Two-dimensional simulation of nanoparticle deposition from high-density plasmas on microstructured surfaces

Selective and controlled deposition of plasma-grown nanoparticles is one of the pressing problems of plasma-aided nanofabrication. The results of advanced numerical simulations of motion of charge-variable nanoparticles in the plasma presheath and sheath areas and in localized microscopic electric fields created by surface microstructures are reported. Conditions for site-selective deposition of such nanoparticles onto individual microstructures and open surface areas within a periodic micropattern are formulated. The effects of plasma parameters, surface potential, and micropattern features on nanoparticle deposition are investigated and explained using particle charging and plasma force arguments. The results are generic and applicable to a broad range of nanoparticle-generating plasmas and practical problems ranging from management of nanoparticle contamination in microelectronics to site-selective nanoparticle deposition into specified device locations, and synthesis of advanced microporous materials and nanoparticle superlattices. © 2007 American Institute of Physics.

Simulation of ion flux distribution in conductive and nonconductive nanotip patterns

The distribution of flux of carbon-bearing cations over nanopatterned surfaces with conductive nanotips and nonconductive nanoislands is simulated using the Monte-Carlo technique. It is shown that the ion current is focused to nanotip surfaces when the negative substrate bias is low and only slightly perturbed at higher substrate biases. In the low-bias case, the mean horizontal ion displacement caused by the nanotip electric field exceeds 10 nm. However, at higher substrate biases, this value reduces down to 2 nm. In the nonconductive nanopattern case, the ion current distribution is highly nonuniform, with distinctive zones of depleted current density around the nanoislands. The simulation results suggest the efficient means to control ion fluxes in plasma-aided nanofabrication of ordered nanopatterns, such as nanotip microemitter structures and quantum dot or nanoparticle arrays. © World Scientific Publishing Company.

Numerical simulation of self-organized nano-islands in plasma-based assembly of quantum dot arrays

This work presents the details of the numerical model used in simulation of self-organization of nano-islands on solid surfaces in plasma-assisted assembly of quantum dot structures. The model includes the near-substrate non-neutral layer (plasma sheath) and a nanostructured solid deposition surface and accounts for the incoming flux of and energy of ions from the plasma, surface temperature-controlled adatom migration about the surface, adatom collisions with other adatoms and nano-islands, adatom inflow to the growing nano-islands from the plasma and from the two-dimensional vapour on the surface, and particle evaporation to the ambient space and the two-dimensional vapour. The differences in surface concentrations of adatoms in different areas within the quantum dot pattern significantly affect the self-organization of the nano-islands. The model allows one to formulate the conditions when certain islands grow, and certain ones shrink or even dissolve and relate them to the process control parameters. Surface coverage by selforganized quantum dots obtained from numerical simulation appears to be in reasonable agreement with the available experimental results.

Numerical simulation of nanoparticle-generating electronegative plasmas in the PECVD of nanostructured silicon film

The results of numerical simulation of the equilibrium parameters of a low pressure nanopowder-generating discharge in silane for the plasma enhanced chemical vapor deposition (PECVD) of nanostructured silicon-based films are presented. It is shown that a low electron temperature and a low density of negative SiH3 - ions are favorable for the PECVD process. This opens a possibility to predict the main parameters of the reactive plasma and plasma-nucleated nanoparticles, and hence, to control the quality of silicon nanofilms.

A novel approach for numerical simulation of plant tissue shrinkage during drying

Drying is a key processing techniques used in food engineering which demands continual developments on advanced analysis techniques in order to optimize the product and the process. In this regard, plant based materials are a frequent subject of interest where microstructural studies can provide a clearer understanding on the fundamental physical mechanisms involved. In this context, considering numerous challenges of using conventional numerical grid-based modelling techniques, a meshfree particle based model was developed to simulate extreme deformations of plant microstructure during drying. The proposed technique is based on a particle based meshfree method: Smoothed Particle Hydrodynamics (SPH) and a Discrete Element Method (DEM). A tissue model was developed by aggrading individual cells modelled with SPH-DEM coupled approach by initializing the cells as hexagons and aggregating them to form a tissue. The model also involves a middle lamella resembling real tissues. Using the model, different dried tissue states were simulated with different moisture content, the turgor pressure, and cell wall contraction effects. Compared to the state of the art grid-based microscale plant tissue drying models, the proposed model is capable of simulating plant tissues at lower moisture contents which results in excessive shrinkage and cell wall wrinkling. Model predictions were compared with experimental findings and a fairly good agreement was observed both qualitatively and quantitatively.

