Metal Clips Induce Folding of a Short Unstructured Peptide into an a-Helix via Turn Conformations in Water. Kinetic versus Thermodynamic Products

Short peptides corresponding to two to four a-helical turns of proteins are not thermodynamically stable helices in water. Unstructured octapeptide Ac-His1*-Ala2-Ala3-His4*-His5*-Glu6-Leu7-His8*-NH2 (1) reacts with two [Pd ((NH2)-N-15(CH2)(2) (NH2)-N-15)(NO3)(2)] in water to form a kinetically stable intermediate, [{Pden}(2)-{(1,4)(5,8)-peptide}](2), in which two 19-membered metallocyclic rings stabilize two peptide turns. Slow subsequent folding to a thermodynamically more stable two-turn a-helix drives the equilibrium to [{Pden}(2)-{(1,5)(4,8)-peptide}] (3), featuring two 22-membered rings. This transformation from unstructured peptide via turns to an a-helix suggests that metal clips might be useful probes for investigating peptide folding.

Measurements of neutral atom diffusion and electron-ion recombination by laser enhanced ionisation and planar laser induced fluorescence in an air-acetylene flame

The spatial and temporal evolution of a depleted atomic distribution created by laser enhanced ionisation (LEI) was employed to determine both a diffusion coefficient for sodium (Na) and an electron (e(-)) and sodium ion recombination rate coefficient in an analytical air-C2H2 flame. A depleted distribution of neutral sodium atoms was produced in a flame by ionising approximately 80% of the irradiated sodium atoms in a well defined region using a two step LEI excitation scheme. Following depletion by ionisation, planar laser induced fluorescence (PLIF) images of the depleted region recorded the diffusion and decay of the depleted Na distribution for different depletion-probe delays. From measurements of the diffused width of the distribution, an accurate diffusion coefficient D = (1.19 +/- 0.03) x 10(-3) m(2) s(-1) for Na was determined in teh burnt gases of the flame. Measurements of the integrated fluorescence intensity in the depleted region for different depletion-probe delays were related to an increase in atomic sodium concentration caused by electron-ion recombination. At high concentrations (greater than or equal to 50 mu g ml(-1)), where the electron and ion concentrations in the depleted region were assumed equal, a recombination rate coefficient of 4.2 x 10(-9) cm(3) s(-1) was calculated. (C) 1997 Elsevier Science B.V.

Effect of target bias on magnetic field enhanced plasma immersion ion implantation

Recent studies have demonstrated that sheath dynamics in plasma immersion ion implantation (PIII) is significantly affected by an external magnetic field, especially in the case when the magnetic field is parallel to the workpiece surface or intersects it at small angles. In this work we report the results from two-dimensional, particle-in-cell (PIC) computer simulations of magnetic field enhanced plasma immersion implantation system at different bias voltages. The simulations begin with initial low-density nitrogen plasma, which extends with uniform density through a grounded cylindrical chamber. Negative bias voltage is applied to a cylindrical target located on the axis of the vacuum chamber. An axial magnetic field is created by a solenoid installed inside the target holder. A set of simulations at a fixed magnetic field of 0.0025 T at the target surface is performed. Secondary electron emission from the target subjected to ion bombardment is also included. It is found that the plasma density around the cylindrical target increases because of intense background gas ionization by the electrons drifting in the crossed E x B fields. Suppression of the sheath expansion and increase of the implantation current density in front of the high-density plasma region are observed. The effect of target bias on the sheath dynamics and implantation current of the magnetic field enhanced PIII is discussed. (C) 2007 Elsevier B.V. All rights reserved.

Numerical simulation of magnetic field enhanced plasma immersion ion implantation

The behavior of plasma and sheath characteristics under the action of an applied magnetic field is important in many applications including plasma probes and material processing. Plasma immersion ion implantation (PIII) has been developed as a fast and efficient surface modification technique of complex shaped three-dimensional objects. The PIII process relies on the acceleration of ions across a high-voltage plasma sheath that develops around the target. Recent studies have shown that the sheath dynamics is significantly affected by an external magnetic field. In this work we describe a two-dimensional computer simulation of magnetic field enhanced plasma immersion implantation system. Negative bias voltage is applied to a cylindrical target located on the axis of a grounded cylindrical vacuum chamber filled with uniform nitrogen plasma. An axial magnetic field is created by a solenoid installed inside the cylindrical target. The computer code employs the Monte Carlo method for collision of electrons and neutrals in the plasma and a particle-in-cell (PIC) algorithm for simulating the movement of charged particles in the electromagnetic field. Secondary electron emission from the target subjected to ion bombardment is also included. It is found that a high-density plasma region is formed around the cylindrical target due to the intense background gas ionization by the magnetized electrons drifting in the crossed ExB fields. An increase of implantation current density in front of high density plasma region is observed. (C) 2007 Elsevier B.V. All rights reserved.

