bluuebunny/crossref_metadata_2025 huggingface dataset:
GROWTH BEHAVIOR OF THE ELECTRODEPOSITED Co-Ni ALLOY NANOWIRES
Authors: GHAHREMANINEZHAD A. , DOLATI A. , KAZEMEINI M.
Published: August 2008

The Co - Ni alloy nanowires were electrodeposited into porous anodic aluminum oxide (AAO) templates. At the first, highly ordered AAO templates were synthesized by two-step anodizing of aluminum to increase pore ordering. Arrays of nanowires with diameter about 30 nm and length about 5000 nm were electrodeposited by alternating current. The composition and structure property of nanowires were investigated by EDX, SEM and TEM techniques. It was found that nanowire composition was related to ions concentration in solution and it was shown that at the optimum potential range of electrodeposition (17-19 V), a change at the potential was shown no strong effect on chemical composition of nanowires. It was observed that nano pores were filled continuously and so nanowires were dense with uniform composition in nanowire length.
MORPHOLOGICAL STUDY OF PULSE CURRENT ELECTRODEPOSITED Zn-Fe ALLOY
Authors: MOHAMMADYANI D. , SOHI M. HEYDARZADEH
Published: August 2008

Zn - Fe alloy electroplated coatings have attracted industrial interest because of their significantly higher corrosion resistance in comparison to pure zinc deposits. In this study pulse currents was applied for electrodeposition of Zn - Fe alloys, using alkaline bath. SEM studies confirmed that pulse electrodeposits are quite dense and smooth. It was also shown that increasing of peak current density (PCD) and duty cycle in pulse electrodeposition coarsen the structure and increase irregularity of the surface. Increasing of the frequency, on the other hand, results in the formation of finer structure.
EFFECT OF SURFACTANT AND SACCHARIN ADDITION ON THE MORPHOLOGY AND WEAR BEHAVIOR OF Ni-Al2O3 NANO-COMPOSITE COATINGS
Authors: ALI AMADEH AHMAD , LARI SEYED MOHAMMAD , MORADI HADI
Published: August 2008

Nano-composite Ni - Al 2 O 3 coatings due to their good wear and corrosion resistance have been widely used in different industries. The agglomeration of nano-particle ceramics in the electrolyte is a serious problem in electrodeposition process that leads to the presence of agglomerated particles in the coating and influences its properties. Using a suitable surfactant can be helpful to control the agglomeration of ceramic particles. In this research nano-composite Ni - Al 2 O 3 coating has been deposited from an alumina containing Watts bath using a square pulse current and Sodium Dodecyl-Sulphate (SDS) as surfactant. It was observed that SDS addition has an important effect on the reduction of particles agglomeration and increases the incorporation of finer particles into the coating. Addition of saccharin to the electrolyte, decreases the grain size and the alumina content in the coating, and also, leads to lower agglomeration and better distribution of ceramic particles. Moreover, the synergistic addition of SDS and saccharin, decreases the grain size, increases the hardness and wear resistance, but has no effect on the crystallographic texture of the coating.
EFFECTS OF CRYSTAL SIZE AND ORIENTATION OF SUBSTRATES ON CELL ADHESION: IMPLICATION FOR MEDICAL IMPLANTS
Authors: FAGHIHI SHAHAB , VALI HOJATOLLAH , TABRIZIAN MARYAM
Published: August 2008

The aim of this study is to investigate the effect of atomic structure of polycrystalline materials on cell-substrate interactions. Samples are prepared from rods and sheets of Ti -6 Al -4 V substrates with predominately two distinct crystallographic orientations as well as nano-structured and annealed titanium fabricated through high-pressure torsion and heat treatment processes. The degree of preosteoblast attachment and rate of growth, which are regulated through the activity and interaction of proteins present in the extracellular matrix, are notably increased on the nano-structured titanium and substrate having predominant [Formula: see text] orientation. The improved cell activity is attributed to the nano-structured feature of these substrates consisting of ultra-fine crystals (< 50 nm) and specific atomic order of [Formula: see text] substrate which provide higher degree of surface wettability. These findings demonstrate the advantages of nano-structured titanium over the conventional and coated titanium implants, as both mechanical properties and cellular response are improved. Furthermore, crystal orientation of the substrates can influence cell responses and, therefore, substrate engineering can be used to improve and control cell-substrate interactions.
MECHANOCHEMICAL SYNTHESIS AND CHARACTERIZATION OF NANOSTRUCTURE FORSTERITE BIOCERAMICS
Authors: FATHI M. H. , KHARAZIHA M.
Published: August 2008

Recent investigations suggest that forsterite ceramics possess good biocompatibility and mechanical properties and might be suitable for potential application like bone implant material. In this study, nanocrystalline forsterite ( Mg2SiO4) powder was prepared by mechanochemical method and subsequent heat treatment and the effect of fluorine ion as catalyst was studied. Mechanochemical process and heat treatment were done on the MgCO3, SiO2and ( NH4)2SiF6powders. The synthesized powders were characterized by X-ray diffraction (XRD), thermogravimetric (TG) analyses and scanning electron microscopy (SEM). The synthesized nano-powder had particle size smaller than 100 nm. The crystallite size of powders after 5 hours mechanical activation was 18 nm. Mechanical activation in the presence of fluorine ion affects the mechanism of forsterite formation and increase the rate of decomposition of MgO and fabrication of forsterite.
FABRICATION OF A NOVEL ADSORBENT FOR MAGNETICALLY REMOVAL OF CR, P AND F IONS BY USING OF NANOMAGNETITE PARTICLES INCORPORATED INTO IRON OXIDE HYDROXIDE MATERIALS
Authors: ESKANDARPOUR A. , TANAHASHI M. , BANDO Y. , IWAI K. , OKIDO M. , ASAI S.
Published: August 2008

