A unified theory of free energy functionals and applications to diffusion.

SignificanceThe free energy functional is a central component of continuum dynamical models used to describe phase transitions, microstructural evolution, and pattern formation. However, despite the success of these models in many areas of physics, chemistry, and biology, the standard free energy frameworks are frequently characterized by physically opaque parameters and incorporate assumptions that are difficult to assess. Here, we introduce a mathematical formalism that provides a unifying umbrella for constructing free energy functionals. We show that Ginzburg-Landau framework is a special case of this umbrella and derive a generalization of the widely employed Cahn-Hilliard equation. More broadly, we expect the framework will also be useful for generalizing higher-order theories, establishing formal connections to microscopic physics, and coarse graining.

Characterizing randomness in photonic glasses using autocorrelation functions of two-dimensional images.

We have developed a simple method to quantify randomness in photonic glasses in relation to the ideal random limit, using autocorrelation functions obtained from two-dimensional images. In our case, the photonic glasses consist of randomly packed silica microspheres which serve as a model system representing isotropic random media. Conventional methods of characterizing randomness in photonic materials often entail technical complexities, such as chemical functionalization, three-dimensional rendering, and particle tracking. Our method circumvents these difficulties based on a mathematical relation that we derive between the autocorrelation function and the radial distribution function. This relation enables us to find the autocorrelation function in the ideal random limit. The autocorrelation function of experimentally fabricated photonic glasses is then obtained from images of a single cross-sectional plane and directly compared to that of the ideal limit. The comparison shows that the autocorrelation function of real structures deviates only slightly from the ideal limit. We find that the deviation can be explained in part by the microsphere polydispersity. Our general method would be useful in characterizing a large class of photonic random media, encompassing biological materials, radiative cooling coatings, and random lasing photonic glasses.

Clinical risk factors for acute ischaemic and haemorrhagic stroke in patients with infective endocarditis.

BACKGROUND: Stroke as a complication of infective endocarditis portends a poor prognosis, yet risk factors for stroke subtypes have not been well defined. AIM: To identify risk factors associated with ischaemic and haemorrhagic strokes. METHODS: A retrospective patient chart review was performed at a single US academic centre to identify risk factors and imaging for patients who were 18 years or older with infectious endocarditis (IE) and stroke diagnoses. Differences in patient characteristics by stroke status were assessed using univariate analysis, χ2 or student's t-test as well as logistic regression models for multivariable analyses and correlation matrices to identify possible collinearity between variables and to obtain odds ratios (OR) and their 95% confidence intervals. RESULTS: A final sample of 1157 participants was used for this analysis. The total number of non-surgical strokes was 178, with a prevalence of 15.4% (78% ischaemic, 10% parenchymal haemorrhages, 8% subarachnoid haemorrhages and 4% mixed ischaemic/haemorrhagic). Multivariate risk factors for ischaemic stroke included prior stroke (OR 2.0, 1.3-3.1), Staphylococcus infection (OR 2.0, 1.3-3.0), mitral vegetations (OR 2.2, 1.4-3.3) and valvular abscess (OR 2.7, 1.7-4.3). Risk factors for haemorrhagic stroke included fungal infection (OR 6.4, 1.2-34.0), male gender (OR 3.5, 1.4-8.3) and rheumatic heart disease (OR 3.3, 1.1-10.4). CONCLUSION: Among patients with IE, there exist characteristics that relate differentially to ischaemic and haemorrhagic stroke risk.

Control of Randomness in Microsphere-Based Photonic Crystals Assembled by Langmuir-Blodgett Process.

Photonic structures in biological systems typically exhibit an appreciable level of disorder within their periodic framework. However, how such disorder within the ordered framework renders unique optical properties has not been fully understood. Toward the goal of improving this understanding, we have investigated Langmuir-Blodgett assembly of microspheres to controllably introduce randomness to photonic structures. We theoretically modeled the assembly process and determined a condition for surface pressure and substrate pulling speed that results in maximum structural order. For each surface pressure, there is an optimum pulling speed and vice versa. Along the trajectory defined by the optimum condition, however, the structural order decreases moderately as the pulling speed increases. This moderate decrease in structural order would be useful for controlled introduction of randomness into the periodic structures. Departing from the trajectory, our experiment reveals that a small change in pulling speed at a given surface pressure can significantly disrupt the structural order. For multilayer assembly, we find that, at a fixed pulling speed, the surface pressure should increase as the number of layers increases to achieve maximum structural order. In totality, we quantitatively present the optimum trajectories for the nth layer assembly relating surface pressure and pulling speed.

