Dependence of folding rates on protein length

Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power law with the chain length N with exponent $\lambda \approx 3.6$ for the Go model, in which all native interactions (i.e., between all side chains and backbone atoms) are uniform. If the interactions between side chains are given by pairwise statistical potentials, which introduce heterogeneity in the contact energies, then the power law fits yield large $\lambda$ values that typically signifies a crossover to an underlying activated process. Accordingly, the dependence of folding time is best described by the stretched exponential \exp(\sqrt{N}). The study also shows that the incorporation of side chains considerably slows down folding by introducing energetic and topological frustration.Comment: 6 pages, 5 eps figure

Aeration Effects on Impact: Drop Test of a Flat Plate

Verbatim reproduction or republication of the papers or articles or part of the articles (e.g., figures or tables) by their authors, after the publication or presentation at the ISOPE meetings and journal, is permitted by the International Society of Offshore and Polar Engineers (ISOPE), provided the full credit is given to the authors, to the publisher, The International Society of Offshore and Polar Engineers (ISOPE), and to the Conference, Symposium or Journal - more specifically not to remove the copyright imprint on page 1 of the paper. The permission does not extend to copying for resale and to re-copyrighting the whole or part of the papers. Posting on your organization's website of the paper(s) you specified is allowed only where only your organization's employees including the students can view free of charge the paper authored or co-authored by your organization's employees, and www.isope.org is provided for the paper(s) in the ISOPE proceedings or journals. Regards, Prof. Jin S Chung Executive Director isope, 495 North Whisman Road, Suite 300 Mountain View, California 94043-5711, USA T 1-650-254-1871; F 1-650-254-2038; [email protected] [email protected], www.isope.org www.deepoceanmining.orgAeration effects on impact have been investigated by dropping a flat plate onto the water surface, in which the water is aerated to various degrees. An experimental study has been carried out in the newly commissioned Ocean Basin at Plymouth University’s COAST Lab. The falling block comprises a rigid impact plate connected to two driver plates and its total mass can be varied between 32 kg and 52 kg. The impact plate is 0.25m long, 0.25 m wide and 0.012 m high. The impact velocity is varied between 4 m/s and 7 m/s. Preliminary results of the impact tests are presented here. Visualised results show that there are significant differences between jet formation after impact of the plate in pure water and in aerated water. There is significant reduction of the maximum pressures from those measured in pure water to those measured in aerated water

Probing the Mechanisms of Fibril Formation Using Lattice Models

Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While these models are, at best, caricatures of peptides, we show that a number of generic features thought to govern fibril assembly are present in the toy model. The monomer, which contains eight beads made from three letters (hydrophobic, polar, and charged), adopts a compact conformation in the native state. The kinetics of fibril assembly occurs in three distinct stages. In each stage there is a cascade of events that transforms the monomers and oligomers to ordered structures. In the first "burst" stage highly mobile oligomers of varying sizes form. The conversion to the aggregation-prone conformation occurs within the oligomers during the second stage. As time progresses, a dominant cluster emerges that contains a majority of the chains. In the final stage, the aggregation-prone conformation particles serve as a template onto which smaller oligomers or monomers can dock and undergo conversion to fibril structures. The overall time for growth in the latter stages is well described by the Lifshitz-Slyazov growth kinetics for crystallization from super-saturated solutions.Comment: 27 pages, 6 figure

Free vibration analysis of laminated composite plates based on FSDT using one-dimensional IRBFN method

This paper presents a new effective radial basis function (RBF) collocation technique for the free vibration analysis of laminated composite plates using the first order shear deformation theory (FSDT). The plates, which can be rectangular or non-rectangular, are simply discretised by means of Cartesian grids. Instead of using conventional differentiated RBF networks, one-dimensional integrated RBF networks (1D-IRBFN) are employed on grid lines to approximate the field variables. A number of examples concerning various thickness-to-span ratios, material properties and boundary conditions are considered. Results obtained are compared with the exact solutions and numerical results by other techniques in the literature to investigate the performance of the proposed method

Evolution of probiotics in aquatic world: Potential effects, the current status in Egypt and recent prospectives

AbstractThe increase in the human population in addition to the massive demand for protein of animal origin forced the authorities to seek for additional sources of feed supplies. Aquaculture is the world worth coming expansion to compensate the shortage in animal protein. Feed in aquaculture plays an important role in the production cycle and exert threshold on both practical and economic aspects. Feed additive sectors are expanding day after day to achieve better growth and health for fish and shrimp and to meet the potential requirements of the culturists. Probiotic proved its successes in human and animal feeding practices and recently gained attention in aquaculture; it has beneficial effects in diseases control and competes with various environmental stressors as well as to promote the growth of the cultured organisms. Probiotics have the privilege to manipulate the non-specific innate immunity among fishes, hence help them into resist many pathogenic agents and are actively used worldwide. The present review is an informative compilation of the probiotics, their mode of action and their useful effects on fishes. The review also highlights the status of probiotics in aquaculture of Egypt, probiotic recent prospective for the possible role of probiotics in fish external and internal environment

A continuum-microscopic method based on IRBFs and control volume scheme for viscoelastic fluid flows

A numerical computation of continuum-microscopic model for visco-elastic flows based on the Integrated Radial Basis Function (IRBF) Control Volume and the Stochastic Simulation Techniques (SST) is reported in this paper. The macroscopic flow equations are closed by a stochastic equation for the extra stress at the microscopic level. The former are discretised by a 1D-IRBF-CV method while the latter is integrated with Euler explicit or Predictor-Corrector schemes. Modelling is very efficient as it is based on Cartesian grid, while the integrated RBF approach enhances both the stability of the procedure and the accuracy of the solution. The proposed method is demonstrated with the solution of the start-up Couette flow of the Hookean and FENE dumbbell model fluids