Structure-mediated thermal transport of monolayer graphene allotropes nanoribbons

We report the study of the thermal transport management of monolayer graphene allotrope nanoribbons (size ∼20 × 4 nm2) by the modulation of their structures via molecular dynamics simulations. The thermal conductivity of graphyne (GY)-like geometries is observed to decrease monotonously with increasing number of acetylenic linkages between adjacent hexagons. Strikingly, by incorporating those GY or GY-like structures, the thermal performance of graphene can be effectively engineered. The resulting hetero-junctions possess a sharp local temperature jump at the interface, and show a much lower effective thermal conductivity due to the enhanced phonon–phonon scattering. More importantly, by controlling the percentage, type and distribution pattern of the GY or GY-like structures, the hetero-junctions are found to exhibit tunable thermal transport properties (including the effective thermal conductivity, interfacial thermal resistance and rectification). This study provides a heuristic guideline to manipulate the thermal properties of 2D carbon networks, ideal for application in thermoelectric devices with strongly suppressed thermal conductivity.

A simulation modeling approach to understanding information technology value cocreation

The business value of information technology (IT) is increasingly being cocreated by multiple parties, opening opportunities for new research initiatives. Previous studies on IT value cocreation mainly focus on analyzing sources of cocreated IT value, yet inadequately accommodating the influence of competition relationships in IT value cocreation activities. To fill the gap, this in-progress paper suggests an agent-based modeling (also simulation) approach to investigating potential influences of the dynamic interplay between cooperation and competition relationships in IT value cocreation settings. In particular, the research proposes a high-level conceptual framework to position general IT value cocreation processes. A relational network view is offered, aiming at decomposing and systemizing several typical cooperation and competition scenarios in practical IT value cocreation settings. The application of a simulation approach to analytical insights and to theory building is illustrated.

B-Raf mutation : a key player in molecular biology of cancer

B-Raf is one of the more commonly mutated proto-oncogenes implicated in the development of cancers. In this review, we consider the mechanisms and clinical impacts of B-Raf mutations in cancer and discuss the implications for the patient in melanoma, thyroid cancer and colorectal cancer, where B-Raf mutations are particularly common.

Carcinoma ex pleomorphic adenoma : a comprehensive review of clinical, pathological and molecular data

Carcinoma ex pleomorphic adenoma (Ca ex PA) is a carcinoma arising from a primary or recurrent benign pleomorphic adenoma. It often poses a diagnostic challenge to clinicians and pathologists. This study intends to review the literature and highlight the current clinical and molecular perspectives about this entity. The most common clinical presentation of CA ex PA is of a firm mass in the parotid gland. The proportion of adenoma and carcinoma components determines the macroscopic features of this neoplasm. The entity is difficult to diagnose pre-operatively. Pathologic assessment is the gold standard for making the diagnosis. Treatment for Ca ex PA often involves an ablative surgical procedure which may be followed by radiotherapy. Overall, patients with Ca ex PA have a poor prognosis. Accurate diagnosis and aggressive surgical management of patients presenting with Ca ex PA can increase their survival rates. Molecular studies have revealed that the development of Ca ex PA follows a multi-step model of carcinogenesis, with the progressive loss of heterozygosity at chromosomal arms 8q, then 12q and finally 17p. There are specific candidate genes in these regions that are associated with particular stages in the progression of Ca ex PA. In addition, many genes which regulate tumour suppression, cell cycle control, growth factors and cell-cell adhesion play a role in the development and progression of Ca ex PA. It is hopeful that these molecular data can give clues for the diagnosis and management of the disease.

Signet-ring cell carcinoma of colorectum : current perspectives and molecular biology

PURPOSE Colorectal signet-ring cell carcinoma (SRCC) is rare, and very little detailed information on the molecular biology of the disease is available. METHODS The literature on the clinical, pathological and, in particular, the molecular biology of this rare entity was critically reviewed. The reviewed articles take into account a total of 1,817 cases of SRCC, but only 143 cases have molecular data available. The characteristics of two patients with colorectal SRCC were also discussed. RESULTS Colorectal SRCC mostly occurs in younger patients, is larger and has different site predilection compared with conventional colorectal adenocarcinoma. It can occur as one of the synchronous cancers in the colorectum. The cancer is usually diagnosed at advanced stages because of the late manifestation of symptoms, and aggressive treatment strategy is required. Limited reports in the literature have shown that the variant of colorectal cancer demonstrated a different pattern of genetic alterations of common growth kinase-related oncogenes (K-ras, BRAF), tumour suppressor genes (p53, p16), gene methylation and cell adhesion-related genes related to the Wingless signalling pathway (E-cadherin and beta-catenin) from conventional colorectal adenocarcinoma. Colorectal SRCC also showed high expression of mucin-related genes and genes related to the gastrointestinal system. There was also a higher prevalence of microsatellite instability-high tumours and low Cox-2 expression in colorectal SRCC as opposed to conventional adenocarcinoma. CONCLUSIONS Colorectal SRCC has unique molecular pathological features. The unique molecular profiles in SRCC may provide molecular-based improvements to patient management in colorectal SRCC.

