Abstract: Wetting efficiency of microstructures or nanostructures patterned on Si wafers is a real challenge in integrated circuits manufacturing. In fact, bad or non-uniform wetting during wet processes limits chemical reactions and can lead to non-complete etching or cleaning inside the patterns and device defectivity. This issue is more and more important with the transistors size shrinkage and concerns mainly high aspect ratio structures. Deep Trench Isolation (DTI) structures enabling pixels’ isolation in imaging devices are subject to this phenomenon. While low-frequency acoustic reflectometry principle is a well-known method for Non Destructive Test applications, we have recently shown that it is also well suited for nanostructures wetting characterization in a higher frequency range. In this paper, we present a high-frequency acoustic reflectometry characterization of DTI wetting through a confrontation of both experimental and modeling results. The acoustic method proposed is based on the evaluation of the reflection of a longitudinal acoustic wave generated by a 100 µm diameter ZnO piezoelectric transducer sputtered on the silicon wafer backside using MEMS technologies. The transducers have been fabricated to work at 5 GHz corresponding to a wavelength of 1.7 µm in silicon. The DTI studied structures, manufactured on the wafer frontside, are crossing trenches of 200 nm wide and 4 µm deep (aspect ratio of 20) etched into a Si wafer frontside. In that case, the acoustic signal reflection occurs at the bottom and at the top of the DTI enabling its characterization by monitoring the electrical reflection coefficient of the transducer. A Finite Difference Time Domain (FDTD) model has been developed to predict the behavior of the emitted wave. The model shows that the separation of the reflected echoes (top and bottom of the DTI) from different acoustic modes is possible at 5 Ghz. A good correspondence between experimental and theoretical signals is observed. The model enables the identification of the different acoustic modes. The evaluation of DTI wetting is then performed by focusing on the first reflected echo obtained through the reflection at Si bottom interface, where wetting efficiency is crucial. The reflection coefficient is measured with different water / ethanol mixtures (tunable surface tension) deposited on the wafer frontside. Two cases are studied: with and without PFTS hydrophobic treatment. In the untreated surface case, acoustic reflection coefficient values with water show that liquid imbibition is partial. In the treated surface case, the acoustic reflection is total with water (no liquid in DTI). The impalement of the liquid occurs for a specific surface tension but it is still partial for pure ethanol. DTI bottom shape and local pattern collapse of the trenches can explain these incomplete wetting phenomena. This high-frequency acoustic method sensitivity coupled with a FDTD propagative model thus enables the local determination of the wetting state of a liquid on real structures. Partial wetting states for non-hydrophobic surfaces or low surface tension liquids are then detectable with this method.
Abstract: Methicillin/multiple-resistant Staphylococcus aureus
(MRSA) are infectious bacteria that are resistant to common
antibiotics. A previous in silico study in our group has identified a
hypothetical protein SAV1226 as one of the potential drug targets. In
this study, we reported the bioinformatics characterization, as well as
cloning, expression, purification and kinetic assays of hypothetical
protein SAV1226 from methicillin/vancomycin-resistant
Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis
revealed a low degree of structural similarity with known proteins.
Kinetic assays demonstrated that hypothetical protein SAV1226 is
neither a domain of an ATP dependent dihydroxyacetone kinase nor
of a phosphotransferase system (PTS) dihydroxyacetone kinase,
suggesting that the function of hypothetical protein SAV1226 might
be misannotated on public databases such as UniProt and
InterProScan 5.
Abstract: With drug resistance becoming widespread in
Plasmodium falciparum infections, the development of the alternative
drugs is the desired strategy for prevention and cure of malaria. Three
drug targets were selected to screen promising drug molecules from
the GSK library of 13469 molecules. Using an in silico structure-based
drug designing approach, the differences in binding energies of
the substrate and inhibitor were exploited between target sites of
parasite and human to design a drug molecule against Plasmodium.
The docking studies have shown several promising molecules from
GSK library with more effective binding as compared to the already
known inhibitors for the drug targets. Though stronger interaction has
been shown by several molecules as compared to the reference, few
molecules have shown the potential as drug candidates though in
vitro studies are required to validate the results. In case of
thymidylate synthase-dihydrofolatereductase (TS-DHFR), three
compounds have shown promise for future studies as potential drugs.
