Molecular structures of magnesium dichloride sheets and nanoballs

The structures and relative stabilities of (MgCl(2))(n)() sheetlike clusters and nanoballs were studied by quantum chemical methods. The sheets as discrete molecules were studied up to Mg(100)Cl(200). Their stabilities increase systematically as a function of the size of the sheet. Periodic ab initio calculations were performed for (001) monolayer sheets of alpha- and beta-MgCl(2), beta-sheet being slightly favored. Nanoballs were constructed from Archimedean polyhedra, producing tetrahedral, octahedral, and icosahedral symmetries, and were studied up to Mg(60)Cl(120). Nanoballs prefer to take the shape of truncated cuboctahedron (Mg(48)Cl(96)). Comparisons to sheetlike clusters and periodic calculations suggest that magnesium dichloride nanoballs are stable.     

BODIL: a molecular modeling environment for structure-function analysis and drug design

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html     

Low Voltage CMOS Power Amplifier with Rail-to-Rail Input and Output

This paper describes a CMOS power amplifier with rail-to-rail input and output, also suitable for low voltage applications. The amplifier uses Simple Miller Compensation with high bandwidth stage to robustly and power efficiently compensate the amplifier. Circuit also includes a common mode adapter block, based on resistive level shift network, to implement rail-to-rail input and optional adaptive biasing block, which can be used to extend bandwidth of the amplifier for large high frequency inputs in continuous-time applications. Measurement results show that the amplifier is capable of driving heavy resistive and capacitive loads having maximum output current exceeding 100 mA, when driving 1 nF ‖ 10 Ω load from 3.0 V supply. Without adaptive biasing the linear amplifier achieves 5.7 MHz unity gain frequency and 61^∘ phase margin when driving 1 nF ‖ 1 kΩ load, while drawing 2.4 mA from 1.5 V supply.     

Crossover scaling of wavelength selection in directional solidification of binary alloys

We simulate cellular and dendritic growth in directional solidification in dilute binary alloys using a phase-field model solved with adaptive-mesh refinement. The spacing of primary branches is examined for a wide range of thermal gradients and alloy compositions and is found to undergo a maximum as a function of pulling velocity, in agreement with experimental observations. We demonstrate that wavelength selection is unambiguously described by a nontrivial crossover scaling function from the emergence of cellular growth to the onset of dendritic fingers. This result is further validated using published experimental data, which obeys the same scaling function.     

Heat transistor: demonstration of gate-controlled electronic refrigeration

We present experiments on a superconductor-normal-metal electron refrigerator in a regime where single-electron charging effects are significant. The system functions as a heat transistor; i.e., the heat flux out from the normal-metal island can be controlled with a gate voltage. A theoretical model developed within the framework of single-electron tunneling provides a full quantitative agreement with the experiment. This work serves as the first experimental observation of Coulombic control of heat transfer and, in particular, of refrigeration in a mesoscopic system.     

Gold as intermolecular glue: a theoretical study of nanostrips based on quinoline-type monomers

A family of infinite nanostrips is computationally predicted. In it monomers of single, double or triple aromatic rings are linked to each other by strong C-Au-C, C-Au <-- N or N --> Au <-- N bonds. Depending on the geometry of the system and saturation of the bonds, these 1-D nanostrips are found to be insulators, narrow- or zero-gap semiconductors, or metals. The calculated dimerization and polymerization energies suggest clear exothermicity of formation. Varying the nitrogen content in the aromatic ring is found to little affect the geometry, and the 1-D band structure of the strips can be interpreted in a rigid-band picture. The orbital character of the states at the Fermi level has been analyzed. One of the new structures is found to be closely similar to graphene with respect to its band structure properties.     

Modeling the growth processes of polyelectrolyte multilayers using a quartz crystal resonator

The layer-by-layer buildup of chitosan/hyaluronan (CH/HA) and poly(l-lysine)/hyaluronan (PLL/HA) multilayers was followed on a quartz crystal resonator (QCR) in different ionic strengths and at different temperatures. These polyelectrolytes were chosen to demonstrate the method whereby useful information is retrieved from acoustically thick polymer layers during their buildup. Surface acoustic impedance recorded in these measurements gives a single or double spiral when plotted in the complex plane. The shape of this spiral depends on the viscoelasticity of the layer material and regularity of the growth process. The polymer layer is assumed to consist of one or two zones. A mathematical model was devised to represent the separation of the layer to two zones with different viscoelastic properties. Viscoelastic quantities of the layer material and the mode and parameters of the growth process were acquired by fitting a spiral to the experimental data. In all the cases the growth process was mainly exponential as a function of deposition cycles, the growth exponent being between 0.250 and 0.275.     

Stearic acid spin labels in lipid bilayers: insight through atomistic simulations

Spin-labeled stearic acid species are commonly used for electron paramagnetic resonance (EPR) studies of cell membranes to investigate phase transitions, fluidity, and other physical properties. In this paper, we use large-scale molecular dynamics simulations to investigate the position and behavior of nitroxide spin labels attached to stearic acid molecules in dipalmitoylphosphatidylcholine (DPPC) bilayers. The results of these studies are potentially very important for the interpretation of EPR spectra, which rely on assumptions about the position of the label in the membrane. Additionally, we investigate the effect of chirality and ionization of the carboxyl group of the label. For a non-ionized species, we observe that spin-label molecules are even able to make flip-flop transitions between the leaflets of the bilayer. Such transitions have been previously observed only in very rare cases in molecular simulations.     

Hydrolytic reactions of thymidine 5'-o-phenyl-N-alkylphosphoramidates, models of nucleoside 5'-monophosphate prodrugs

To obtain detailed data on the kinetics of hydrolytic reactions of triester-like nucleoside 5'-O-aryl-N-alkylphosphoramidates, potential prodrugs of antiviral nucleoside monophosphates, the hydrolysis of diastereomeric (Rp/Sp) thymidine 5'-{O-phenyl-N-[(1S)-2-oxo-2-methoxy-1-methylethyl]phosphoramidate} (3), a phosphoramidate derived from the methyl ester of L-alanine, has been followed by reversed-phase HPLC over the range from Ho=0 to pH 8 at 90 degrees C. According to the time-dependent product distributions, the hydrolysis of 3 proceeds at pH<4 by two parallel routes, namely by nucleophilic displacement of the alaninyl ester moiety by a water molecule and by hydrolysis of the carboxylic ester linkage that allows intramolecular attack of the carboxy group on the phosphorus atom, thereby resulting in the departure of either thymidine or phenol without marked accumulation of any intermediates. Both routes represent about half of the overall disappearance of 3. The departure of phenol eventually leads to the formation of thymidine 5'-phosphate. At pH>5, the predominant reaction is hydrolysis of the carboxylic ester linkage followed by intramolecular displacement of a phenoxide ion by the carboxylate ion and hydrolysis of the resulting cyclic mixed anhydride into an acyclic diester-like thymidine 5'-phosphoramidate. The latter product accumulated quantitatively without any indication of further decomposition. Hydroxide-ion-catalyzed P--OPh bond cleavage of the starting material 3 occurred as a side reaction. Comparative measurements with thymidine 5'-{N-[(1S)-2-oxo-2-methoxy-1-methylethyl]phosphoramidate} (4) revealed that, under acidic conditions, this diester-like compound is hydrolyzed by P--N bond cleavage three orders of magnitude more rapidly than the triester-like 3. At pH>5, the stability order is reversed, with 3 being hydrolyzed six times as rapidly as 4. Mechanisms of the partial reactions are discussed.