Enhanced corrosion resistance of AISI H13 steel treated by nitrogen plasma immersion ion implantation

Electrochemical corrosion measurements of AISI H13 steel treated by Pill process in 3.5% (wt) NaCl solution were investigated. So far the corrosion behavior of AISI H 13 steel by Pill has not been studied. The electrochemical results are correlated with the surface morphology, nitrogen content and hardness of the nitride layer. Ion implantation of nitrogen into H 13 steel was carried out by Pill technique. SEM examination revealed a generalized corrosion and porosity over all analyzed sample surfaces. Penetration of nitrogen reaching more than 20 gm was achieved at 450 degrees C and hardness as high as 1340 HV (factor of 2.7 enhancement over standard tempered and annealed H 13) was reached by a high power, 9 h Pill treatment. The corrosion behavior of the samples was studied by potentiodynamic polarization method. The noblest corrosion behavior was observed for the samples treated by PIII at 450 degrees C, during 9 h. Anodic branches of polarization curves of PIII processed samples show a passive region associated with the formation of a protective film. The passive region current density of PIII treated H13 samples (3.5 x 10(-6) A/cm(2)) is about 270 times lower than the one of untreated specimens, which demonstrates the higher corrosion resistance for the Pill treated H 13 samples. (c) 2007 Elsevier B.V. All rights reserved.

Numerical simulation of magnetic-field-enhanced plasma immersion ion implantation in cylindrical geometry

Recent studies have demonstrated that the sheath dynamics in plasma immersion ion implantation (PIII) is significantly affected by an external magnetic field. In this paper, a two-dimensional computer simulation of a magnetic-field-enhanced PHI system is described. Negative bias voltage is applied to a cylindrical target located on the axis of a grounded vacuum chamber filled with uniform molecular nitrogen plasma. A static magnetic field is created by a small coil installed inside the target holder. The vacuum chamber is filled with background nitrogen gas to form a plasma in which collisions of electrons and neutrals are simulated by the Monte Carlo algorithm. It is found that a high-density plasma is formed around the target due to the intense background gas ionization by the magnetized electrons drifting in the crossed E x B fields. The effect of the magnetic field intensity, the target bias, and the gas pressure on the sheath dynamics and implantation current of the PHI system is investigated.

Diverse Amorphous Carbonaceous Thin Films Obtained by Plasma Enhanced Chemical Vapor Deposition and Plasma Immersion Ion Implantation and Deposition

Diverse amorphous hydrogenated carbon and similar films containing additional elements were produced by Plasma Enhanced Chemical Vapor Deposition (PECVD) and by Plasma Immersion Ion Implantation and Deposition (PIIID). Thus a-C:H, a-C:H:F, a-C:H:N, a-C:H:Cl and a-C:H:O:Si were obtained, starting from the same feed gases, using both techniques. The same deposition system supplied with radiofrequency (RF) power was used to produce all the films. A cylindrical stainless steel chamber equipped with circular electrodes mounted horizontally was employed. RF power was fed to the upper electrode; substrates were placed on the lower electrode. For PIIID negative high tension pulses were also applied to the lower electrode. Raman spectroscopy confirmed that all the films are amorphous. Chemical characterization of each pair of films was undertaken using Infrared Reflection Absorption Spectroscopy and X-ray Photoelectron Spectroscopy. The former revealed the presence of specific structures, such as C-H, C-O, O-H. The latter allowed calculation of the ratio of hetero-atoms to carbon atoms in the films, e. g. F:C, N:C, and Si:C. Only relatively small differences in elemental composition were detected between films produced by the two methods. The deposition rate in PIIID is generally reduced in relation to that of PECVD; for a-C:H:Cl films the reduction factor is almost four.