Symmetry-breaking nanostructures on crystalline silicon for enhanced light trapping in thin film solar cells.

We introduce a new approach to systematically break the symmetry in periodic nanostructures on a crystalline silicon surface. Our focus is inverted nanopyramid arrays with a prescribed symmetry. The arrangement and symmetry of nanopyramids are determined by etch mask design and its rotation with respect to the [110] orientation of the Si(001) substrate. This approach eliminates the need for using expensive off-cut silicon wafers. We also make use of low-cost, manufacturable, wet etching steps to fabricate the nanopyramids. Our experiment and computational modeling demonstrate that the symmetry breaking can increase the photovoltaic efficiency in thin-film silicon solar cells. For a 10-micron-thick active layer, the efficiency improves from 27.0 to 27.9% by enhanced light trapping over the broad sunlight spectrum. Our computation further reveals that this improvement would increase from 28.1 to 30.0% in the case of a 20-micron-thick active layer, when the unetched area between nanopyramids is minimized with over-etching. In addition to the immediate benefit to solar photovoltaics, our method of symmetry breaking provides a useful experimental platform to broadly study the effect of symmetry breaking on spectrally tuned light absorption and emission.

On coarse projective integration for atomic deposition in amorphous systems.

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the "equation-free" framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of this technique in realistic settings is the "lifting" operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO2 using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.

Effect of wall-molecule interactions on electrokinetic transport of charged molecules in nanofluidic channels during FET flow control.

The interactions between charged molecules and channel surfaces are expected to significantly influence the electrokinetic transport of molecules and their separations in nanochannels. This study reports the effect of wall-molecule interactions on flow control of negatively charged Alexa 488 and positively charged Rhodamine B dye molecules in an array of nanochannels (100 nm wx 500 nm dx 14 mm l) embedded in fluidic field effect transistors (FETs). For FET flow control, a third electrical potential, known as a gate bias, is applied to the channel walls to manipulate their zeta-potential. Electroosmotic flow of charged dye molecules is accelerated or reversed according to the polarity and magnitude of the gate bias. During FET flow control, we monitor how the electrostatic interaction between charged dye molecules and channel walls affects the apparent velocity of molecules, using laser-scanning confocal fluorescence microscopy. We observe that the changes in flow speed and direction of negatively charged Alexa 488 is much more pronounced than that of positively charged Rhodamine B in response to the gate bias that causes either repulsive or attractive electrostatic interactions. This observation is supported by calculations of concentration-weighted velocity profiles of the two dye molecules during FET flow control. The velocity profile of negatively charged Alexa 488 is much more pronounced at the center of each nanochannel than near its walls since Alexa 488 molecules are repelled from negatively charged channel walls. This pronounced center velocity further responds to the gate bias, increasing the average velocity by as much as 23% when -30 V is applied to the gate (zeta-potential = -80.6 mV). In contrast, the velocity profile of positively charged Rhodamine B is dispersed over the entire channel width due to dye-wall attraction and adsorption. Our experimental observations and calculations support the hypothesis that valence-charge-dependent electrostatic interaction and its manipulation by the gate bias would enhance molecular separations of differentially charged molecules in nanofluidic FETs.

Impact of leakage current and electrolysis on FET flow control and pH changes in nanofluidic channels.

