Walk Methodology Research Articles

Multiscale modeling of randomly interwoven fibers for prediction of KM2 Kevlar yarn strength and damage

Modeling Kevlar yarn response as a function of twist requires creating a model at the filament level that incorporates capturing the mechanical interaction of numerous fibers. The inherent complexity of building a multiscale interwoven fibrous structure manually is prohibitive for such an endeavor; therefore, computer-aided simulations are preferred. In this study, a random walk methodology was employed to generate a fibrous structure along the axis of a yarn. Since the directionality of the fibers is randomly oriented along the axis, the fibers can wind around each other and tangle or terminate on demand. The resultant geometry can represent the tortuous path that yarn filaments experience. Yarn twist can be introduced through imposing a rotation matrix to the geometry or conducting an initial analysis that applies the preload. The analysis method employed in this paper captures the correct prestress of the twisted yarns at zero, three, and ten twists per inch. The analysis then loaded the yarn until filament fracture occurred. The predicted ultimate load was within 5% for all three twists per inch analyzed. The zero twists per inch linear response matched test results to within 5%.

Transition processes through a longitudinal integrated clerkship: a qualitative study of medical students' experiences.

This paper describes the transition processes experienced by Year3 medical students during their longitudinal integrated clerkship (LIC). The authors conceptualise the stages that encompass the transition through a LIC. The purpose of this study was to understand the perspectives of 12 Northern Ontario School of Medicine (NOSM) Year3 medical students about their transition process. Data were collected longitudinally through three conversational interviews with each of these students, occurring before, during and after the clerkship. The authors used a guided walk methodology to explore students' everyday lives and elicit insights about the transition process, prompted by the locations and clinical settings in which the clerkship occurred. Participants identified three interconnected stages in the transition process: (i) shifting from classroom to clinical learning; (ii) dealing with disorientation and restoring balance, and (iii) seeing oneself as a physician. Interview data provided evidence for the adaptive strategies the participants developed in response to these stages. Based on these findings, the transition process during a LIC can be characterised as one of entering the unfamiliar, with few forewarnings about the changes, of experiencing moments of confusion and burnout, and of eventual gains in confidence and competence in the clinical roles of a physician. Recommendations are made regarding future research opportunities to further scholarship on transitions.

On the upscaling of chemical transport in fractured rock

AbstractThe impact of flow heterogeneity on chemical transport from single to multiple fractures is investigated. The emphasis is on the dynamic nature of the specific surface area (SSA) due to heterogeneity of the flow, relative to a purely geometrical definition. The flow‐dependent SSA is interpreted probabilistically, following inert tracer particles along individual fractures. Upscaling to a fracture network is proposed as a time domain random walk based on the statistics of SSA for single fractures. Statistics of SSA are investigated for three correlation structures of transmissivity: multi‐Gaussian and two non‐multi‐Gaussian. The mean of SSA stabilizes after ∼20 fractures at different values depending on whether the cubic or quadratic hydraulic law is assumed. The results are tested against comprehensive DFN simulations based on site‐specific data but also against direct estimates from a wider range of tracer tests. The proposed time domain random walk methodology sets bounds for SSA in a 75% confidence interval as ∼1800 1/m and 27,000 1/m, with a median of 14,000 1/m; these values capture reasonably well both the DFN simulation and tracer test SSA data. Presented results may be particularly relevant when quantifying uncertainty of reactive transport modeling in fractured rock.

