Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

A Hybrid Scheme Based on Finite Element/Volume Methods for Two Immiscible Fluid Flows

We have successfully extended our implicit hybrid finite element/volume (FE/FV) solver to flows involving two immiscible fluids. The solver is based on the segregated pressure correction or projection method on staggered unstructured hybrid meshes. An intermediate velocity field is first obtained by solving the momentum equations with the matrix-free implicit cell-centered FV method. The pressure Poisson equation is solved by the node-based Galerkin FE method for an auxiliary variable. The auxiliary variable is used to update the velocity field and the pressure field. The pressure field is carefully updated by taking into account the velocity divergence field. This updating strategy can be rigorously proven to be able to eliminate the unphysical pressure boundary layer and is crucial for the correct temporal convergence rate. Our current staggered-mesh scheme is distinct from other conventional ones in that we store the velocity components at cell centers and the auxiliary variable at vertices. The fluid interface is captured by solving an advection equation for the volume fraction of one of the fluids. The same matrix-free FV method, as the one used for momentum equations, is used to solve the advection equation. We will focus on the interface sharpening strategy to minimize the smearing of the interface over time. We have developed and implemented a global mass conservation algorithm that enforces the conservation of the mass for each fluid.

Optimization of Organic-Inorganic Inter-phase in Hybrid Systems Based on Waterborne Polyurethanes and Silica Nanostructures

215 p.

Growth of yellowfin tuna, Thunnus albacares, in the Eastern Pacific Ocean based on otolith increments

ENGLISH: The growth of yellowfin tuna in the eastern Pacific is described in terms of several measurements taken from the fish and their otoliths (sagittae). Equations are also developed to predict age from the readily available dimensions of fork length and head length. The data for all of these relationships were obtained from a sample of 196 fish collected during 1977 through 1979 from purse seiners fishing north of the equator and east of 137°W. The fork-length range of the sample was 30-170 cm. The number of increments on a sagitta of each fish was used as a direct estimate of its age in days. The correspondence between increments and days has been validated for yellowfin in the length range of 40-110 cm. Circumstantial evidence indicates that the relationship also applies in the intervals of 0-40 cm and 110-170 cm. This circumstancial evidence was derived from: 1) literature on validated increments during early growth for other species, 2) knowledge that structures assumed to be daily increments on yellowfin otoliths have subsequently been validated in the corresponding zone on bluefin otoliths, and 3) a comparison of the growth curve based on increments to others obtained from length frequency modal analysis. Based on this information the age estimates over the entire size range of sampled fish are believed to be accurate. In addition to the general growth and age-predictive relationships, the major conclusions of the study are that: 1) Sexually dimorphic growth exists in terms of fork length, fish weight and the length of the otolith counting path for the entire data set. Examination of the data for 1977 and 1979 also revealed that the fork-length growth of each sex differed within years. 2) For combined sexes there were significant differences among the fork-length growth curves for yellowfin sampled in different years. 3) Yellowfin caught inshore (within 275 miles of the coast) were heavier than those caught offshore for fork lengths between 30 and 110 cm. The situation was reversed for lengths greater than 110 cm. 4) Back-calculated spawning months were distributed uniformly throughout the year in 1974 and 1977, but in 1975-1976 and 1978 spawning activity was apparently concentrated in the latter half of the year. SPANISH: El crecimiento del atún aleta amarilla en el Pacífico oriental se describe en términos de varias medidas obtenidas de peces y otolitos (sagita). Se formularon también ecuaciones para pronosticar la edad, según las dimensiones fácilmente disponibles de la longitud horquilla y longitud de la cabeza. Los datos de todas estas relaciones fueron obtenidos mediante una muestra de 196 peces recolectados desde 1977hasta 1979, en barcos cerqueros que estaban pescando al norte de la línea ecuatorial y al este de los 137°W. El intervalo de la longitud horquilla de la muestra fue de 30-170 cm. Se empleó el número de incrementos en la sagita de cada pez como un estimado directo de la edad en días. Se ha comprobado la relación entre los incrementos y los días en el intervalo de longitud de 40-110 cm del aleta amarilla. La evidencia circunstancial indica que se aplica también la relación a los intervalos de 0-40 cm y 110-170 cm. Esta evidencia circunstancial se dedujo: 1) de las publicaciones sobre incrementos comprobados de otras especies durante el primer crecimiento, 2) del conocimientoque las estructuras que se supone son incrementos diarios en los otolitos del aleta amarilla han sido comprobadas luego en la parte correspondiente de otolitos del aleta azul y 3) por una comparación de la curva de crecimiento, basada en incrementos relacionados a otras curvas obtenidas según el análisis modal frecuencia-talla. Se cree, basados en esta información, que las estimaciones de la edad sobre toda la amplitud de talla de los peces muestreados, es acertada. Además de la relación del crecimiento general y del pronóstico de la edad, las principales conclusiones de este estudio son: 1) En toda la serie de datos existe el crecimiento sexualmente dimórfico en términos de longitud horquilla, peso del pez y longitud del plano de conteo del otolito. El examen de los datos de 1977 y 1979, revelan también que el crecimiento longitud horquilla de cada sexo es diferente en los años. 2) En los sexos combinados hubo diferencias significativas entre las curvas de crecimiento longitud horquilla del aleta amarilla muestreado en diferentes años. 3) El aleta amarilla capturado cerca a la costa (en las primeras 275 millas) fue más pesado que el capturado en las aguas mar afuera, correspondiente a la longitud horquilla entre 30 y 110 cm. La situación fue inversa para tallas de más de 110 cm. 4) En 1974 y 1977, los meses retrocalculados del desove se distribuyeron uniformemente durante el año, pero en 1975-1976 y 1978, la actividad del desove se concentró aparentemente en el último semestre del año. (PDF contains 62 pages.)