We have fabricated multiple-internal-reflection Si infrared waveguides integrated with an array of nanochannels sealed with an optically transparent top cover. The channel walls consist of a thin layer of SiO2 for electrical insulation, and gate electrodes surround the channel sidewalls and bottom to manipulate their surface charge and zeta-potential in a fluidic field effect transistor (FET) configuration. This nanofluidic device is used to probe the transport of charged molecules (Alexa 488) and to measure the pH shift in nanochannels in response to an electrical potential applied to the gate. During gate biasing for FET operation, laser-scanning confocal fluorescence microscopy (LS-CFM) is used to visualize the flow of fluorescent dye molecules (Alexa 488), and multiple internal reflection-Fourier transform infrared spectroscopy (MIR-FTIRS) is used to probe the characteristic vibrational modes of fluorescein pH indicator and measure the pH shift. The electroosmotic flow of Alexa 488 is accelerated in response to a negative gate bias, whereas its flow direction is reversed in response to a positive gate bias. We also measure that the pH of buffered electrolyte solutions shifts by as much as a pH unit upon applying the gate bias. With prolonged application of gate bias, however, we observe that the initial response in flow speed and direction as well as pH shift becomes reversed. We attribute these anomalous flow and pH shift characteristics to a leakage current that flows from the Si gate through the thermally grown SiO2 to the electrolyte solution.

Experimentally and theoretically observed native pH shifts in a nanochannel array.

Lab-on-a-chip (LOC) technology provides a powerful platform for simultaneous separation, purification, and identification of low concentration multicomponent mixtures. As the characteristic dimension of LOC devices decreases down to the nanoscale, the possibility of containing an entire lab on a single chip is becoming a reality. This research examines one of the unique physical characteristics of nanochannels, in which native pH shifts occur. As a result of the electrical double layer taking up a significant portion of a 100 nm wide nanochannel, electroneutrality no longer exists in the channel causing a radial pH gradient. This work describes experimentally observed pH shifts as a function of ionic strength using the fluorescent pH indicator 5-(and-6)-carboxy SNARF-1 and compares it to a model developed using Comsol Multiphysics. At low ionic strengths (approximately 3 mM) the mean pH shift is approximately 1 pH unit whereas at high ionic strengths (approximately 150 mM) the mean pH shift is reduced to 0.1 pH units. An independent analysis using fluorescein pH indicator is also presented supporting these findings. Two independent non-linear simulations coupling the Nernst-Planck equation describing transport in ionic solutions subjected to an electric field and Poisson's equation to describe the electric field as it relates to the charge distribution are solved using a finite element solver. In addition, the effects of chemical activities are considered in the simulations. The first numerical simulation is based on a surface zeta-potential which significantly underestimates the experimental results for most ionic strengths. A modified model assuming that SNARF and fluorescein molecules are able to diffuse into the hydrolyzed SiO2 phase, and in the case of the SNARF molecule, able to bind to neutral regions of the SiO2 phase agrees quantitatively with experimental results.

Synthesis and Characterization of Germanium Coordination Compounds for Production of Germanium Nanomaterials.

A series of novel germanium(II) precursors was synthesized to initiate an investigation between the precursors' structures and the morphologies of the resulting nanoparticles. The precursors were synthesized from the reaction of Ge[N(SiMe3)2]2 or [Ge(OBut)2]2 and the appropriate ligand: N,N'-dibenzylethylenediamine (H2-DBED), tert-butanol (H-OBut), 2,6-di-methyl phenol (H-DMP), 2,6-di-phenyl phenol (H-DPP), tert-butyldimethylsilanol (H-DMBS), triphenylsilanol (H-TPS), triphenylsilanethiol (H-TPST), and benzenethiol (H-PS). The products were identified as: [Ge(µc-DBED)]2 (1, µc= bridging chelating), [Ge(µ-DMP)(DMP)]2 (2), Ge(DPP)2 (3), [Ge(µ-OBut)(DMBS)]2, (4), [Ge(µ-DMBS)(DMBS)]2 (5), Ge(TPS)3(H) (6), [Ge(µ-TPST)(TPST)]2 (7), and Ge(PS)4 (8). The Ge(II) metal centers were found to adopt a pyramidal geometry for 1, 2, 4, 5, 7, a bent arrangement for 3, and a tetrahedral coordination for the Ge(IV) species 6 and 8. Using a simple solution precipitation methodology, Ge(0) nanomaterials were isolated as dots and wires for the majority of precursors. Compound 7 led to the isolation of amorphous GexSy. The nanomaterials isolated were characterized by TEM, EDS, and powder XRD. A correlation between the precursor's arrangement and final observed nanomorphology was proffered as part of the 'precursor structure affect' phenomenon.