Fiberwalk: a random walk approach to fiber representative volume element creation

Attaining accurate representative geometry for a finite element analysis at various scales can be a challenging research task. Added complications arise when the geometry is representing a manufactured or biological composite. In this study, a representative geometry of linear fibrous composites was created at the microscale and is employed to reproduce crystalline microfibril stacking of Kevlar to form a single fibril joined by a non-ordered crystal structure. The structure can have ellipsoidal or rectangular microfibrils stacked in ellipsoidal or rectangular fibrils and may have any desired packing ratio within the 1–100% range. In order to build a fibrous structure along a path, a Random Walk methodology was used. Since the directionality of the fibers is random, but always stepping from one side of the path toward the other, the fibers can wind around each other and tangle or terminate if needed. Another key concept of this method is the addition of a rotation matrix operation for the path of the fibers. This allows the path around the three local coordinates to be in a linear or sinusoidal direction. The resultant geometry produced can represent the tortuous path nanofibrils undergo. Moreover, rotation about the path axis allows for the twisted geometry of ring spun yarn, and metal cable to be reproduced. Inclusion of spherical objects to the path of the fibers has been accommodated to reproduce fiber projection around, or end at, an obstruction in their path. This approach allows representing impurities at the fibril, fiber, or yarn level of composite fabric manufacturing.

High throughput sequencing of the Angiostrongylus cantonensis genome: a parasite spreading worldwide

Angiostrongylus cantonensis is a parasitic nematode of rodents and a leading aetiological agent of eosinophilic meningitis in humans. Definitive diagnosis is difficult, often relying on immunodiagnostic methods which utilize crude antigens. New immunodiagnostic methods based on recombinant proteins are being developed, and ideally these methods would be made available worldwide. Identification of diagnostic targets, as well as studies on the biology of the parasite, are limited by a lack of molecular information on Angiostrongylus spp. available in databases. In this study we present data collected from DNA random high-throughput sequencing together with proteomic analyses and a cDNA walking methodology to identify and obtain the nucleotide or amino acid sequences of unknown immunoreactive proteins. 28 080 putative ORFs were obtained, of which 3371 had homology to other deposited protein sequences. Using the A. cantonensis genomic sequences, 156 putative ORFs, matching peptide sequences obtained from previous proteomic studies, were considered novel, with no homology to existing sequences. Full-length coding sequences of eight antigenic target proteins were obtained. In this study we generated not only the complete nucleotide sequences of the antigenic protein targets but also a large amount of genomic data which may help facilitate future genomic, proteomic, transcriptomic or metabolomic studies on Angiostrongylus.

Single Nucleotide Polymorphisms of Helicobacter pylori dupA that Lead to Premature Stop Codons

The detection of the putative disease-specific Helicobacter pylori marker duodenal ulcer promoting gene A (dupA) is currently based on PCR detection of jhp0917 and jhp0918 that form the gene. However, mutations that lead to premature stop codons that split off the dupA leading to truncated products cannot be evaluated by PCR. We directly sequence the complete dupA of 75 dupA-positive strains of H. pylori isolated from patients with gastritis (n = 26), duodenal ulcer (n = 29), and gastric carcinoma (n = 20), to search for frame-shifting mutations that lead to stop codon. Thirty-four strains had single nucleotide mutations in dupA that lead to premature stop codon creating smaller products than the predicted 1839 bp product and, for this reason, were considered as dupA-negative. Intact dupA was more frequently observed in strains isolated from duodenal ulcer patients (65.5%) than in patients with gastritis only (46.2%) or with gastric carcinoma (50%). In logistic analysis, the presence of the intact dupA independently associated with duodenal ulcer (OR = 5.06; 95% CI = 1.22-20.96, p = .02). We propose the primer walking methodology as a simple technique to sequence the gene. When we considered as dupA-positive only those strains that carry dupA gene without premature stop codons, the gene was associated with duodenal ulcer and, therefore, can be used as a marker for this disease in our population.

