optimally solving two nonlinear and inconsistent — in the conventional meaning — equations sets by the method of minimization of quadratic residuals. The authors outline the methods for calculating material constants, which were used to derive analytical expressions that optimally approximate the test results for 10Kh15N27T3MR steel at 600°C under various stresses. A method of piecewise-linear approximation of creep rupture strength test results, which involves the use of a two-segment broken line, is put forward. It implies that the locations of kinks as well as other numerical characteristics of the broken line are determined from the condition of the line’s optimal arrangement relative to the experimental data points. The method takes a more comprehensive account of various damage accumulation mechanisms in steel under various stress levels. __________ Translated from Problemy Prochnosti, No. 4, pp. 25–35, July–August, 2008.     

Modeling the Ultrasonic Radiation of a Planar Transducer Through a Plane Fluid—Solid Interface

Three types of transducer beam models are developed for obtaining the bulk waves generated by a plane piston transducer radiating through a planar fluid—solid interface. The first type, called the surface integral model, is based on a Rayleigh—Sommerfeld-like integral that requires a two-dimensional surface integral to be evaluated. The second model, called the boundary diffraction wave (BDW) paraxial model, simplifies the two-dimensional integration of the surface integral model to a one-dimensional line integration. The third type of model, called the edge element model, is shown to be a novel way of efficiently evaluating the two-dimensional surface integration of the surface integral model. The limitations of these models for simulating inspections near critical refracted angles and near the interface are discussed. It is shown that the introduction of the paraxial approximation in the BDW model allows that model to be computed with a very large (300—1) speed advantage over the surface integral while retaining the same accuracy in most cases. The edge element model, while having a smaller (5—1) advantage over the direct numerical integration of the surface integral model, retains the accuracy of the surface integral model in cases where the paraxial approximation fails and can be easily generalized to more complex testing situations (focused probes, curved interfaces, etc.).     

Identification of singular interfaces with Δ<Emphasis Type="Bold">g</Emphasis>s and its basis of the O-lattice

This article identifies singular interfaces according to singularity in terms of structural defects, including dislocations and ledges. Defect singularities are defined by the elimination of one or more classes of defects, which must be present in the vicinal interfaces. In addition to the three commonly classified structural interfaces, a new type of interface—the CS-coherent interface—is introduced. Singularities in dislocation and ledge structures have been integrated in the study of orientation relationships (OR). The dislocation structures are determined through the O-lattice theory, originally proposed by Bollmann. The basic concepts of the O-lattice and related formulas from the original theory and extended studies are briefly reviewed. According to the theory, singular interfaces exhibiting singularity in the dislocation structures have been identified. An interface that is singular with respect to the interface orientation must be normal to at least one Δg, a vector connecting two reciprocal points from different lattices. An interface that is singular also with respect to the OR must obey one or more Δg parallelism rules. The selection of proper Δgs for different preferred states of interfaces are explained. Identification of singular interfaces with measurable Δgs provides a convenient and effective approach to the interpretation of the observed facets and ORs. The ambiguity about the selection of the deformation matrix (A) for the O-lattice calculation and the advantage of the O-lattice approach over the approach using the Frank–Bilby equation for the calculation of the interfacial dislocations are clarified. Limitations of the present approach and further study are discussed.     

Engaging and Supporting Problem Solving in Engineering Ethics

Learning to solve ethical problems is essential to the education of all engineers. Engineering ethics problems are complex and ill structured with multiple perspectives and interpretations to address in their solution. In two experiments, we examined alternative strategies for engaging ethical problem solving. In Experiment 1, students studied two versions of an online learning environment consisting of everyday ethics problems. Students using question hypertext links to navigate applied more perspectives and canons and wrote stronger overall solutions to ethics problems than those using embedded hypertext links. In Experiment 2, students engaged in a more generative task, evaluating alternative arguments for solutions to the cases or generating and supporting their own solutions. Both groups better supported their solutions and generated more counterclaims than control students. These studies focused on solving realistic case‐based ethics problems as an effective method for addressing ABET's ethics criteria.     