Monitoring FET flow control and wall adsorption of charged fluorescent dye molecules in nanochannels integrated into a multiple internal reflection infrared waveguide.

Using Si as the substrate, we have fabricated multiple internal reflection infrared waveguides embedded with a parallel array of nanofluidic channels. The channel width is maintained substantially below the mid-infrared wavelength to minimize infrared scattering from the channel structure and to ensure total internal reflection at the channel bottom. A Pyrex slide is anodically bonded to the top of the waveguide to seal the nanochannels, while simultaneously enabling optical access in the visible range from the top. The Si channel bottom and sidewalls are thermally oxidized to provide an electrically insulating barrier, and the Si substrate surrounding the insulating SiO(2) layer is selectively doped to function as a gate. For fluidic field effect transistor (FET) control, a DC potential is applied to the gate to manipulate the surface charge on SiO(2) channel bottom and sidewalls and therefore their zeta-potential. Depending on the polarity and magnitude, the gate potential can accelerate, decelerate, or reverse the flow. Here, we demonstrate that this nanofluidic infrared waveguide can be used to monitor the FET flow control of charged, fluorescent dye molecules during electroosmosis by multiple internal reflection Fourier transform infrared spectroscopy. Laser scanning confocal fluorescence microscopy is simultaneously used to provide a comparison and verification of the IR analysis. Using the infrared technique, we probe the vibrational modes of dye molecules, as well as those of the solvent. The observed infrared absorbance accounts for the amount of dye molecules advancing or retracting in the nanochannels, as well as adsorbing to and desorbing from the channel bottom and sidewalls.

Water-soluble germanium(0) nanocrystals: cell recognition and near-infrared photothermal conversion properties.

Surfactant-passivated germanium nanocrystals (Ge(0) NCs) 3-5 nm in diameter were synthesized and encapsulated with functionalized phospholipids to yield water-soluble Ge(0) NCs. Upon encapsulation, the NCs retained their cubic crystalline phase and displayed good resistance to oxidation, as determined by transmission electron microscopy and X-ray photoelectron spectroscopy. As a test of their cell compatibility, the ability of carboxyfluorescein (CF)-labeled dinitrophenyl (DNP)-functionalized Ge(0) NCs to crosslink dinitrophenol-specific immunoglobulin E antibodies on the surface of mast cells (RBL-2H3) was examined in vitro. Treatment with a multivalent DNP antigen (i.e., DNP-Ge(0) NCs or CF-DNP-Ge(0) NCs) caused crosslinking of FcepsilonRI receptors and cellular responses, which were evaluated with morphological and colorimetric assays and live-cell fluorescence microscopy. Incubation of RBL-2H3 cells with Ge(0) NCs for approximately 24 h gave less than a 2 % increase in cell death as compared to DNP-functionalized bovine serum albumin. When irradiated with near-infrared (NIR) radiation (lambda(exc)=770 nm, 1.1 W cm(-2)) from a continuous-wave Ti:sapphire laser, the bulk-solution temperature of a toluene solution containing 20 mg mL(-1) Ge(0) NCs increased by approximately 35 degrees C within 5 min. Phospholipid-encapsulated water-soluble Ge(0) NCs at concentrations of 1.0 mg mL(-1) also displayed stable photothermal behavior under repetitive and prolonged NIR laser exposures in water, to yield a temperature increase of approximately 20 degrees C within 5 min (lambda(exc)=770 nm, 0.9 W cm(-2)). The photothermal efficiency of water-soluble Ge(0) NCs compares favorably with a recent report for Au nanoshells.

Solution synthesis of germanium nanowires using a Ge2+ alkoxide precursor.

