A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.Comment: preprint, draft, 2 tables, 47 references, 7 files, Codes that can solve three dimensional linear elastostatic problems using constant boundary elements (of triangular shape) while ignoring body forces are provided as supplementary files; codes are distributed under the MIT License in three versions: i) MATLAB version ii) Fortran 90 version (sequential code) iii) Fortran 90 version (parallel code

Simulations using meshfree methods

In this paper, attempt is made to solve a few problems using the Polynomial Point Collocation Method (PPCM), the Radial Point Collocation Method (RPCM), Smoothed Particle Hydrodynamics (SPH), and the Finite Point Method (FPM). A few observations on the accuracy of these methods are recorded. All the simulations in this paper are three dimensional linear elastostatic simulations, without accounting for body forces.Comment: preprint (draft) + 3 figures, 1 table, 2 appendices, 2 images, 1 MATLAB cod

Performance of three commercial lipases in a model enzyme modified cheese system : a thesis presented in partial fulfilment of the requirements for the degree of Master of Technology in Food Technology at Massey University

The effects of Amano 'R' (from Penicillium roqueforti), Palatase (from Mucor miehei) and kid lipase (from kid goat) activity on hydrolysis of triglycerides in a constant enzyme modified cheese (EMC) base have been investigated. The effects of incubation time, temperature, enzyme concentration, pH, water activity (a w ) and salt-in-moisture content on enzyme activity were studied. Under the same conditions (0.15% enzyme, 30°C, 24 h), Palatase and Amano 'R' showed a greater extent of hydrolysis (total free fatty acids) than Kid lipase. The total free fatty acids (FFAs) released by Palatase, Amano 'R' and Kid lipase were 224, 188 and 20.5 mmol FFA. kg EMC. -1 , respectively. The optimum temperature for hydrolysis by Amano 'R', Palatase and Kid lipase was around 30°C, 55°C and 45°C respectively. Amano 'R' was very heat sensitive, compared to the other two enzymes. Hydrolysis increased with increasing initial pH. The optimum pH's determined for Amano 'R', Palatase and Kid lipase were 7.5, 8.0 and 5.5 respectively. Enzyme activity decreased slightly as water activity decreased and salt-in-moisture content increased, for all enzymes. The incubation time and enzyme concentration showed the expected trend. At all process conditions, a high percentage (about 55%) of the fatty acids released by kid lipase was butyric acid. Both Palatase and Amano 'R' were relatively non selective and released large amounts of all fatty acids. Compared to Palatase, Amano 'R' selectively released a higher percentage of butyric acid (about 15% compared to 10%). Generally, the rate of release of butyric acid was greater at lower incubation temperatures for all enzymes. Also, the percentage of butyric acid release decreased with increasing initial pH for Palatase lipase

Identifying leading indicators of product recalls from online reviews using positive unlabeled learning and domain adaptation

Consumer protection agencies are charged with safeguarding the public from hazardous products, but the thousands of products under their jurisdiction make it challenging to identify and respond to consumer complaints quickly. From the consumer's perspective, online reviews can provide evidence of product defects, but manually sifting through hundreds of reviews is not always feasible. In this paper, we propose a system to mine Amazon.com reviews to identify products that may pose safety or health hazards. Since labeled data for this task are scarce, our approach combines positive unlabeled learning with domain adaptation to train a classifier from consumer complaints submitted to the U.S. Consumer Product Safety Commission. On a validation set of manually annotated Amazon product reviews, we find that our approach results in an absolute F1 score improvement of 8% over the best competing baseline. Furthermore, we apply the classifier to Amazon reviews of known recalled products; the classifier identifies reviews reporting safety hazards prior to the recall date for 45% of the products. This suggests that the system may be able to provide an early warning system to alert consumers to hazardous products before an official recall is announced

Scalability of Genetic Programming and Probabilistic Incremental Program Evolution

This paper discusses scalability of standard genetic programming (GP) and the probabilistic incremental program evolution (PIPE). To investigate the need for both effective mixing and linkage learning, two test problems are considered: ORDER problem, which is rather easy for any recombination-based GP, and TRAP or the deceptive trap problem, which requires the algorithm to learn interactions among subsets of terminals. The scalability results show that both GP and PIPE scale up polynomially with problem size on the simple ORDER problem, but they both scale up exponentially on the deceptive problem. This indicates that while standard recombination is sufficient when no interactions need to be considered, for some problems linkage learning is necessary. These results are in agreement with the lessons learned in the domain of binary-string genetic algorithms (GAs). Furthermore, the paper investigates the effects of introducing utnnecessary and irrelevant primitives on the performance of GP and PIPE.Comment: Submitted to GECCO-200

Chemoselective Formation of Unsymmetrically Substituted Ethers from Catalytic Reductive Coupling of Aldehydes and Ketones with Alcohols in Aqueous Solution

A well-defined cationic Ru–H complex catalyzes reductive etherification of aldehydes and ketones with alcohols. The catalytic method employs environmentally benign water as the solvent and cheaply available molecular hydrogen as the reducing agent to afford unsymmetrical ethers in a highly chemoselective manner

Scope and Mechanistic Analysis for Chemoselective Hydrogenolysis of Carbonyl Compounds Catalyzed by a Cationic Ruthenium Hydride Complex with a Tunable Phenol Ligand

A cationic ruthenium hydride complex, [(C6H6)(PCy3)(CO)RuH]+BF4– (1), with a phenol ligand was found to exhibit high catalytic activity for the hydrogenolysis of carbonyl compounds to yield the corresponding aliphatic products. The catalytic method showed exceptionally high chemoselectivity toward the carbonyl reduction over alkene hydrogenation. Kinetic and spectroscopic studies revealed a strong electronic influence of the phenol ligand on the catalyst activity. The Hammett plot of the hydrogenolysis of 4-methoxyacetophenone displayed two opposite linear slopes for the catalytic system 1/p-X-C6H4OH (ρ = −3.3 for X = OMe, t-Bu, Et, and Me; ρ = +1.5 for X = F, Cl, and CF3). A normal deuterium isotope effect was observed for the hydrogenolysis reaction catalyzed by 1/p-X-C6H4OH with an electron-releasing group (kH/kD = 1.7–2.5; X = OMe, Et), whereas an inverse isotope effect was measured for 1/p-X-C6H4OH with an electron-withdrawing group (kH/kD = 0.6–0.7; X = Cl, CF3). The empirical rate law was determined from the hydrogenolysis of 4-methoxyacetophenone: rate = kobsd[Ru][ketone][H2]−1 for the reaction catalyzed by 1/p-OMe-C6H4OH, and rate = kobsd[Ru][ketone][H2]0 for the reaction catalyzed by 1/p-CF3-C6H4OH. Catalytically relevant dinuclear ruthenium hydride and hydroxo complexes were synthesized, and their structures were established by X-ray crystallography. Two distinct mechanistic pathways are presented for the hydrogenolysis reaction on the basis of these kinetic and spectroscopic data