A new chemical adsorbent for fluoride, phosphate and chromium removals for use in a high magnetic filtration process was produced by applying a novel nanomagnetite aggregation process through the generating procedure of an iron oxide hydroxide. The experimental work to produce the new adsorbent can be divided into two sequential steps: (1) the formation of nanomagnetite particles by means of a chemical precipitation and (2) embedding the nanomagnetite particles, in a solute state, into an iron oxyhydroxide crystal aggregates, before crystallization, to form the new adsorbent. The experimental results obtained from VSM, zeta potential, adsorption trials and SEM pictures obviously reveal a great alteration in the main properties of the new adsorbent comparing to the base iron component material. The new adsorbent not only has a much higher ions adsorption capacity but also can effectively comes to work with a magnetically assisted water treating system due to its enhanced magnetic susceptibility.
EFFECTS OF PROCESS CONTROL AGENTS ON THE SYNTHESIS OF NANO-CRYSTALLINE BARIUM HEXAFERRITE
Authors: JAHANGIR S. , ATAIE A. , NIKKHAH-MOSHAEE R.
Published: August 2008

Nano size particles of barium hexaferrite were produced by conventional mixed oxide ceramic method from BaCO 3 and α Fe 2 O 3 as starting materials with a Fe / Ba molar ratio of 11. The mixture of precursors was intensively milled by high energy ball mill and the The influence of various process control agents (PCA) on the process has been investigated. Analysis of the XRD patterns indicates that PCA can strongly alter the morphology and phase composition of ball milled powder particles. In all milled samples, BaCO 3 completely decomposed and slight displacement of reflections of hematite phase due to the dissolving of various ions like Ba or C in its lattice is observed. Nano size particles exhibiting angular shape together with some amorphous structure were observed in the sample processed in the presence of NaCl . Barium hexaferrite magnetic phase was partially formed in sample milled in the presence of stearic acid.
OPTIMIZATION OF THE MOLARITY OF NaOH AS PRECIPITATING AGENT FOR THE SYNTHESIS OF Ni FERRITE NANOCRYSTALLINE POWDERS BY COPRECIPITATION METHOD
Authors: DEHGHAN R. , EBRAHIMI S. A. SEYYED , BADIEI A.
Published: August 2008

In this study, the effects of the molarity of the precipitating agent on the synthesis of nanostructured NiFe 2 O 4 powders by coprecipitation, followed by calcination were investigated and its optimum amount was also determined. Ni -ferrite powder was synthesized for the first time by dissolving Fe and Ni chlorides and ammonium ferrous sulfate in deionized water with different molar proportions. While stirring, the precipitating agent of NaOH was added to the solution with different molarities and after 1 hour of aging, the resultant precipitate was washed with deionized water and acetone.

It was concluded that single phase nickel ferrite nanocrystalline powders can be prepared by use of 2.2M NaOH , with crystallite size of 30-50 nm.
INFLUENCE OF pH ON PHYSICAL PROPERTIES OF NICKEL-ZINC NANOCRYSTALLINE POWDERS SYNTHESIZED BY A SOL-GEL AUTO-COMBUSTION METHOD
Authors: BARATI M. R. , EBRAHIMI S. A. SEYYED , BADIEI A.
Published: August 2008

In this research a sol-gel auto-combustion route has been proposed to synthesize nickel-zinc ferrite nanocrystalline powder, using metal nitrates, citric acid as fuel and ammonia as pH adjusting agent. The influence of pH value of the solution on phase evolution, crystallite size and morphology of as-burnt powders were investigated by XRD, SEM and TEM techniques. The results revealed that with pH=7 the single phase nickel-zinc ferrite nanocrystalline powders with crystallite size of about 27nm were formed directly after auto combustion process.
AN INVESTIGATION OF DISPERSION AND STABILITY OF CARBON BLACK NANO PARTICLES IN WATER VIA UV-VISIBLE SPECTROSCOPY
Authors: SHARIF SH. M. , KHATIBI E. , SARPOOLAKI H. , FARD F. GOLESTANI
Published: August 2008

Study of the quality of carbon black dispersion by using UV-Visible Spectroscopy was carried out. Carbon materials have a main absorption around 200 nm (UV region) due to π→π* excitation. Based on UV absorption of carbon black and the parameter affects the absorption, UV Visible spectroscopy was used to study CB dispersion. Result showed that Triton X-100 was proper kinds of dispersant which resulted in higher UV absorption compared to other used dispersants. Also proper weight ratio of Triton X-100 to initial carbon solid was calculated of 50 wt% which no significant change was observed for sample containing higher amount of dispersant. Finally AFM images and PSA results asserted the results obtained from UV-Visible Spectroscopy.
CHEMICAL SYNTHESIS OF NANO-TITANIUM DIBORIDE POWDERS BY BOROTHERMIC REDUCTION
Authors: FARD H. SINAEI POUR , BAHARVANDI H. R. , ABDIZADEH H. , SHAHBAHRAMI B.
Published: August 2008