Abstract: Doxorubicin, also known as Adriamycin, is an
anthracycline class of drug used in cancer chemotherapy. It is used in
the treatment of non-Hodgkin’s lymphoma, multiple myeloma, acute
leukemia, breast cancer, lung cancer, endometrium cancer and ovary
cancers. It functions via intercalating DNA and ultimately killing
cancer cells. The major side effects of doxorubicin are hair loss,
myelosuppression, nausea & vomiting, oesophagitis, diarrhea, heart
damage and liver dysfunction. The minor modifications in the
structure of compound exhibit large variation in the biological
activity, has prompted us to carry out the synthesis of sulfonamide
derivatives. Sulfonamide is an important feature with broad spectrum
of biological activity such as antiviral, antifungal, diuretics, antiinflammatory,
antibacterial and anticancer activities. Structure of the
synthesized compound N-(1-methyl-2-oxo-2-N-methyl anilinoethyl)
benzene sulfonamide confirmed by proton nuclear magnetic
resonance (1H NMR),13C NMR, Mass and FTIR spectroscopic tools
to assure the position of all protons and hence stereochemistry of the
molecule. Further we have reported the binding potential of
synthesized sulfonamide analogues in comparison to doxorubicin
drug using Auto Dock 4.2 software. Computational binding energy
(B.E.) and inhibitory constant (Ki) has been evaluated for the
synthesized compound in comparison of doxorubicin against Poly
(dA-dT).Poly (dA-dT) and Poly (dG-dC).Poly (dG-dC) sequences.
The in vitro cytotoxic study against human breast cancer cell lines
confirms the better anticancer activity of the synthesized compound
over currently in use anticancer drug doxorubicin. The IC50 value of
the synthesized compound is 7.12 μM whereas for doxorubicin is 7.2
μM.
Abstract: Advanced head and neck cancers are aggressive
tumours, which require aggressive treatment. Treatment efficiency is
often hindered by cancer cell repopulation during radiotherapy,
which is due to various mechanisms triggered by the loss of tumour
cells and involves both stem and differentiated cells. The aim of the
current paper is to present in silico simulations of radiotherapy
schedules on a virtual head and neck tumour grown with biologically
realistic kinetic parameters. Using the linear quadratic formalism of
cell survival after radiotherapy, altered fractionation schedules
employing various treatment breaks for normal tissue recovery are
simulated and repopulation mechanism implemented in order to
evaluate the impact of various cancer cell contribution on tumour
behaviour during irradiation. The model has shown that the timing of
treatment breaks is an important factor influencing tumour control in
rapidly proliferating tissues such as squamous cell carcinomas of the
head and neck. Furthermore, not only stem cells but also
differentiated cells, via the mechanism of abortive division, can
contribute to malignant cell repopulation during treatment.
Abstract: Three dimensional non-Interlaced carbon fibre
reinforced silicon carbide (3-D-Cf/SiC) composites with pyrocarbon
interphase were fabricated using isothermal chemical vapor
infiltration (ICVI) combined with polymer impregnation pyrolysis
(PIP) process. Polysilazane (PSZ) is used as a preceramic polymer to
obtain silicon carbide matrix. Thermo gravimetric analysis (TGA),
Infrared spectroscopic analysis (IR) and X-ray diffraction (XRD)
analysis were carried out on PSZ pyrolysed at different temperatures
to understand the pyrolysis and obtaining the optimum pyrolysing
condition to yield β-SiC phase. The density of the composites was
1.94 g cm-3 after the 3-D carbon preform was SiC infiltrated for 280 h
with one intermediate polysilazane pre-ceramic PIP process.
Mechanical properties of the composite materials were investigated
under tensile, flexural, shear and impact loading. The values of
tensile strength were 200 MPa at room temperature (RT) and 195
MPa at 500°C in air. The average RT flexural strength was 243 MPa.
The lower flexural strength of these composites is because of the
porosity. The fracture toughness obtained from single edge notched
beam (SENB) technique was 39 MPa.m1/2. The work of fracture
obtained from the load-displacement curve of SENB test was 22.8
kJ.m-2. The composites exhibited excellent impact resistance and the
dynamic fracture toughness of 44.8 kJ.m-2 is achieved as determined
from instrumented Charpy impact test. The shear strength of the
composite was 93 MPa, which is significantly higher compared 2-D
Cf/SiC composites. Microstructure evaluation of fracture surfaces
revealed the signatures of fracture processes and showed good
support for the higher toughness obtained.
