Isotopic fractionation in proteins as a measure of hydrogen bond length

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor (I) is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds, we calculate (I) as a function of the proton donor-acceptor distance R. For numerical results, we use a parameterization of the model for symmetric 0-H. ``.0 bonds R. H. McKenzie, Chem. Phys. Lett. 535, 196 (2012)]. We consider the relative contributions of the 0-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunneling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total (I) as a function of R with NMR experimental results for enzymes, and in particular with an earlier model parametrization (D(R), used previously to determine bond lengths. (C) 2015 AIP Publishing LLC.

Similarity of Matrices Over Local Rings of Length Two

Let R be a (commutative) local principal ideal ring of length two, for example, the ring R = Z/p(2)Z with p prime. In this paper, we develop a theory of normal forms for similarity classes in the matrix rings M-n (R) by interpreting them in terms of extensions of R t]-modules. Using this theory, we describe the similarity classes in M-n (R) for n <= 4, along with their centralizers. Among these, we characterize those classes which are similar to their transposes. Non-self-transpose classes are shown to exist for all n > 3. When R has finite residue field of order q, we enumerate the similarity classes and the cardinalities of their centralizers as polynomials in q. Surprisingly, the polynomials representing the number of similarity classes in M-n (R) turn out to have non-negative integer coefficients.

Correlation equations for average deposition rate coefficients of nanoparticles in a cylindrical pore

Nanoparticle deposition behavior observed at the Darcy scale represents an average of the processes occurring at the pore scale. Hence, the effect of various pore-scale parameters on nanoparticle deposition can be understood by studying nanoparticle transport at pore scale and upscaling the results to the Darcy scale. In this work, correlation equations for the deposition rate coefficients of nanoparticles in a cylindrical pore are developed as a function of nine pore-scale parameters: the pore radius, nanoparticle radius, mean flow velocity, solution ionic strength, viscosity, temperature, solution dielectric constant, and nanoparticle and collector surface potentials. Based on dominant processes, the pore space is divided into three different regions, namely, bulk, diffusion, and potential regions. Advection-diffusion equations for nanoparticle transport are prescribed for the bulk and diffusion regions, while the interaction between the diffusion and potential regions is included as a boundary condition. This interaction is modeled as a first-order reversible kinetic adsorption. The expressions for the mass transfer rate coefficients between the diffusion and the potential regions are derived in terms of the interaction energy profile. Among other effects, we account for nanoparticle-collector interaction forces on nanoparticle deposition. The resulting equations are solved numerically for a range of values of pore-scale parameters. The nanoparticle concentration profile obtained for the cylindrical pore is averaged over a moving averaging volume within the pore in order to get the 1-D concentration field. The latter is fitted to the 1-D advection-dispersion equation with an equilibrium or kinetic adsorption model to determine the values of the average deposition rate coefficients. In this study, pore-scale simulations are performed for three values of Peclet number, Pe = 0.05, 5, and 50. We find that under unfavorable conditions, the nanoparticle deposition at pore scale is best described by an equilibrium model at low Peclet numbers (Pe = 0.05) and by a kinetic model at high Peclet numbers (Pe = 50). But, at an intermediate Pe (e.g., near Pe = 5), both equilibrium and kinetic models fit the 1-D concentration field. Correlation equations for the pore-averaged nanoparticle deposition rate coefficients under unfavorable conditions are derived by performing a multiple-linear regression analysis between the estimated deposition rate coefficients for a single pore and various pore-scale parameters. The correlation equations, which follow a power law relation with nine pore-scale parameters, are found to be consistent with the column-scale and pore-scale experimental results, and qualitatively agree with the colloid filtration theory. These equations can be incorporated into pore network models to study the effect of pore-scale parameters on nanoparticle deposition at larger length scales such as Darcy scale.