Thin-ship theory and influence of rake and flare

The basic computational task of the thin-ship theory of free-surface potential flow about a ship that advances at constant speed along a straight path in calm water, of large depth and lateral extent, is considered. Specifically, a straightforward method for evaluating the pressure and the wave profile at a ship hull (the wave drag, hydrodynamic lift and pitch moment, and sinkage and trim are also considered) in accordance with Michell’s thin-ship theory is given. A main ingredient of this method is a simple analytical approximation to the local-flow component in the expression for the Green function (associated with the classical Michell–Kelvin linearized free-surface boundary condition) of thin-ship theory. This practical Green function is used to evaluate and analyze steady flow about a four-parameter family of ship bows with rake and flare. In particular, the variations of the bow-wave height and location with respect to the draft-based Froude number, the entrance angles at the top and bottom waterlines, and the rake angle are explored via a systematic parametric study. This parametric study provides estimates—immediately useful for design—of the influence of rake and flare on the height and the location of a ship bow wave, and shows that rake and flare effects can be significant, especially at low Froude numbers.     

MQSPR modeling in materials informatics: a way to shorten design cycles?

We demonstrate applications of quantitative structure–property relationship (QSPR) modeling to supplement first-principles computations in materials design. We have here focused on the design of polymers with specific electronic properties. We first show that common materials properties such as the glass transition temperature (T _g) can be effectively modeled by QSPR to generate highly predictive models that relate polymer repeat unit structure to T _g. Next, QSPR modeling is shown to supplement and guide first-principles density functional theory (DFT) computations in the design of polymers with specific dielectric properties, thereby leveraging the power of first-principles computations by providing high-throughput capability. Our approach consists of multiple rounds of validated MQSPR modeling and DFT computations to optimize the polymer skeleton as well as functional group substitutions thereof. Rigorous model validation protocols insure that the statistical models are able to make valid predictions on molecules outside the training set. Future work with inverse QSPRs has the potential to further reduce the time to optimize materials properties.     

Identification of the vortex mechanism of front stabilization in modeling of asymmetric flow of an incompressible fluid along a cylinder with a protruding disk

Based on numerical solution of the Navier—Stokes equations by the finite-difference method and physical modeling in a wind tunnel of laminar flow along a cylinder with a protruding disk the vortex mechanism of front stabilization and reduction in the drag of blunt bodies is investigated.     

Do international management researchers need a code of ethics?

Abstract and Key Results

Probing material properties with sharp indenters: a retrospective

A retrospective on the use of sharp, fixed-profile indenters as materials probes is presented. Indentation is proposed as a simple but powerful methodology for evaluating basic mechanical properties—elastic modulus, hardness, toughness—in all classes of materials. Indentation also provides unique insight into fundamental deformation and fracture processes. Of particular interest is the existence of intrinsic size effects as characteristic contact dimensions pass from macro- to micro- to nano-scale dimensions. The utility of indentations as ‘controlled flaws’ in the context of strength of materials is outlined. The roles of two other important material factors—rate effects and microstructure—are considered. Examples of technological and biological applications are presented as illustrations of the widespread power of the technique. Strengths and limitations of the methodology as a routine testing protocol are discussed.     

Ein Mitbegründer der modernen Medizin- und Wissenschaftsethik: John Gregory (1724–1773) und seineLectures on the Duties and Qualifications of a Physician

The scottish physician and philosopher John Gregory (1724–1773) published in 1770Lectures On The Duties and Qualifications Of A Physician. Besides giving many very concrete and pragmatic rules and proposals concerning medical etiquette and decency, like most medical “codifiers” did before and after him, Gregory also develops a truely “ethical”—in the sense of (moral-) philosophically based—“system of conduct in a physician”. His concept of practicing and teaching ethics in medicine and research combines Bacon's (1561–1626) philosophy of nature and science with both, the general moral philosophy of the religious sceptic David Hume (1711–1776) and the traditional christian-occidental virtues and deontologies upheld by the movement of the so-called “Common-Sense Philosophy”. By thus combinig conservative moral traditions with the modern enlightenment philosophy of empirism, Gregory's teachings establish ethics in medicine and science on a very broad compromise. It can be proved that his very comprehensiveLectures had—particularly via the famousCode of Medical Ethics of Thomas Percival (1740–1804)—a decisive influence on our contemporary concepts of bioethics.      