CFD convective flow simulation of the varying properties of CO2-H20 mixtures in geothermal systems

Numerical simulation of a geothermal reservoir, modelled as a bottom-heated square box, filled with water-CO2 mixture is presented in this work. Furthermore, results for two limiting cases of a reservoir filled with either pure water or CO2 are presented. Effects of different parameters including CO2 concentration as well as reservoir pressure and temperature on the overall performance of the system are investigated. It has been noted that, with a fixed reservoir pressure and temperature, any increase in CO2concentration leads to better performance, i.e. stronger convection and higher heat transfer rates. With a fixed CO2 concentration, however, the reservoir pressure and temperature can significantly affect the overall heat transfer and flow rate from the reservoir. Details of such variations are documented and discussed in the present paper.

Computational fluid dynamics simulation and turbomachinery code validation of a high pressure ratio radial-inflow turbine

The present study explores reproducing the closest geometry of a high pressure ratio single stage radial-inflow turbine applied in the Sundstrans Power Systems T-100 Multipurpose Small Power Unit. The commercial software ANSYS-Vista RTD along with a built in module, BladeGen, is used to conduct a meanline design and create 3D geometry of one flow passage. Carefully examining the proposed design against the geometrical and experimental data, ANSYS-TurboGrid is applied to generate computational mesh. CFD simulations are performed with ANSYS-CFX in which three-dimensional Reynolds-Averaged Navier-Stokes equations are solved subject to appropriate boundary conditions. Results are compared with numerical and experimental data published in the literature in order to generate the exact geometry of the existing turbine and validate the numerical results against the experimental ones.

Towards a multi-element simulation of heavily over-consolidated bagasse using a material subroutine

A better understanding of the behaviour of prepared cane and bagasse, and the ability to model the mechanical behaviour of bagasse as it is squeezed in a milling unit to extract juice, would help identify how to improve the current process. There are opportunities to decrease bagasse moisture from a milling unit. The behaviour of bagasse in chutes is poorly understood. Previous investigations have shown that juice flow through bagasse obeys Darcy’s permeability law, that the grip of the rough surface of the grooves on the bagasse can be represented by the Mohr-Coulomb failure criterion for soils, and that the internal mechanical behaviour of the bagasse is critical state behaviour similar to that for sand and clay. Progress has been made in the last 11 years towards implementing a mechanical model for bagasse in finite element software. The objective is to be able to correctly simulate various simple mechanical loading conditions measured in the laboratory. Combining these behaviours together is thought to have a high probability of reproducing the complicated stress conditions in a milling unit. This paper reports on progress made towards modelling the fifth and final (and most challenging) of the simple loading conditions: the shearing of heavily over-consolidated bagasse, using a specific model for bagasse in a multi-element simulation.

Molecular basis for lysine specificity in the yeast ubiquitin-conjugating enzyme Cdc34

Ubiquitin (Ub)-conjugating enzymes (E2s) and ubiquitin ligases (E3s) catalyze the attachment of Ub to lysine residues in substrates and Ub during monoubiquitination and polyubiquitination. Lysine selection is important for the generation of diverse substrate-Ub structures, which provides versatility to this pathway in the targeting of proteins to different fates. The mechanisms of lysine selection remain poorly understood, with previous studies suggesting that the ubiquitination site(s) is selected by the E2/E3-mediated positioning of a lysine(s) toward the E2/E3 active site. By studying the polyubiquitination of Sic1 by the E2 protein Cdc34 and the RING E3 Skp1/Cul1/F-box (SCF) protein, we now demonstrate that in addition to E2/E3-mediated positioning, proximal amino acids surrounding the lysine residues in Sic1 and Ub are critical for ubiquitination. This mechanism is linked to key residues composing the catalytic core of Cdc34 and independent of SCF. Changes to these core residues altered the lysine preference of Cdc34 and specified whether this enzyme monoubiquitinated or polyubiquitinated Sic1. These new findings indicate that compatibility between amino acids surrounding acceptor lysine residues and key amino acids in the catalytic core of ubiquitin-conjugating enzymes is an important mechanism for lysine selection during ubiquitination.