Optical, mechanical and surface properties of amorphous carbonaceous thin films obtained by plasma enhanced chemical vapor deposition and plasma immersion ion implantation and deposition

Diverse amorphous hydrogenated carbon-based films (a-C:H, a-C:H:F, a-C:H:N, a-C:H:Cl and a-C:H:Si:O) were obtained by radiofrequency plasma enhanced chemical vapor deposition (PECVD) and plasma immersion ion implantation and deposition (PIIID). The same precursors were used in the production of each pair of each type of film, such as a-C:H, using both PECVD and PIIID. Optical properties, namely the refractive index, n, absorption coefficient, α, and optical gap, ETauc, of these films were obtained via transmission spectra in the ultraviolet-visible near-infrared range (wavelengths from 300 to 3300 nm). Film hardness, elastic modulus and stiffness were obtained as a function of depth using nano-indentation. Surface energy values were calculated from liquid drop contact angle data. Film roughness and morphology were assessed using atomic force microscopy (AFM). The PIIID films were usually thinner and possessed higher refractive indices than the PECVD films. Determined refractive indices are consistent with literature values for similar types of films. Values of ETauc were increased in the PIIID films compared to the PECVD films. An exception was the a-C:H:Si:O films, for which that obtained by PIIID was thicker and exhibited a decreased ETauc. The mechanical properties - hardness, elastic modulus and stiffness - of films produced by PECVD and PIIID generally present small differences. An interesting effect is the increase in the hardness of a-C:H:Cl films from 1.0 to 3.0 GPa when ion implantation is employed. Surface energy correlates well with surface roughness. The implanted films are usually smoother than those obtained by PECVD. ©2013 Elsevier B.V. All rights reserved.

Study of magnetic field enhanced plasma immersion ion implantation in Silicon

A comparison between experimental measurements and numerical calculations of the ion current distribution in plasma immersion ion implantation (PIII) with external magnetic field is presented. Later, Silicon samples were implanted with nitrogen ion to analyze the effect on them. The magnetic field considered is essentially non-uniform and is generated by two magnetic coils installed on vacuum chamber. The presence of both, electric and magnetic field in PIII create a crossed ExB field system, promoting drift velocity of the plasma around the target. The results found shows that magnetized electrons drifting in ExB field provide electron-neutral collision. The efficient ionization increases the plasma density around the target where a magnetic confinement is formed. As result, the ion current density increases, promoting significant changes in the samples surface properties, especially in the surface wettability.

Computational investigations of ion conduction mechanisms using enhanced sampling methods

Proper ion channels’ functioning is a prerequisite for a normal cell and disorders involving ion channels, or channelopathies, underlie many human diseases. Long QT syndromes (LQTS) for example may arise from the malfunctioning of hERG channel, caused either by the binding of drugs or mutations in HERG gene. In the first part of this thesis I present a framework to investigate the mechanism of ion conduction through hERG channel. The free energy profile governing the elementary steps of ion translocation in the pore was computed by means of umbrella sampling simulations. Compared to previous studies, we detected a different dynamic behavior: according to our data hERG is more likely to mediate a conduction mechanism which has been referred to as “single-vacancy-like” by Roux and coworkers (2001), rather then a “knock-on” mechanism. The same protocol was applied to a model of hERG presenting the Gly628Ser mutation, found to be cause of congenital LQTS. The results provided interesting insights about the reason of the malfunctioning of the mutant channel. Since they have critical functions in viruses’ life cycle, viral ion channels, such as M2 proton channel, are considered attractive targets for antiviral therapy. A deep knowledge of the mechanisms that the virus employs to survive in the host cell is of primary importance in the identification of new antiviral strategies. In the second part of this thesis I shed light on the role that M2 plays in the control of electrical potential inside the virus, being the charge equilibration a condition required to allow proton influx. The ion conduction through M2 was simulated using metadynamics technique. Based on our results we suggest that a potential anion-mediated cation-proton exchange, as well as a direct anion-proton exchange could both contribute to explain the activity of the M2 channel.