Abstract: The MyD88 is an evolutionarily conserved host-expressed adaptor protein that is essential for proper TLR/ IL1R immune-response signaling. A previously identified complete cDNA (1626 bp) of OfMyD88 comprised an ORF of 867 bp encoding a protein of 288 amino acids (32.9 kDa). The gDNA (3761 bp) of OfMyD88 revealed a quinquepartite genome organization composed of 5 exons (with the sizes of 310, 132, 178, 92 and 155 bp) separated by 4 introns. All the introns displayed splice signals consistent with the consensus GT/AG rule. A bipartite domain structure with two domains namely death domain (24-103) coded by 1st exon, and TIR domain (151-288) coded by last 3 exons were identified through in silico analysis. Moreover, homology modeling of these two domains revealed a similar quaternary folding nature between human and rock bream homologs. A comprehensive comparison of vertebrate MyD88 genes showed that they possess a 5-exonic structure.In this structure, the last three exons were strongly conserved, and this suggests that a rigid structure has been maintained during vertebrate evolution.A cluster of TATA box-like sequences were found 0.25 kb upstream of cDNA starting position. In addition, putative 5'-flanking region of OfMyD88 was predicted to have TFBS implicated with TLR signaling, including copies of NFkB1, APRF/ STAT3, Sp1, IRF1 and 2 and Stat1/2. Using qPCR technique, a ubiquitous mRNA expression was detected in liver and blood. Furthermore, a significantly up-regulated transcriptional expression of OfMyD88 was detected in head kidney (12-24 h; >2-fold), spleen (6 h; 1.5-fold), liver (3 h; 1.9-fold) and intestine (24 h; ~2-fold) post-Fla challenge. These data suggest a crucial role for MyD88 in antibacterial immunity of teleosts.
Abstract: Altered drug binding may be an important factor in isoniazid (INH) resistance, rather than major changes in the enzyme’s activity as a catalase or peroxidase (KatG). The identification of structural or functional defects in the mutant KatGs responsible for INH resistance remains as an area to be explored. In this connection, the differences in the binding affinity between wild-type (WT) and mutants of KatG were investigated, through the generation of three mutants of KatG, Ser315Thr [S315T], Ser315Asn [S315N], Ser315Arg [S315R] and a WT [S315]) with the help of software-MODELLER. The mutants were docked with INH using the software-GOLD. The affinity is lower for WT than mutant, suggesting the tight binding of INH with the mutant protein compared to WT type. These models provide the in silico evidence for the binding interaction of KatG with INH and implicate the basis for rationalization of INH resistance in naturally occurring KatG mutant strains of Mycobacterium tuberculosis.
Abstract: A thin gold metal layer was deposited on the top of
silicon oxide films containing embedded Si nanocrystals (Si-nc). The
sample was annealed in a gas containing nitrogen, and subsequently
characterized by photoluminescence. We obtained 3-fold
enhancement of photon emission from the Si-nc embedded in silicon
dioxide covered with a Gold layer as compared with an uncovered
sample. We attribute this enhancement to the increase of the
spontaneous emission rate caused by the coupling of the Si-nc
emitters with the surface plasmons (SP). The evolution of PL
emission with laser irradiated time was also collected from covered
samples, and compared to that from uncovered samples. In an
uncovered sample, the PL intensity decreases with time,
approximately with two decay constants. Although the decrease of
the initial PL intensity associated with the increase of sample
temperature under CW pumping is still observed in samples covered
with a gold layer, this film significantly contributes to reduce the
permanent deterioration of the PL intensity. The resistance to
degradation of light-emitting silicon nanocrystals can be increased by
SP coupling to suppress the permanent deterioration. Controlling the
permanent photodeterioration can allow to perform a reliable optical
gain measurement.
Abstract: Currently, mathematical and computer modeling are widely used in different biological studies to predict or assess behavior of such a complex systems as a biological are. This study deals with mathematical and computer modeling of bi-substrate enzymatic reactions, which play an important role in different biochemical pathways. The main objective of this study is to represent the results from in silico investigation of bi-substrate enzymatic reactions in the presence of uncompetitive inhibitors, as well as to describe in details the inhibition effects. Four models of uncompetitive inhibition were designed using different software packages. Particularly, uncompetitive inhibitor to the first [ES1] and the second ([ES1S2]; [FS2]) enzyme-substrate complexes have been studied. The simulation, using the same kinetic parameters for all models allowed investigating the behavior of reactions as well as determined some interesting aspects concerning influence of different cases of uncompetitive inhibition. Besides, it has been shown that uncompetitive inhibitors exhibit specific selectivity depending on mechanism of bi-substrate enzymatic reaction.