Phage M13Ko7 Detection With Biosensor Based On Imaging Ellipsometry And Afm Microscopic Confirmation

A rapid detection and identification of pathogens is important for minimizing transfer and spread of disease. A label-free and multiplex biosensor based on imaging ellipsometry (BIE) had been developed for the detection of phage M13KO7. The surface of silicon wafer is modified with aldehyde, and proteins can be patterned homogeneously and simultaneously on the surface of silicon wafer in an array format by a microfluidic system. Avidin is immobilized on the surface for biotin-anti-M13 immobilization by means of interaction between avidin and biotin, which will serve as ligand against phage M13KO7. Phages M13KO7 are specifically captured by the ligand when phage M13KO7 solution passes over the surface, resulting in a significant increase of mass surface concentration of the anti-M13 binding phage M13KO7 layer, which could be detected by imaging ellipsometry with a sensitivity of 10(9) pfu/ml. Moreover, atomic force microscopy is also used to confirm the fact that phage M13KO7 has been directly captured by ligands on the surface. It indicates that BIE is competent for direct detection of phage M13KO7 and has potential in the field of virus detection. (C) 2008 Elsevier B.V. All rights reserved.

Detection of hepatitis B virus markers using a biosensor based on imaging ellipsometry

A biosensor based on imaging ellipsometry (BIE) has been developed and validated in 169 patients for detecting five markers of hepatitis B virus (HBV) infection. The methodology has been established to pave the way for clinical diagnosis, including ligand screening, determination of the sensitivity, set-up of cut-off values (CoVs) and comparison with other clinical methods. A matrix assay method was established for ligand screening. The CoVs of HBV markers were derived with the help of receiver operating characteristic curves. Enzyme-linked immunosorbent assay (ELISA) was the reference method. Ligands with high bioactivity were selected and sensitivities of 1 ng/mL and 1 IU/mL for hepatitis B surface antigen (HBsAg) and surface antibody (anti-HBs) were obtained respectively. The CoVs of HBsAg, anti-HBs, hepatitis B e antigen, hepatitis B e antibody and core antibody were as follows: 15%, 18%, 15%, 20% and 15%, respectively, which were the percentages over the values of corresponding ligand controls. BIE can simultaneously detect up to five markers within 1 h with results in acceptable agreement with ELISA, and thus shows a potential for diagnosing hepatitis B with high throughput.

Report on estimating the size of dolphin schools, based on data obtained during a charter cruise of the M/V Gina Anne, October 11 -November 25, 1979

Estimates of dolphin school sizes made by observers and crew members aboard tuna seiners or by observers on ship or aerial surveys are important components of population estimates of dolphins which are involved in the yellowfin tuna fishery in the eastern Pacific. Differences in past estimates made from tuna seiners and research ships and aircraft have been noted by Brazier (1978). To compare various methods of estimating dolphin school sizes a research cruise was undertaken with the following major objectives: 1) compare estimates made by observers aboard a tuna seiner and in the ship's helicopter, from aerial photographs, and from counts made at the backdown channel, 2) compare estimates of observers who are told the count of the school size after making their estimate to the observer who is not aware of the count to determine if observers can learn to estimate more accurately, and 3) obtain movie and still photographs of dolphin schools of known size at various stages of chase, capture and release to be used for observer training. The secondary objectives of the cruise were to: 1) obtain life history specimens and data from any dolphins that were killed incidental to purse seining. These specimens and data were to be analyzed by the U.S. National Marine Fisheries Service ( NMFS ) , 2) record evasion tactics of dolphin schools by observing them from the helicopter while the seiner approached the school, 3) examine alternative methods for estimating the distance and bearing of schools where they were first sighted, 4) collect the Commission's standard cetacean sighting, set log and daily activity data and expendable bathythermograph data. (PDF contains 31 pages.)

Performance analysis of bit error rate for free space optical communication with tip-tilt compensation based on gamma-gamma distribution

In this paper, the gamma-gamma probability distribution is used to model turbulent channels. The bit error rate (BER) performance of free space optical (FSO) communication systems employing on-off keying (OOK) or subcarrier binary phase-shift keying (BPSK) modulation format is derived. A tip-tilt adaptive optics system is also incorporated with a FSO system using the above modulation formats. The tip-tilt compensation can alleviate effects of atmospheric turbulence and thereby improve the BER performance. The improvement is different for different turbulence strengths and modulation formats. In addition, the BER performance of communication systems employing subcarrier BPSK modulation is much better than that of compatible systems employing OOK modulation with or without tip-tilt compensation.