Damızlık Değerlerinin Kalman Süzgeci ile Tahmini: Süt Sığırlarından Toplanan Vücut Kondüsyon Puanları İçin Bir Uygulama

Summary The aim of this study was to investigate usefulness of Kalman Filter (KF) Random Walk methodology (KF-RW) for prediction of breeding values in animals. We used body condition score (BCS) from dairy cattle for illustrating use of KF-RW. BCS was measured by Swiss Holstein Breeding Association during May 2004-March 2005 for 7 times approximately at monthly intervals from dairy cows (n=80) stationed at the Chamau research farm of Eidgenossische Technische Hochschule (ETH), Switzerland. Benefits of KF were demonstrated using random walk models via simulations. Breeding values were predicted over days in milk for BCS by KF-RW. Variance components were predicted by Gibbs sampling. Locally weighted scatter plot smoothing (LOWESS) and KF-RW were compared under different longitudinal experimental designs, and results showed that KF-RW gave more reasonable estimates especially for lower smoother span of LOWESS. Estimates of variance components were found more accurate when the number of observations and number of subjects increased and increasing these quantities decreased standard errors. Fifty subjects with 10 observations each, started to give reasonable estimates. Posterior means for variance components were found (with standard errors) 0.03 (0.006) for animal genetic variance 0.04 (0.007) for permanent environmental variance and 0.21 (0.02) for error variance. Since KF gives online estimation of breeding values and does not need to store or invert matrices, this methodology could be useful in animal breeding industry for obtaining online estimation of breeding values over days in milk.

Experimental evidence of the role of compound counting processes in random walk approaches to fractional dynamics

We present dielectric spectroscopy data obtained for gallium-doped Cd(0.99)Mn(0.01)Te:Ga mixed crystals, which exhibit a very special case of the two-power-law relaxation pattern with the high-frequency power-law exponent equal to 1. We explain this behavior, which cannot be fitted by any of the well-known empirical relaxation functions, in a subordinated diffusive framework. We propose a diffusion scenario based on a renormalized clustering of a random number of spatio-temporal steps in the continuous-time random walk. Such a construction substitutes the renewal counting process, which is used in the classical continuous time random walk methodology, with a compound counting one. As a result, we obtain an appropriate relaxation function governing the observed nonstandard pattern, and we show the importance of the compound counting processes in studying fractional dynamics of complex systems.

Ergodic transport through aquifers of non‐Gaussian log conductivity distribution and occurrence of anomalous behavior

Three‐dimensional advective transport of passive solutes through isotropic porous formations of stationary non‐Gaussian log conductivity distributions is investigated by using an approximate semianalytical model, which is compared with accurate numerical simulations. The study is a continuation of our previous works in which formation heterogeneity is modeled using spherical nonoverlapping inclusions and an approximate analytical model was developed. Flow is solved for average uniform velocity, and transport of an ergodic plume is quantified by mass flux (traveltime distribution) at a control plane. The analytical model uses a self‐consistent argument, and it is based on the solution for an isolated inclusion submerged in homogeneous background matrix of effective conductivity. As demonstrated in the past, this analytical model accurately predicted the entire distributions of traveltimes in formations of Gaussian log conductivity distributions, as validated by numerical simulations. The present study (1) extends the results to formations of non‐Gaussian log conductivity structures (the subordination model), (2) extends the approximate analytical model to cubical blocks that tessellate the entire domain, (3) identifies a condition in conductivity distribution, at the tail of low values, that renders transport anomalous with macrodispersivity growing without bounds, and (4) provides links of our work to continuous time random walk (CTRW) methodology, as applied to subsurface transport. It is found that a class of CTRW solutions proposed in the past cannot be based on solution of flow in formations with conductivity distribution of finite integral scale.

Continuous Self-Avoiding Walk with Application to the Description of Polymer Chains

We develop the continuous self-avoiding walk (CSAW) methodology for investigating temperature dependent thermodynamic properties of finite polymer chains without imposing a lattice. This leads to a new concept: the free energy theta temperature, T(theta)(F), at which the free energy is proportional to chain length. Above T(theta)(F), the polymer chain-solvent mixture leads to a single phase, whereas below T(theta)(F) the polymer solvent system has a positive surface tension with a tendency to phase separation to form a globular phase. For finite chains this coil-globule transition lies above the geometric theta temperature at which the distribution describes a Gaussian coil. CSAW provides the basis for a new approach to predict globular properties of real polymers.