Titanium diboride ( TiB 2) is one of the candidate materials for high temperature structural applications and also for control rod elements in high temperature nuclear reactors. In this paper the nano-sized titanium diboride powders were synthesized through a borothermic reduction by using TTIP and B 4 C as titanium and boron sources. Three different concentration of TTIP solutions were prepared: 0.033, 0.050 and 0.10 M. After heat treating of products between 900 to 1200°C, the scanning electron microscopy (SEM) images and X-ray diffraction patterns of powder indicated that by using the 0.10 M TTIP, the only product was TiB 2; otherwise the product was TiB 2- B 4 C composite.
GROWTH OF TiO2 NANOPARTICLES BY PULSED LASER ABLATION (PLA) IN LIQUID MEDIA AND STUDY OF PHOTOCATALYTIC PROPERTIES
Authors: SHADMEHR S. , MAHDAVI S. M. , TAGHAVINIA N. , AZARIAN A.
Published: August 2008

We synthesized TiO 2 nanoparticles by pulsed laser ablation of titanium target immersed in an aqueous solution of surfactant sodium dodecyl sulfate (SDS) or deionized water. The surfactant concentration dependence on size of TiO 2 nanoparticles was investigated. The maximum amount of nanoparticles (with mean size of 40 nm in diameter) was obtained in an aqueous solution of 0.001 M SDS. We have also studied the effect of laser wavelength on growth of TiO 2 nanoparticles. UV/visible spectroscopy and Scanning Electron Microscopy observations were employed for characterization of optical properties and particle sizes respectively. As TiO 2 is a famous photocatalyst, we have also done photocatalytic test by Methyl Orange under UV irradiation for prepared samples.
EFFECTS OF CALCINATIONS TEMPERATURE ON THE STRUCTURE OF CuO-ZrO2 NANOPARTICLES
Authors: VAHIDSHAD Y. , ABDIZADEH H. , BAHARVANDI H. R. , BASERI M. AKBARI
Published: August 2008

Nano sized copper oxide-zirconia particles were prepared by using a sol-gel technique. The phase change with the calcinations temperature was also investigated for the sample containing 30 wt% copper. It was found that the calcinations temperature strongly influenced the interaction between the active species and support and hence the structure and catalytic performance. Low calcinations temperature yielded poorly crystallized catalysts and favored the formation of a Cu ( OH )2 and Zr ( OH )4 like structure. The results show that cubic ZrO 2 and copper oxide were present below calcinations at 400°C, and cubic ZrO 2 with some amount of monoclinic ZrO 2 and tetragonal ZrO 2, as well as copper oxide, formed after calcinations at 500°C. However, below heating at 500°C, amorphous compounds were obtained; suggesting that 500°C could be a phase transition point. The incorporation of copper in the ZrO 2 lattice resulted in a loss of order in the ZrO 2 structure when calcined at 500°C, with a further increase in the calcinations temperature leading to the phase change. In this work, the latest results on nano crystalline CuO - ZrO 2 as the catalyst for hydrogen synthesis from methanol is reported. The effect of calcinations temperature on the nanoparticle structure of catalyst is focused.
EFFECT OF AGING AND CALCINATION ON MORPHOLOGY AND PROPERTIES OF SYNTHESIZED NANOCRYSTALLINE TiO2
Authors: NAMIN H. ESLAMI , HASHEMIPOUR H. , RANJBAR M.
Published: August 2008

Titanium dioxide nanoparticles were prepared by precipitation of aqueous TiCl 4 solution with ammonium hydroxide as precipitation agent. Freshly prepared Titania gel is allowed to crystallize under refluxing and stirring condition for 6 h over 90°C and oven dried over night in temperature above 100 C. X-ray diffraction studies on oven dried powder indicate formation of anatase phase TiO 2 with average crystalline size of 4.5 nm. Powders with variable amount of anatase and rutile phase were prepared by calcination of pure anatase in the temperature range 400-1000 c for 4 h. the XRD patterns show that phase transition from anatase to rutile occur in calcination above 600°C. The morphology and microstructure characteristics were obtained by XRD, TEM. and TGA.
OPTIMIZATION OF COATING PROCESS OF HEMATITE NANO PARTICLES ON MICA FLAKES BY RESPONSE SURFACE METHODOLOGY
Authors: TOHIDIFAR M. R. , TAHERI-NASSAJ E. , ALIZADEH P.
Published: August 2008

The present paper attempts as how the pigments comprising of nano-sized hematite particles deposited on mica surfaces in optimum conditions offer an excellent pearlescent properties. To record the influencing parameters on the synthesis process, response surface methodology (RSM) technique was used where temperature of reaction, synthesis time and concentration of urea were selected as variable parameters. Taking into account colorimetric parameters, the whole process was then analyzed by "Design Expert" software that finally gave following optimum factors: reaction temperature=82.02°C, synthesis time=11.98 h, urea concentration=37.5 g/l. Once the above optimum parameters selected, seemingly, the spherical hematite particles of about 60 nm in diameter are deposited uniformly on mica surfaces.
FABRICATION OF IRON-ALUMINA NANOCOMPOSITE POWDER BY HIGH ENERGY BALL MILLING OF HEMATITE-ALUMINUM POWDER MIXTURE
Authors: KHODAEI M. , KARIMZADEH F. , ENAYATI M. H.
Published: August 2008