Abstract: The mechanism of nickel (Ni) metallization in silicon-germanium (Si0.5Ge0.5) alloy nanowire (NW) was studied. Transmission electron microscope imaging with in-situ annealing was conducted at temperatures of 200oC to 600°C. During rapid formation of Ni germanosilicide, loss of material from from the SiGe NW occurred which led to the formation of a thin Ni germanosilicide filament and eventual void. Energy dispersive X-ray spectroscopy analysis along the SiGe NW before and after annealing determined that Ge atoms tend to out-diffuse from the Ni germanosilicide towards the Ni source in the course of annealing. A model for the Ni germanosilicide formation in SiGe NW is proposed to explain this observation.
Abstract: Adenylate kinase (AK) catalyse the phosphotransferase
reaction plays an important role in cellular energy homeostasis. The
inhibitors of bacterial AK are useful in the treatment of several
bacterial infections. To the novel inhibitors of AK, docking studies
performed by using the 3D structure of Bacillus stearothermophilus
adenylate kinase from protein data bank (IZIP). 46 Quinoxaline
analogues were docked in 1ZIP and selected the highly interacting
compounds based on their binding energies, for further studies
Abstract: The use of synthetic retardants in polymeric insulated
cables is not uncommon in the high voltage engineering to study
electrical treeing phenomenon. However few studies on organic
materials for the same investigation have been carried. .This paper
describes the study on the effects of Oil Palm Empty Fruit Bunch
(OPEFB) microfiller on the tree initiation and propagation in silicone
rubber with different weight percentages (wt %) of filler to insulation
bulk material. The weight percentages used were 0 wt % and 1 wt %
respectively. It was found that the OPEFB retards the propagation of
the electrical treeing development. For tree inception study, the
addition of 1(wt %) OPEFB has increase the tree inception voltage of
silicone rubber. So, OPEFB is a potential retardant to the initiation
and growth of electrical treeing occurring in polymeric materials for
high voltage application. However more studies on the effects of
physical and electrical properties of OPEFB as a tree retardant
material are required.
Abstract: A major challenge in biomaterials research is the
regulation of protein adsorption which is a key factor for controlling
the subsequent cell adhesion at implant surfaces. The aim of the
present study was to control the adsorption of fibronectin (FN) and
the attachment of MG-63 osteoblasts with an electronic
nanostructure. Shallow doping line lattices with a period of 260 nm
were produced for this purpose by implantation of phosphorous in
silicon wafers. Protein coverage was determined after incubating the
substrate with FN by means of an immunostaining procedure and the
measurement of the fluorescence intensity with a TECAN analyzer.
We observed an increased amount of adsorbed FN on the
nanostructure compared to control substrates. MG-63 osteoblasts
were cultivated for 24h on FN-incubated substrates and their
morphology was assessed by SEM. Preferred orientation and
elongation of the cells in direction of the doping lattice lines was
observed on FN-coated nanostructures.
Abstract: In the Fe-3%Si sheets, grade Hi-B, with AlN and MnS
as inhibitors, the Goss grains which abnormally grow do not have a
size greater than the average size of the primary matrix. In this
heterogeneous microstructure, the size factor is not a required
condition for the secondary recrystallization. The onset of the small
Goss grain abnormal growth appears to be related to a particular
behavior of their grain boundaries, to the local texture and to the
distribution of the inhibitors. The presence and the evolution of
oriented clusters ensure to the small Goss grains a favorable
neighborhood to grow. The modified Monte-Carlo approach, which
is applied, considers the local environment of each grain. The grain
growth is dependent of its real spatial position; the matrix
heterogeneity is then taken into account. The grain growth conditions
are considered in the global matrix and in different matrixes
corresponding to A component clusters. The grain growth behaviour
is considered with introduction of energy only, energy and mobility,
energy and mobility and precipitates.
Abstract: As application of re-activation of backside on power
device Insulated Gate Bipolar Transistor (IGBT), laser annealing was
employed to irradiate amorphous silicon substrate, and resistivities
were measured using four point probe measurement. For annealing
the amorphous silicon two lasers were used at wavelength of visible
green (532 nm) together with Infrared (793 nm). While the green
laser efficiently increased temperature at top surface the Infrared
laser reached more deep inside and was effective for melting the
top surface. A finite element method was employed to evaluate time
dependent thermal distribution in silicon substrate.