A review and numerical assessment of the random walk particle tracking method

We review the basic mathematical concepts of random walk particle tracking (RWPT) and its advantages and limitations. Three different numerical approaches to overcome the local mass conservation problem of the random walk methodology are examined: (i) the interpolation method, (ii) the reflection principle, and (iii) the generalized stochastic differential equations (GSDE). Analytical solutions of the spatial moments for a two-layer system are compared to model predictions using the different techniques and results demonstrate that the interpolation method reproduces correctly average velocity, but fails to reproduce macrodispersion at higher hydraulic conductivity contrasts between the two layers. On the contrary, the reflection principle and the GSDE approach underestimate average velocity, but reproduce macrodispersion better for high contrasts. The different behavior is based on an artificial shift of mass for increasing heterogeneities for the GSDE approach and the reflection principle, whereas the interpolation method suffers from the smoothing of the dispersion tensor. The behavior of these approaches was furthermore analyzed in two-dimensional heterogeneous hydraulic conductivity fields, which are characterized by different random function models. Solute transport was simulated correctly by all three approaches for the reference fields having Gaussian structures or non-Gaussian structures with an isotropic spatial correlation, even for a variance of the natural log of hydraulic conductivity of σ ln K 2 = 4. However, for the non-Gaussian model with a strong anisotropic spatial correlation and a variance of σ ln K 2 = 2 and higher, the interpolation method was the only technique modelling solute transport correctly. Furthermore, we discuss the general applicability of random walk particle tracking in comparison to the standard transport models and conclude that in advection-dominated problems using a high spatial discretization or requiring the performance of many model runs, RWPT represents a good alternative for modelling contaminant transport.

Cloning the human betaretrovirus proviral genome from patients with primary biliary cirrhosis.

Patients with primary biliary cirrhosis (PBC) have both serologic and tissue evidence of infection. A recently identified human betaretrovirus was originally cloned from the biliary epithelium cDNA library of a patient with PBC. By conducting a BLASTN search, the initial partial pol gene fragment was found to have 95% to 97% nucleotide homology with mouse mammary tumor virus (MMTV) and with retrovirus sequences derived from human breast cancer samples. Using an anti-p27(CA) MMTV antibody, viral proteins were detected in the perihepatic lymph nodes but not in liver tissue samples from patients with PBC, suggesting a higher viral burden in lymphoid tissue. Therefore, in the current study, we used lymph node DNA to clone the proviral genome of the human betaretrovirus from two patients with PBC using a polymerase chain reaction (PCR) walking methodology with conserved primers complementary to MMTV. The human betaretrovirus genome contains five potential open reading frames (ORF) for Gag, protease (Pro), polymerase (Pol), envelope (Env), and superantigen (Sag) proteins that are collinear with their counterparts in MMTV. Alignment studies performed with characterized MMTV and human breast cancer betaretrovirus amino acid sequences revealed a 93% to 99% identity with the p27 capsid proteins, a 93% to 97% identity with the betaretrovirus envelope proteins, and a 76% to 85% identity with the more variable superantigen proteins. Phylogenetic analysis of known betaretrovirus superantigen proteins showed that the human and murine sequences did not cluster as two distinct species. In conclusion, human betaretrovirus nucleic acid sequences have been cloned from patients with PBC. They share marked homology with MMTV and human breast cancer-derived retrovirus sequences.

Quadratic diffusion Monte Carlo and pure estimators for atoms

The implementation and reliability of a quadratic diffusion Monte Carlo method for the study of ground-state properties of atoms are discussed. We show in the simple yet nontrivial calculation of the binding energy of the Li atom that the method presented is effectively second-order in the time step. The fulfillment of the expected quadratic behavior relies on some basic requirements of the trial wave function used for importance sampling, in the context of the fixed-node approximation. Expectation values of radial operators are calculated by means of a pure estimation based on the forward walking methodology. It is shown that accurate results without extrapolation errors can be obtained with a pure algorithm, explicitely reported, that can be easily implemented in any previous diffusion Monte Carlo program.