Diagnosis of the load-carrying capacity of pipes containing a longitudinal crack when loaded by an axial force and internal pressure

A method is developed for evaluating the load-carrying capacity and safe life of pipes with a through longitudinal crack when loaded by an axial force and internal pressure. The method is based on the use of previously developed nomograms of strain and limit load. The first nomogram is calculated on the basis of constitutive relations of the theory of plasticity, while the second is calculated in accordance with a fracture criterion for biaxial loading. The proposed method makes it possible to determine one of three parameters — critical crack length, limiting pressure, or limiting axial load — without preliminary calculations if the other two parameters are already known. As an example, nomograms are presented for a steel 15G2 pipe having a diameter of 1420 mm and wall thickness of 21.5 mm and containing a longitudinal crack. Translated from Problemy Prochnosti, No. 12, pp. 16–23, December, 1994.     

Analysis of the random errors of digital algorithms for measuring the frequency of laser-doppler anemometers by numerical modeling

An analysis is made of the errors of digital algorithms for measuring the frequency of the Doppler signal of a laser-Doppler anemometer (LDA) by numerical modeling. An examination is made of methods of evaluating the period of the high-frequency duty cycle of a single-particle signal from an LDA with respect to the coordinates of the “zeros” of the process. Methods of evaluating the frequency of the signal from the position of the maximum of the modulus of spectral density are also discussed. Results are presented from studies of the dependence of the measurement error on the parameters of a discretized LDA signal and the signal/noise ratio. The conditions necessary for restricting the maximum measurement error to 0.1–0.3% are determined. Translated from Izmeritel'naya Tekhnika, No. 7, pp. 36–38, July, 1995.     

Combined modeling and experimental studies of hydroxylated silica nanoparticles

Nanotechnology offers several opportunities to solve problems related with Oil and Gas industry. One of them is the possibility to use hard nanoparticles to control the wettability phenomena between the three-phase system (oil–water–minerals) at reservoir conditions of temperature, pressure, and salinity. Here, we present a combined experimental and modeling study of hydroxylated silica nanoparticles as candidate for improved oil recovery applications. In this work, we mainly focus on development of more realistic SiO₂-nanoparticle models and validating them against the experimental data. An efficient Monte Carlo scheme is proposed to generate realistic SiO₂ nanoparticle atomistic models (3–5 nm). Structural and spectroscopic properties such as Raman and Infrared were obtained through Molecular Dynamics (MD) calculations using a force field that mimics an ab initio data. We have also used Fourier transform infrared spectroscopy to identify chemical functional groups present in 5 nm unmodified (bare) silica nanoparticle dispersions. A good agreement between the MD simulations and experiments has been observed.     

Import-export of knowledge between scientific subject categories: The iceberg hypothesis

The capacity to attract citations from other disciplines — or knowledge export — has always been taken into account in evaluating the quality of scientific papers or journals. Some of the JCR’s (ISI’s Journal Citation Report) Subject Categories have a greater exporting character than others because they are less isolated. This influences the rank/JIF (ISI’s Journal Impact Factor) distribution of the category. While all the categories fit a negative power law fairly well, those with a greater External JIF give distributions with a more sharply defined peak and a longer tail — something like an iceberg. One also observes a major relationship between the rates of export and import of knowledge.     

Fiber-reinforced hyperelastic solids: a realizable homogenization constitutive theory

A new homogenization theory to model the mechanical response of hyperelastic solids reinforced by a random distribution of aligned cylindrical fibers is proposed. The central idea is to devise a special class of microstructures—by means of an iterated homogenization procedure in finite elasticity together with an exact dilute result for sequential laminates—that allows to compute exactly the macroscopic response of the resulting fiber-reinforced materials. The proposed framework incorporates direct microstructural information up to the two-point correlation functions, and requires the solution to a Hamilton–Jacobi equation with the fiber concentration and the macroscopic deformation gradient playing the role of “time” and “spatial” variables, respectively. In addition to providing constitutive models for the macroscopic response of fiber-reinforced materials, the proposed theory also gives information about the local fields in the matrix and fibers, which can be used to study the evolution of microstructure and the development of instabilities. As a first application of the theory, closed-form results for the case of Neo-Hookean solids reinforced by a transversely isotropic distribution of anisotropic fibers are worked out. These include a novel explicit criterion for the onset of instabilities under general finite-strain loading conditions.