A Crack Perpendicular to the Bimaterial Interface in Finite Solid

The dislocation simulation method is used in this paper to derive the basic equations for a crack perpendicular to the bimaterial interface in a finite solid. The complete solutions to the problem, including the T stress and the stress intensity factors are obtained. The stress field characteristics are investigated in detail. It is found that when the crack is within a weaker material, the stress intensity factor is smaller than that in a homogeneous material and it decreases when the distance between the crack tip and interface decreases. When the crack is within a stiffer material, the stress intensity factor is larger than that in a homogeneous material and it increases when the distance between the crack tip and interface decreases. In both cases, the stress intensity factor will increase when the ratio of the size of a sample to the crack length decreases. A comparison of stress intensity factors between a finite problem and an infinite problem has been given also. The stress distribution ahead of the crack tip, which is near the interface, is shown in details and the T stress effect is considered.

Finite Element Solutions for Plane Strain Mode I Crack with Strain Grading Effect

In this paper, a new phenomenological theory with strain gradient effects is proposed to account for the size dependence of plastic deformation at micro- and submicro-length scales. The theory fits within the framework of general couple stress theory and three rotational degrees of freedom omega(i) are introduced in addition to the conventional three translational degrees of freedom mu(i). omega(i) is called micro-rotation and is the sum of material rotation plus the particles' relative rotation. While the new theory is used to analyze the crack tip field or the indentation problems, the stretch gradient is considered through a new hardening law. The key features of the theory are that the rotation gradient influences the material character through the interaction between the Cauchy stresses and the couple stresses; the term of stretch gradient is represented as an internal variable to increase the tangent modulus. In fact the present new strain gradient theory is the combination of the strain gradient theory proposed by Chen and Wang (Int. J. Plast., in press) and the hardening law given by Chen and Wang (Acta Mater. 48 (2000a) 3997). In this paper we focus on the finite element method to investigate material fracture for an elastic-power law hardening solid. With remotely imposed classical K fields, the full field solutions are obtained numerically. It is found that the size of the strain gradient dominance zone is characterized by the intrinsic material length l(1). Outside the strain gradient dominance zone, the computed stress field tends to be a classical plasticity field and then K field. The singularity of stresses ahead of the crack tip is higher than that of the classical field and tends to the square root singularity, which has important consequences for crack growth in materials by decohesion at the atomic scale. (C) 2002 Elsevier Science Ltd. All rights reserved.

Analysis of instability of a cylindrical soap film of finite dimensions

By means of experiments of instability of a uniform cylindrical soap film, Boys had showed that the bubble molded by the film is unstable when its length is greater than its circumference. Recently that is generally called the Rayleigh Criterion. In this paper, a linear theory in hydrodynamics is applied to analyze the stability of the cylindrical soap film supported by two equal size disks; all conditions of the stationary wave on the end plates of two disks are given. From here we get that the Rayleigh Criterion on the stability of the cylindrical soap film is proved.

Tensionless Contact Of A Finite Beam Resting On Reissner Foundation

A more generalized model of a beam resting on a tensionless Reissner foundation is presented. Compared with the Winkler foundation model, the Reissner foundation model is a much improved one. In the Winkler foundation model, there is no shear stress inside the foundation layer and the foundation is assumed to consist of closely spaced, independent springs. The presence of shear stress inside Reissner foundation makes the springs no longer independent and the foundation to deform as a whole. Mathematically, the governing equation of a beam on Reissner foundation is sixth order differential equation compared with fourth order of Winkler one. Because of this order change of the governing equation, new boundary conditions are needed and related discussion is presented. The presence of the shear stress inside the tensionless Reissner foundation together with the unknown feature of contact area/length makes the problem much more difficult than that of Winkler foundation. In the model presented here, the effects of beam dimension, gap distance, loading asymmetry and foundation shear stress on the contact length are all incorporated and studied. As the beam length increases, the results of a finite beam with zero gap distance converge asymptotically to those obtained by the previous model for an infinitely long beam. (C) 2008 Elsevier Ltd. All rights reserved.