In this study, hematite ( Fe2O3) and aluminum ( Al ) powder mixtures were mechanically alloyed in a high-energy shaker ball mill to synthesize the iron-alumina ( Fe - Al2O3) nanocomposite powder. The structural changes and phase developments occurring during mechanochemical process were studied by X-ray diffractometery (XRD) and scanning electron microscopy (SEM). The results showed that mechanochemical reaction of Fe2O3and Al completed after 3 hours of milling time in a nanocrystalline Fe and Al2O3embedded form and further milling produced a Fe - Al2O3nanocomposite powder. Kinetics consideration according to the calculated adiabatic temperature demonstrated the sudden displacement reaction during mechanical alloying that accord well with XRD results. Also, particle size decrease as well as crystallite size with increasing the milling time.
FABRICATION OF ALUMINA/ZIRCONIA (YSZ) NANOCOMPOSITES BY GELCASTING PROCESS
Authors: SAADAT SOMAYE , MALEKSAEEDI SAEED , PAYDAR MOHAMMAD HOSSEIN , AHMADI HAFEZ
Published: August 2008

Gelcasting process as a promising method for fabrication of reliable ceramics has been utilized to develop alumina-zirconia nanocomposites from nanosized powders. Sedimentation and viscosity measurement were performed to find the accurate dispersing condition for production of alumina-zirconia nanocomposite slurry with high solid loading and low viscosity. The gelcasting was accomplished by in situ polymerization of an acrylamide base monomer. The effects of solid loading, viscosity and deairing were also studied. Finally, crack and flaw free samples with relative densities of 99%, were achieved from the optimal slurry with 35vol. % solid loading, by performing sintering at 1600°C for 2 hours. SEM micrographs showed dense microstructure with fine and homogenous dispersion of zirconia phase in the alumina matrix.
MECHANICAL AND THERMAL PROPERTIES OF MONTMORILLONITE-EPOXY NANOCOMPOSITE
Authors: MAROUF B. T. , BAGHERI R. , PEARSON R. A.
Published: August 2008

In this investigation, the mechanical and thermal properties of the montmorillonite-epoxy nanocomposites were studied. The epoxy compounds were prepared by in situ polymerization and the intercalation dispersion were obtained as evidenced using X-ray diffraction (XRD) and transmission electron microscopy (TEM). The results reveal remarkable stiffening effect and slight toughening effect of the MMT in the epoxy resin and an insight about the crack tip and notch tip toughening mechanism. According to the DMA, the glass transition temperature increases as increasing the MMT content.
THE EFFECT OF ALUMINUM ELECTROPOLISHING ON NANO-PORES ARRANGEMENT IN ANODIC ALUMINA MEMBRANES
Authors: RAHIMI M. H. , TABAIAN S. H. , MARASHI S. P. HOVEYDA , AMIRI M. , DALALY M. M. , SARAMAD SHAHYAR , RAMAZANI AHMAD , ZOLFAGHARI ALIREZA
Published: August 2008

Surface conditions of aluminum can influence the final arrangement of nano-pores in fabrication of ordered nanoporous anodic alumina membranes (AAMs). This study is mainly focused on the different applied voltages of aluminum electropolishing by keeping all the other parameters constant. After heat treatment (stress relieving and annealing at 500°C) of pure aluminum sheets, the samples were electropolished at different voltages (10-60V) to obtain desirable surface smoothness, while the temperature of the container was kept constant. The current-time curves were recorded during electropolishing process. The surface roughness obtained in each applied voltage was examined using optical microscope and atomic force microscope (AFM). The process was followed by two-step anodization in order to reach ordered nano-pores. Finally, the influence of surface roughness on regularity of nano-pores was observed using scanning electron microscope (SEM). The SEM images were analyzed to investigate the morphology and the degree of self ordering of pores of the samples by using a new designed analytical method aiming MATLAB and fast Fourier transform (FFT) technique. It was concluded that the electropolishing voltage and the resulted surface roughness and also formed defects can competitively affect the arrangement of membrane's nano-pores. A desired smoothness obtained from electropolishing voltage of 30V. Also 40V provided the best order with respect to the other voltages.
ZnO NANORODS GROWN BY CARBOTHERMAL EVAPORATION
Authors: JANFESHAN BITA , BAHREVAR MOHAMMADALI , AHMADI KAMRAN
Published: August 2008

ZnO nanorods and bamboo-like structures were fabricated by carbothermal evaporation in Ar gas and air atmosphere on Au -coated silicon wafers. Deposition in air atmosphere led to the fabrication of nanostructured ZnO . Investigation of substrate distance from the source material revealed that thinner nanorods are grown at shorter distances.
LIQUID PHASE SINTERING OF SUB MICRON WC COMPOSITES CONTAINING NEW BINDERS BASED ON BORON DOPED ALUMINIDES
Authors: AHMADIAN M. , WEXLER D. , CHANDRA T. , CALKA A.
Published: August 2008

Densification behavior of sub micron tungsten carbide composites based on boron doped Fe 60 Al 40 and Ni 3 Al binders were investigated. Soft cobalt binder phase in WC hard metals was replaced by harder and tougher Fe 60 Al 40 and Ni 3 Al intermetallics with boron level up to 0.1wt%. Intermetallic binders were prepared in ultrafine form under controlled atmosphere using ring grinding, blended with sub micron WC powder and then uniaxilly hot pressed under 20 MPa pressure in argon atmosphere for 4 minutes duration at temperatures of 1450 °C, 1500 °C and 1550 °C. It was found that the density of composites increased significantly and WC grain size increased slightly with increase in sintering temperature. The composites exhibited highest density (about 99.5 %TD) and minimal grain growth in WC at sintering temperature of 1500 °C. The presence of boron was found to facilitate densification during liquid phase sintering and boron also resulted in achieving uniform microstructure with continuous binder phase, nearly full density and high faceted features in the structure.
ULTRAFINE PRIMARY SILICON PARTICLES IN PHOSPHORUS-MODIFIED HYPEREUTECTIC AL-SI ALLOY POWDERS PRODUCED BY SAMD METHOD
Authors: DELSHAD-KHATIBI P. , AKHLAGHI F.
Published: August 2008