Abstract: Tuberculosis (TB) is a bacterial infectious disease caused by the obligate human pathogen, Mycobacterium tuberculosis. Multidrug-resistant tuberculosis (MDR-TB) is a global reality that threatens tuberculosis control. Resistance to antibiotic Rifampicin, occurs in 95% of cases through nucleotide substitutions in an 81-bp core region of the rpoB i.e; beta subunit of DNA dependant RNA polymerase. In this paper, we studied the Rifampicin-rpoB receptor interactions In silico. First, homology modeling was performed to obtain the three dimensional structure of Mycobacterium rpoB. Sixty analogs of Rifampicin were prepared using Marvin sketch software. Both original Rifampicin and the analogs were docked with rpoB and energy values were obtained. Out of sixty analogs, 43 analogs had lesser energy values than conventional Rifampicin and hence are predicted to have greater binding affinity to rpoB. Thus, this study offers a route for the development of Rifampicin analogs against multi drug resistant Mycobacterium rpoB.
Abstract: The mathematical modeling of different biological
processes is usually used to predict or assess behavior of systems in
which these processes take place. This study deals with mathematical
and computer modeling of bi-substrate enzymatic reactions with
ping-pong mechanism, which play an important role in different
biochemical pathways. Besides that, three models of competitive
inhibition were designed using different software packages. The main
objective of this study is to represent the results from in silico
investigation of bi-substrate enzymatic reactions with ordered pingpong
mechanism in the presence of competitive inhibitors, as well as
to describe in details the inhibition effects. The simulation of the
models with certain kinetic parameters allowed investigating the
behavior of reactions as well as determined some interesting aspects
concerning influence of different cases of competitive inhibition.
Simultaneous presence of two inhibitors, competitive to the S1 and S2
substrates have been studied. Moreover, we have found the pattern of
simultaneous influence of both inhibitors.
Abstract: RF performance of SOI CMOS device has attracted
significant amount of interest recently. In order to improve RF
parameters, Strained Si/Relaxed Si0.8Ge0.2 investigated as a
replacement for Si technology .Enhancement of carrier mobility
associated with strain engineering makes Strained Si a promising
candidate for improving RF performance of CMOS technology.
From the simulation, the cut-off frequency is estimated to be 224
GHZ, whereas in SOI at similar bias is about 188 GHZ. Therefore,
Strained Si exhibits 19% improvement in cut-off frequency over
similar Si counterpart. In this paper, Ion/Ioff ratio is studied as one of
the key parameters in logic and digital application. Strained Si/SiGe
demonstrates better Ion/Ioff characteristic than SOI, in similar channel
length of 100 nm.Another important key analog figures of merit such
as Early Voltage (VEA) ,transconductance vs drain current (gm /Ids)
are studied. They introduce the efficiency of the devices to convert
dc power into ac frequency.
Abstract: The aim of this study was to compare the solubility of selected volatile organic compounds in water and silicon oil using the simple static headspace method. The experimental design allowed equilibrium achievement within 30 – 60 minutes. Infinite dilution activity coefficients and Henry-s law constants for various organics representing esters, ketones, alkanes, aromatics, cycloalkanes and amines were measured at 303K. The measurements were reproducible with a relative standard deviation and coefficient of variation of 1.3x10-3 and 1.3 respectively. The static determined activity coefficients using shaker flasks were reasonably comparable to those obtained using the gas liquid - chromatographic technique and those predicted using the group contribution methods mainly the UNIFAC. Silicon oil chemically known as polydimethysiloxane was found to be better absorbent for VOCs than water which quickly becomes saturated. For example the infinite dilution mole fraction based activity coefficients of hexane is 0.503 and 277 000 in silicon oil and water respectively. Thus silicon oil gives a superior factor of 550 696. Henry-s law constants and activity coefficients at infinite dilution play a significant role in the design of scrubbers for abatement of volatile organic compounds from contaminated air streams. This paper presents the phase equilibrium of volatile organic compounds in very dilute aqueous and polymeric solutions indicating the movement and fate of chemical in air and solvent. The successful comparison of the results obtained here and those obtained using other methods by the same authors and in literature, means that the results obtained here are reliable.