Molecular/Cluster Statistical Thermodynamics Methods To Simulate Quasi-Static Deformations At Finite Temperature

The rapid evolution of nanotechnology appeals for the understanding of global response of nanoscale systems based on atomic interactions, hence necessitates novel, sophisticated, and physically based approaches to bridge the gaps between various length and time scales. In this paper, we propose a group of statistical thermodynamics methods for the simulations of nanoscale systems under quasi-static loading at finite temperature, that is, molecular statistical thermodynamics (MST) method, cluster statistical thermodynamics (CST) method, and the hybrid molecular/cluster statistical thermodynamics (HMCST) method. These methods, by treating atoms as oscillators and particles simultaneously, as well as clusters, comprise different spatial and temporal scales in a unified framework. One appealing feature of these methods is their "seamlessness" or consistency in the same underlying atomistic model in all regions consisting of atoms and clusters, and hence can avoid the ghost force in the simulation. On the other hand, compared with conventional MD simulations, their high computational efficiency appears very attractive, as manifested by the simulations of uniaxial compression and nanoindenation. (C) 2008 Elsevier Ltd. All rights reserved.

The Effects of Backfill Soil Properties on Wave-induced Pore Pressures around a Trenched Pipeline

Offshore pipelines are always trenched into seabed to reduce wave-induced forces and thereby to enhance their stability. The trenches are generally backfilled either by in-site sediments or by depositing selected backfill materials over the pipeline from bottom-dump barge. The actual waves in shallow water zone are always characterized as nonlinear. The proper evaluation of the wave-induced pressures upon pipeline is important for coastal geotechnical engineers. However, most previous investigations of the wave–seabed–pipe interaction problem have been concerned only with a single sediment layer and linear wave loading. In this paper, based on Biot’s consolidation theory, a two-dimensional finite element model is developed to investigate non-linear wave induced pore pressures around trenched pipeline. The influences of the permeability of backfill soil and the geometry profiles of trenches upon soil responses around pipeline are studied respectively.

A mathematical study of finite-amplitude rock-folding

The problem of the finite-amplitude folding of an isolated, linearly viscous layer under compression and imbedded in a medium of lower viscosity is treated theoretically by using a variational method to derive finite difference equations which are solved on a digital computer. The problem depends on a single physical parameter, the ratio of the fold wavelength, L, to the "dominant wavelength" of the infinitesimal-amplitude treatment, L_d. Therefore, the natural range of physical parameters is covered by the computation of three folds, with L/L_d = 0, 1, and 4.6, up to a maximum dip of 90°.

Significant differences in fold shape are found among the three folds; folds with higher L/L_d have sharper crests. Folds with L/L_d = 0 and L/L_d = 1 become fan folds at high amplitude. A description of the shape in terms of a harmonic analysis of inclination as a function of arc length shows this systematic variation with L/L_d and is relatively insensitive to the initial shape of the layer. This method of shape description is proposed as a convenient way of measuring the shape of natural folds.

The infinitesimal-amplitude treatment does not predict fold-shape development satisfactorily beyond a limb-dip of 5°. A proposed extension of the treatment continues the wavelength-selection mechanism of the infinitesimal treatment up to a limb-dip of 15°; after this stage the wavelength-selection mechanism no longer operates and fold shape is mainly determined by L/L_d and limb-dip.

Strain-rates and finite strains in the medium are calculated f or all stages of the L/L_d = 1 and L/L_d = 4.6 folds. At limb-dips greater than 45° the planes of maximum flattening and maximum flattening rat e show the characteristic orientation and fanning of axial-plane cleavage.