In the present study, alloy powder batches of Al-20Si (wt. %) were generated by SAMD technique using NaCl as the solid media. The method consists of introducing and mixing a specified amount of NaCl particles (mean diameter 254 μm) in aluminum melt at the temperature of 710°C. Melt disintegration occurs in 5 min by kinetic energy transfer from a rotating impeller (1400 rpm) to the metal via the solid atomizing medium ( NaCl particles). The resulting mixture of aluminum droplets and NaCl particles are subsequently quenched in water to dissolve NaCl and solidify Al droplets to produce powder particles. In order to investigate the effect of phosphorus modification on the size and morphology of the primary Si particles, the SAMD technique was also performed to produce Al-20Si -0.015P powder particles. The resultant powders were screened through 6 different sized sieves ranging from 38 to 500 μm and different powder fractions were cold mounted, polished and studied by optical microscopy.

It was concluded that for both un-modified and modified alloys, there was a decrease in the size of primary Si particles corresponding to a decrease in the powder particle size. However, the same sized phosphorus modified powders exhibited considerably finer primary Si particles in which the average size of these ultrafine Si particles was about 1.1 μm for the smallest sieved particles.
PROTEIN FOLDING AS A PHYSICAL STOCHASTIC PROCESS
Authors: HUANG KERSON
Published: August 2008

We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as hydrogen bonding, which can be taken into account by imposing conditions on SAW. The resulting model is termed CSAW (conditioned self-avoiding walk). Conceptually, the mathematical basis is a generalized Langevin equation. In practice, the model is implemented on a computer by combining SAW and Monte Carlo. To illustrate the flexibility and capabilities of the model, we consider a number of examples, including folding pathways, elastic properties, helix formation, and collective modes.
OPTIMAL METHODS FOR RE-ORDERING DATA MATRICES IN SYSTEMS BIOLOGY AND DRUG DISCOVERY APPLICATIONS
Authors: DIMAGGIO PETER A. , MCALLISTER SCOTT R. , FLOUDAS CHRISTODOULOS A. , FENG XIAO-JIANG , RABINOWITZ JOSHUA D. , RABITZ HERSCHEL A.
Published: August 2008

The analysis of large-scale data sets via clustering techniques is utilized in a number of applications. Many of the methods developed employ local search or heuristic strategies for identifying the "best" arrangement of features according to some metric. In this article, we present rigorous clustering methods based on the optimal re-ordering of data matrices. Distinct mixed-integer linear programming (MILP) models are utilized for the clustering of (a) dense data matrices, such as gene expression data, and (b) sparse data matrices, which are commonly encountered in the field of drug discovery. Both methods can be used in an iterative framework to bicluster data and assist in the synthesis of drug compounds, respectively. We demonstrate the capability of the proposed optimal re-ordering methods on several data sets from both systems biology and molecular discovery studies and compare our results to other clustering techniques when applicable.
THE SOLUTION OF THE DISTANCE GEOMETRY PROBLEM IN PROTEIN MODELING VIA GEOMETRIC BUILDUP
Authors: WU DI , WU ZHIJUN , YUAN YAXIANG
Published: August 2008

A well-known problem in protein modeling is the determination of the structure of a protein with a given set of inter-atomic or inter-residue distances obtained from either physical experiments or theoretical estimates. A general form of the problem is known as the distance geometry problem in mathematics, the graph embedding problem in computer science, and the multidimensional scaling problem in statistics. The problem has applications in many other scientific and engineering fields as well such as sensor network localization, image recognition, and protein classification. We describe the formulations and complexities of the problem in its various forms, and introduce a geometric buildup approach to the problem. Central to this approach is the idea that the coordinates of the atoms in a protein can be determined one atom at a time, with the distances from the determined atoms to the undetermined ones. It can determine a structure more efficiently than other conventional approaches, yet without requiring more distance constraints than necessary.
THE DIFFERENTIAL GEOMETRY OF PROTEINS AND ITS APPLICATIONS TO STRUCTURE DETERMINATION
Authors: GORIELY ALAIN , HAUSRATH ANDREW , NEUKIRCH SÉBASTIEN
Published: August 2008

Understanding the three-dimensional structure of proteins is critical to understand their function. While great progress is being made in understanding the structures of soluble proteins, large classes of proteins such as membrane proteins, large macromolecular assemblies, and partially organized or heterogeneous structures are being comparatively neglected. Part of the difficulty is that the coordinate models we use to represent protein structure are discrete and static, whereas the molecules themselves are flexible and dynamic. In this article, we review methods to develop a continuous description of proteins more general than the traditional coordinate models and which can describe smooth changes in form. This description can be shown to be strictly equivalent to the traditional atomic coordinate description.
A NEW NEUROSURGICAL TOOL INCORPORATING DIFFERENTIAL GEOMETRY AND CELLULAR AUTOMATA TECHNIQUES
Authors: OSHMYANSKY ALEXANDER R. , MAINI PHILIP K.
Published: August 2008