Enhanced 3-dimensional carbon nanotube based anodes for lithium-ion battery applications

A prototype 3-dimensional (3D) anode, based on multiwall carbon nanotubes (MWCNTs), for Li-ion batteries (LIBs), with potential use in Electric Vehicles (EVs) was investigated. The unique 3D design of the anode allowed much higher areal mass density of MWCNTs as active materials, resulting in more amount of Li+ ion intake, compared to that of a conventional 2D counterpart. Furthermore, 3D amorphous Si/MWCNTs hybrid structure offered enhancement in electrochemical response (specific capacity 549 mAhg–1 ). Also, an anode stack was fabricated to further increase the areal or volumetric mass density of MWCNTs. An areal mass density of the anode stack 34.9 mg/cm2 was attained, which is 1,342% higher than the value for a single layer 2.6 mg/cm2. Furthermore, the binder-assisted and hot-pressed anode stack yielded the average reversible, stable gravimetric and volumetric specific capacities of 213 mAhg–1 and 265 mAh/cm3, respectively (at 0.5C). Moreover, a large-scale patterned novel flexible 3D MWCNTs-graphene-polyethylene terephthalate (PET) anode structure was prepared. It generated a reversible specific capacity of 153 mAhg–1 at 0.17C and cycling stability of 130 mAhg –1 up to 50 cycles at 1.7C.

Enhanced 3-Dimensional Carbon Nanotube Based Anodes for Li-ion Battery Applications

A prototype 3-dimensional (3D) anode, based on multiwall carbon nanotubes (MWCNTs), for Li-ion batteries (LIBs), with potential use in Electric Vehicles (EVs) was investigated. The unique 3D design of the anode allowed much higher areal mass density of MWCNTs as active materials, resulting in more amount of Li+ ion intake, compared to that of a conventional 2D counterpart. Furthermore, 3D amorphous Si/MWCNTs hybrid structure offered enhancement in electrochemical response (specific capacity 549 mAhg-1). Also, an anode stack was fabricated to further increase the areal or volumetric mass density of MWCNTs. An areal mass density of the anode stack 34.9 mg/cm2 was attained, which is 1,342% higher than the value for a single layer 2.6 mg/cm2. Furthermore, the binder-assisted and hot-pressed anode stack yielded the average reversible, stable gravimetric and volumetric specific capacities of 213 mAhg-1 and 265 mAh/cm3, respectively (at 0.5C). Moreover, a large-scale patterned novel flexible 3D MWCNTs-graphene-polyethylene terephthalate (PET) anode structure was prepared. It generated a reversible specific capacity of 153 mAhg-1 at 0.17C and cycling stability of 130 mAhg-1 up to 50 cycles at 1.7C.

Vascular Endothelial Growth Factor Increases During Blood-brain Barrier-enhanced Permeability Caused By Phoneutria Nigriventer Spider Venom.

Phoneutria nigriventer spider accidental envenomation provokes neurotoxic manifestations, which when critical, results in epileptic-like episodes. In rats, P. nigriventer venom (PNV) causes blood-brain barrier breakdown (BBBb). The PNV-induced excitotoxicity results from disturbances on Na(+), K(+) and Ca(2+) channels and glutamate handling. The vascular endothelial growth factor (VEGF), beyond its angiogenic effect, also, interferes on synaptic physiology by affecting the same ion channels and protects neurons from excitotoxicity. However, it is unknown whether VEGF expression is altered following PNV envenomation. We found that adult and neonates rats injected with PNV showed immediate neurotoxic manifestations which paralleled with endothelial occludin, β-catenin, and laminin downregulation indicative of BBBb. In neonate rats, VEGF, VEGF mRNA, and Flt-1 receptors, glutamate decarboxylase, and calbindin-D28k increased in Purkinje neurons, while, in adult rats, the BBBb paralleled with VEGF mRNA, Flk-1, and calbindin-D28k increases and Flt-1 decreases. Statistically, the variable age had a role in such differences, which might be due to age-related unequal maturation of blood-brain barrier (BBB) and thus differential cross-signaling among components of the glial neurovascular unit. The concurrent increases in the VEGF/Flt-1/Flk-1 system in the cerebellar neuron cells and the BBBb following PNV exposure might imply a cytokine modulation of neuronal excitability consequent to homeostatic perturbations induced by ion channels-acting PNV neuropeptides. Whether such modulation represents neuroprotection needs further investigation.