An environmentally based growth model that uses finite difference calculus with maximum likelihood method: its application to the brackish water bivalve Corbicula japonica in Lake Abashiri, Japan

We present a growth analysis model that combines large amounts of environmental data with limited amounts of biological data and apply it to Corbicula japonica. The model uses the maximum-likelihood method with the Akaike information criterion, which provides an objective criterion for model selection. An adequate distribution for describing a single cohort is selected from available probability density functions, which are expressed by location and scale parameters. Daily relative increase rates of the location parameter are expressed by a multivariate logistic function with environmental factors for each day and categorical variables indicating animal ages as independent variables. Daily relative increase rates of the scale parameter are expressed by an equation describing the relationship with the daily relative increase rate of the location parameter. Corbicula japonica grows to a modal shell length of 0.7 mm during the first year in Lake Abashiri. Compared with the attain-able maximum size of about 30 mm, the growth of juveniles is extremely slow because their growth is less susceptible to environmental factors until the second winter. The extremely slow growth in Lake Abashiri could be a geographical genetic variation within C. japonica.

Compressive failure of finite size unidirectional composite laminates with a region of fibre waviness

The compressive behaviour of finite unidirectional composites with a region of misaligned reinforcement is investigated via finite element analyses. Models with and without fibre bending stiffness are compared, confirming that compressive strength is accurately predicted without modelling fibre bending stiffness for real composite components which typically have waviness defects of several millimetres wavelength. Various defect parameters are investigated. Results confirm the well-known sensitivity of compressive strength to misalignment angle, and also show that compressive strength falls rapidly with the proportion of laminate width covered by the wavy region. A simple empirical equation is proposed to model the effect of a single patch of waviness in finite specimens. Other parameters such as length and position of the wavy region are found to have a smaller effect on compressive strength. The modelling approach is finally adapted to model distributed waviness and thus determine the compressive strength of composites with realistic waviness defects. © 2011 Elsevier Ltd. All rights reserved.

Finite element modelling of the sismic behaviour of water front structures

Water front structures have suffered significant damage in many of the recent earthquakes. These include gravity type quay walls, vertically composite walls, cantilever retaining walls, anchored bulkheads and similar structures. One of the primary causes for the poor performance of these classes of structures is the liquefaction of the foundation soil and in some instances liquefaction of the backfill soil. The liquefaction of the soil in-front of the quay wall tends to cause large lateral displacements and rotation of the wall. Often such gravity walls are placed on rubble mound deposited onto the sea bed.This paper presents finite element analyses of such a problem in which strength degradation of the foundation soil and the backfill material will be modelled using PZ mark III constitutive model. The performance of the wall in terms of its lateral displacement, vertical settlement and/or the rotation suffered by the wall will be presented. In addition, the contours of the horizontal and vertical effective stresses and the excess pore pressure ratio will be presented at different time instants together with hyrdraulic gradients. Immediately after the earthquake, the hydraulic gradients indicate migration of pore water into the region below the wall, suggesting further softening of the foundation soil below the wall.

On the transition from finite-volume negatively buoyant releases to continuous fountains

An experimental investigation to identify the source conditions that distinguish finite-volume negatively buoyant fluid projectile behaviour from fountain behaviour in quiescent environments of uniform density is described. Finite-volume releases are governed by their source Froude number Fr D and the aspect ratio L/D of the release, where L denotes the length of the column of fluid dispensed vertically from the nozzle of diameter D. We establish the influence of L/D on the peak rise heights of a release formed by dispensing saline solution into fresh water for 0

Lateral response of monopiles using centrifuge testing and finite element analysis

Offshore wind capacity is expected to grow exponentially over the next decade resulting in the production of a considerable amount of renewable energy. Monopiles are currently the most popular type of foundation for supporting offshore wind turbines in shallow to medium depth waters. In this paper, the load-deformation response of a 3.8 m diameter monopile installed in soft clays when subjected to axial and lateral loading is investigated using centrifuge testing and soil pore-fluid coupled three-dimensional finite element analysis. Monopile deformation is principally assessed in terms of its lateral displacements and bending moments. Its behaviour as a short rigid pile is discussed using concepts such as its rotation at mudline and the pile depth at which pivoting occurs. © 2014 Taylor & Francis Group.