Using optical coherence imaging, it is possible to visualize seizure progression intraoperatively. However, it is difficult to pinpoint an exact epileptic focus. This is crucial in attempts to minimize the amount of resection necessary during surgical therapeutic interventions for epilepsy and is typically done approximately from visual inspection of optical coherence imaging stills. In this paper, we create an algorithm with the potential to pinpoint the source of a seizure from an optical coherence imaging still. To accomplish this, a grid is overlaid on optical coherence imaging stills. This then serves as a grid for a two-dimensional cellular automation. Each cell is associated with a Riemannian curvature tensor representing the curvature of the brain's surface in all directions for a cell. Cells which overlay portions of the image which show neurons that are firing are considered "depolarized".
MODELING THE GROWTH AND INVASION OF GLIOMAS, FROM SIMPLE TO COMPLEX: THE GOLDIE LOCKS PARADIGM
Authors: ROCKNE RUSSELL , ALVORD ELLSWORTH C. , REED P. J. , SWANSON KRISTIN R.
Published: August 2008

As with all mathematical modeling, the scope of the question to be explored determines the scope of the most appropriate model. The case is no different for the modeling of primary brain tumors (gliomas), ranging from too simple, not accounting for the major feature of gliomas (extensive invasion), to too complicated, with too many variables and no easy way to translate from culture media in vitro to brain tissue in vivo. We settle on a "just right" approach which utilizes currently available magnetic resonance imaging (MRI) to estimate two defining characteristics, net rates of proliferation (ρ) and diffusion (D). Most importantly, these parameters are predictive of clinical behavior, and can be tailored to individual patients in vivo and in real time. These two rates combine to generate a linear radial growth pattern of the MRI visible portion of each glioma. Further, we introduce a novel method for the calculation of glioma invasion through grey and white matter.
GEOMETRY, ACTIVITY-DEPENDENT MECHANISMS, MEMBRANE KINETICS AND CHANNEL DENSITY DISTRIBUTION INTERPLAY IN SINGLE NEURON PLASTICITY: A COMPUTATIONAL STUDY
Authors: CATALDO ENRICO , BRUNELLI MARCELLO , AV-RON EVYATAR , CAI YIDAO , BAXTER DOUGLAS A.
Published: August 2008

Conduction of action potentials throughout the complex morphology of neurons may be modulated in an activity-dependent manner. Among modulatory mechanisms, afterhyperpolarization (AHP) plays an important role. To investigate how the AHP modulatory capabilities on transmission were dependent on the axonal geometry as well as on membrane properties such as channel kinetics, channel density distribution and membrane noise, multi-compartment computational neural models were built, using the neurosimulator SNNAP. Two kinetic schema for the sodium and potassium channels were compared. The simulations suggest that channel kinetics profoundly influence the AHP-dependent modulation of action potential conduction through points of impedance mismatch in the highly branched neurites of neurons.
MODELS OF ALLEE EFFECTS AND THEIR IMPLICATIONS FOR POPULATION AND COMMUNITY DYNAMICS
Authors: BEREC LUDĚK
Published: August 2008

Allee effects are broadly defined as a decline in individual fitness at low population sizes or densities. Although the roots of the concept go back at least to 1920's, until recently, Allee effects eked out on the periphery of ecological theory, in the shade of the prominently discussed negative density dependence. The situation has changed dramatically in the last ten years or so, and we can find an ever increasing number of studies considering Allee effects from an ever increasing range of disciplines. Mathematical models have always been an important tool by which to assess impacts of Allee effects for population and community dynamics. Actually, much of what we know about Allee effects comes from mathematical models. Up to now, Allee effects have been examined in the context of most existing model structures, and significantly altered our picture of population and community dynamics based on assuming negative density dependence only.
THE DECOUPLING AND SOLUTION OF LOGISTIC AND CLASSICAL TWO-SPECIES LOTKA-VOLTERRA DYNAMICS WITH VARIABLE PRODUCTION RATES
Authors: PEARCE CHARLES E. M. , LEIPNIK ROY B.
Published: August 2008

Central to the dynamics of population biology are various versions of the Lotka-Volterra equations. Particular cases may be used to model competitive, commensal, predatory and other behaviour. Similar equations describe macro-economic interactions, epidemics and other processes of mass action. Refinements of many versions of these equations have been exhibited in the BIOMAT meetings to describe new biological features. The solutions to such equations may display a variety of forms. Broadly speaking, quite a lot of qualitative information may often be obtained about the solutions. In many cases it is convenient to eliminate time from the equations, so obtaining equations for the joint values of population sizes. By contrast, determining explicit expressions for the evolution with time of the component population sizes frequently appears to be infeasible, although numerical procedures may be available.
ALLEE EFFECT, EMIGRATION AND IMMIGRATION IN A CLASS OF PREDATOR-PREY MODELS
Authors: GONZÁLEZ-OLIVARES EDUARDO , MENA-LORCA JAIME , MENESES-ALCAY HÉCTOR , GONZÁLEZ-YAÑEZ BETSABÉ , FLORES JOSÉ D.
Published: August 2008

In this work we analyze a predator-prey model proposed by A. Kent et al. in Ecol. Model.162, 233 (2003), in which two aspect of the model are considered: an effect of emigration or immigration on prey population to constant rate and a prey threshold level for predators. We prove that the system when the immigration effect is introduced in the model has a dynamics that is similar to the Rosenzweig-MacArthur model. Also, when emigration is considered in the model, we show that the behavior of the system is strongly dependent on this phenomenon, this due to the fact that trajectories are highly sensitive to the initial conditions, in similar way as when Allee effect is assumed on prey. Furthermore, we determine constraints in the parameters space for which two stable attractor exist, indicating that the extinction of both population is possible in addition with the coexistence of oscillating of populations size in a unique stable limit cycle. We also show that the consideration of a threshold level of prey population for the predator is not essential in the dynamics of the model.
EPIDEMIC PREDICTIONS AND PREDICTABILITY IN COMPLEX ENVIRONMENTS
Authors: COLIZZA VITTORIA , BARRAT ALAIN , BARTHÉLEMY MARC , VESPIGNANI ALESSANDRO
Published: August 2008

The spread of epidemics is inevitably entangled with human behavior, social contacts, and population flows among different geographical regions. The collection and analysis of datasets which trace the activities and interactions of individuals, social patterns, transportation infrastructures and travel fluxes, have unveiled the presence of connectivity patterns characterized by complex features encoded in large-scale heterogeneities and unbounded statistical fluctuations. These features dramatically affect the behavior of dynamical processes occurring on networks, and are responsible for the observed statistical properties of the processes' dynamics and evolution patterns. Here we will present a large-scale stochastic computational approach for the study of the global spread of emergent infectious diseases which explicitly incorporates real world transportation networks and census data.
MANAGEMENT OF COMPLEX SYSTEMS: MODELING THE BIOLOGICAL PEST CONTROL
Authors: RAFIKOV MARAT , BALTHAZAR JOSÉ MANOEL , VON BREMEN HUBERTUS F.
Published: August 2008

The aim of this paper is to study the cropping system as complex one, applying methods from theory of dynamic systems and from the control theory to the mathematical modeling of the biological pest control. The complex system can be described by different mathematical models. Based on three models of the pest control, the various scenarios have been simulated in order to obtain the pest control strategy only through natural enemies' introduction.
GRASSHOPPER DENSITY POPULATION CLASSIFICATION WITH NEURAL NETWORKS
Authors: HERNÁNDEZ ISAIAS CHAIREZ , REYES J. NATIVIDAD GURROLA , GUTIERREZ CIPRIANO GARCIA , CHAIREZ FRANCISCO ECHAVARRIA
Published: August 2008

Satellite images of the grassland area in Durango México were obtained of altitude, slope, average annual temperature, annual precipitation, type of vegetation, type of soil, normal vegetation index, percentage of herbaceous and percentage of bares soil, in order to relate them with grasshopper density population (GDP) surveyed in 35 sampling sites from June to November in 2003 in the study area. A stepwise regression analysis was performed with the most abundant grasshopper species Phoetaliotes nebrascensis (Thomas), Melanoplus lakinus (Scudder) and Boopedon nubilum (Say) with data extracted from the satellite images. Results showed R > 0.798, F(4,27) > 9.86 and P > 0.000016. The significant variables were normal vegetation index, type of vegetation, altitude and precipitation. GDP raster maps were interpolated using the stepwise regression equations. Then, classification neural networks models were used in order to classify GDP maps. Analysis of percentage of classification error showed that the adequate number of hidden neurons was between six and twelve. Results of error classification were 21% for P. nebrascensis, 5% for M. lakinus and 20% for B. nubilum. Neural networks are practical tools to classify grasshopper population and it will help to take control measurements in overpopulated areas.
A STORY OF GROWING CONFUSION: GENES AND THEIR REGULATION
Authors: PROHASKA SONJA J. , STADLER PETER F.
Published: August 2008

High-throughput experiments have produced convicing evidence for an extensive contribution of diverse classes of RNAs in the expression of genetic information. Instead of a simple arrangement of mostly protein-coding genes, the human transcriptome features a complex arrangement of overlapping transcripts, many of which do not code for proteins at all, while others "sample" exons from several different "genes". The complexity of the transcriptome and the prevalence of noncoding transcripts forces us to reconsider both the concept of the "gene" itself and our understanding of the mechanisms that regulate "gene expression".
SYNCHRONIZATION PHENOMENA IN PROTOCELL MODELS
Authors: FILISETTI ALESSANDRO , SERRA ROBERTO , CARLETTI TIMOTEO , POLI IRENE , VILLANI MARCO
Published: August 2008

This work aims to consider simplified models of protocells in order to describe their general behaviors. The advantage of the modelling approach is that the early protocells of life-forms on Earth are not reproduced in the present time. However, the problem is considered as a right track to understand the origin of life as well as to work with more objective synthesis of new drugs.
Ocean Circulation Kinetic Energy: Reservoirs, Sources, and Sinks
Authors: Ferrari Raffaele , Wunsch Carl
Published: August 2008

The ocean circulation is a cause and consequence of fluid scale interactions ranging from millimeters to more than 10,000 km. Although the wind field produces a large energy input to the ocean, all but approximately 10% appears to be dissipated within about 100 m of the sea surface, rendering observations of the energy divergence necessary to maintain the full water-column flow difficult. Attention thus shifts to the physically different kinetic energy (KE) reservoirs of the circulation and their maintenance, dissipation, and possible influence on the very small scales representing irreversible molecular mixing. Oceanic KE is dominated by the geostrophic eddy field, and depending on the vertical structure (barotropic versus low-mode baroclinic), direct and inverse energy cascades are possible. The pathways toward dissipation of the dominant geostrophic eddy KE depend crucially on the direction of the cascade but are difficult to quantify because of serious observational difficulties for wavelengths shorter than approximately 100–200 km. At high frequencies, KE is dominated by internal waves with near-inertial frequencies (frequencies near the local Coriolis parameter), whose shears appear to be a major source of wave breaking and mixing in the ocean interior.
Determination of the Cleavage Plane in EarlyC. elegansEmbryos
Authors: Galli Matilde , van den Heuvel Sander
Published: August 2008

Cells split in two at the final step of each division cycle. This division normally bisects through the middle of the cell and generates two equal daughters. However, developmental signals can change the plane of cell cleavage to facilitate asymmetric segregation of fate determinants and control the position and relative sizes of daughter cells. The anaphase spindle instructs the site of cell cleavage in animal cells, hence its position is critical in the regulation of symmetric vs asymmetric cell division. Studies in a variety of models identified evolutionarily conserved mechanisms that control spindle positioning. However, how the spindle determines the cleavage site is poorly understood. Recent results in Caenorhabditis elegans indicate dual functions for a Gα pathway in positioning the spindle and cleavage furrow. We review asymmetric division of the C. elegans zygote, with a focus on microtubule-cortex interactions that position the spindle and cleavage plane.
Planar Cell Polarity Signaling: From Fly Development to Human Disease
Authors: Simons Matias , Mlodzik Marek
Published: August 2008

Most, if not all, cell types and tissues display several aspects of polarization. In addition to the ubiquitous epithelial cell polarity along the apical-basolateral axis, many epithelial tissues and organs are also polarized within the plane of the epithelium. This is generally referred to as planar cell polarity (PCP; or historically, tissue polarity). Genetic screens in Drosophila pioneered the discovery of core PCP factors, and subsequent work in vertebrates has established that the respective pathways are evolutionarily conserved. PCP is not restricted only to epithelial tissues but is also found in mesenchymal cells, where it can regulate cell migration and cell intercalation. Moreover, particularly in vertebrates, the conserved core PCP signaling factors have recently been found to be associated with the orientation or formation of cilia. This review discusses new developments in the molecular understanding of PCP establishment in Drosophila and vertebrates; these developments are integrated with new evidence that links PCP signaling to human disease.
Toward a New Sociology of Rights: A Genealogy of “Buried Bodies” of Citizenship and Human Rights
Authors: Somers Margaret R. , Roberts Christopher N.J.
Published: August 2008

Although a thriving social science literature in citizenship has emerged in the past two decades, to date there exists neither a sociology of rights nor a sociology of human rights. Theoretical obstacles include the association of rights with the philosophical discourse of normativity, the abstraction of universalism, and the individualism attributed to rights-bearers. Parallel historical obstacles dating from the Universal Declaration of Human Rights (UDHR) in 1948 include American exceptionalism and racism, cultural relativism, the institutional primacy of sovereignty, and the privileging of civil rights over socioeconomic rights. Except in the United States, today human rights discourse is the lingua franca of global struggles*; building a sociology of rights as a collective project is now imperative. This article unearths and reconstructs 60 years of political clashes, intellectual debates, and struggles for inclusion and recognition surrounding human rights and citizenship—much of which has been hidden from history (especially African American human rights movements). We introduce a nascent but uncoordinated social science attention to rights and develop criteria for a new sociology of rights. At the nexus of human rights and citizenship rights we identify the public good of a “right to have rights,” which expresses the institutional, social, and moral preconditions for human recognition and inclusion. The concept offers a promising avenue of social science inquiry. [*Erratum]
After Inclusion
Authors: Carbado Devon , Fisk Catherine , Gulati Mitu
Published: August 2008

What forms of discrimination are likely to be salient in the coming decade? This review flags a cluster of problems that roughly fall under the rubric of inclusive exclusions or discrimination by inclusion. Much contemporary discrimination theory and empirical work is concerned not simply with mapping the forces that keep people out of the labor market but also with identifying the forces that push them into hierarchical structures within workplaces and labor markets. Underwriting this effort is the notion that, although determining what happens before and during the moment in which a prospective employee is excluded from an employment opportunity remains crucial to antidiscrimination theory and practice, significant employment discrimination problems can occur after a person is hired and becomes an employee. These problems transcend racial and sexual harassment. They include a range of subtle institutional practices and interpersonal dynamics that create systemic advantages for some employees and disadvantages for others. We predict that the next generation of race discrimination scholarship will engage these “after inclusion” workplace difficulties theoretically, empirically, and doctrinally.
Providing Expert Knowledge in an Adversarial Context: Social Cognitive Science in Employment Discrimination Cases
Authors: Fiske Susan T. , Borgida Eugene
Published: August 2008

Quality science provides the foundation for expert testimony in court, a claim illustrated here by three established principles of social cognition frequently applied to litigation in employment discrimination cases. First, dual processes, automatic and controlled, underlie “hidden” bias. The Implicit Association Test exemplifies one controversial but scientifically tractable application of such automaticity principles. Second, encoding and attention reveal incredibly early bias. Their potential application via neuroscience in the courtroom will challenge both science and the law. Third, mental construal produces categorical representation. Legal applications show categories’ tenacity despite commonsense expectations about the impact of individuating information. Psychological scientists, expert witnesses, legal scholars, legal practitioners, and organizational managers each benefit when quality science is imported into legal contexts. Normal science disagreements should not mistakenly tarnish the credibility of quality science.