A simple solution synthesis of germanium (Ge0) nanowires under mild conditions (<400 degrees C and 1 atm) was demonstrated using germanium 2,6-dibutylphenoxide, Ge(DBP)2 (1), as the precursor where DBP = 2,6-OC6H3(C(CH3)3)2. Compound 1, synthesized from Ge(NR2)2 where R = SiMe3 and 2 equiv of DBP-H, was characterized as a mononuclear species by single-crystal X-ray diffraction. Dissolution of 1 in oleylamine, followed by rapid injection into a 1-octadecene solution heated to 300 degrees C under an atmosphere of Ar, led to the formation of Ge0 nanowires. The Ge0 nanowires were characterized by transmission electron microscopy (TEM), X-ray diffraction analysis, and Fourier transform infrared spectroscopy. These characterizations revealed that the nanowires are single crystalline in the cubic phase and coated with oleylamine surfactant. We also observed that the nanowire length (0.1-10 microm) increases with increasing temperature (285-315 degrees C) and time (5-60 min). Two growth mechanisms are proposed based on the TEM images intermittently taken during the growth process as a function of time: (1) self-seeding mechanism where one of two overlapping nanowires serves as a seed, while the other continues to grow as a wire; and (2) self-assembly mechanism where an aggregate of small rods (<50 nm in diameter) recrystallizes on the tip of a longer wire, extending its length.

Anhydrous solution synthesis of germanium nanocrystals from the germanium(II) precursor Ge[N(SiMe3)2]2.

A convenient, simple, single-source solution synthesis of Ge nanocrystals via thermal reduction of Ge(II) precursor Ge[N(SiMe3)2]2 in a non-coordinating solvent at 300 degrees C and 1 atm Ar is described.

Adsorption kinetics of 1-alkanethiols on hydrogenated Ge(111).

We have investigated the liquid-phase self-assembly of 1-alkanethiols (HS(CH2)n-1CH3, n = 8, 16, and 18) on hydrogenated Ge(111), using attenuated total reflection Fourier transform infrared spectroscopy as well as water contact angle measurements. The infrared absorbance of C-H stretching modes of alkanethiolates on Ge, in conjunction with water contact angle measurements, demonstrates that the final packing density is a function of alkanethiol concentration in 2-propanol and its chain length. High concentration and long alkyl chain increase the steady-state surface coverage of alkanethiolates. A critical chain length exists between n = 8 and 16, above which the adsorption kinetics is comparable for all long alkyl chain 1-alkanethiols. The steady-state coverage of hexadecanethiolates, representing long-chain alkanethiolates, reaches a maximum at approximately 5.9 x 10(14) hexadecanethiolates/cm2 in 1 M solution. The characteristic time constant to reach a steady state also decreases with increasing chain length. This chain length dependence is attributed to the attractive chain-to-chain interaction in long-alkyl-chain self-assembled monolayers, which reduces the desorption-to-adsorption rate ratio (kd/ka). We also report the adsorption and desorption rate constants (ka and kd) of 1-hexadecanethiol on hydrogenated Ge(111) at room temperature. The alkanethiol adsorption is a two-step process following a first-order Langmuir isotherm: (1) fast adsorption with ka = 2.4 +/- 0.2 cm3/(mol s) and kd = (8.2 +/- 0.5) x 10(-6)(s-1); (2) slow adsorption with ka = 0.8 +/- 0.5 cm3/(mol s) and kd = (3 +/- 2) x 10(-6) s(-1).

Peering into the self-assembly of surfactant templated thin-film silica mesophases.

It is now recognized that self-assembly is a powerful synthetic approach to the fabrication of nanostructures with feature sizes smaller than achievable with state of the art lithography and with a complexity approaching that of biological systems. For example, recent research has shown that silica/surfactant self-assembly combined with evaporation (so-called evaporation induced self-assembly EISA) can direct the formation of porous and composite thin-film mesostructures characterized by precise periodic arrangements of inorganic and organic constituents on the 1-50-nm scale. Despite the potential utility of these films for a diverse range of applications such as sensors, membranes, catalysts, waveguides, lasers, nano-fluidic systems, and low dielectric constant (so-called low k) insulators, the mechanism of EISA is not yet completely understood. Here, using time-resolved grazing incidence small-angle X-ray scattering (GISAXS) combined with gravimetric analysis and infrared spectroscopy, we structurally and compositionally characterize in situ the evaporation induced self-assembly of a homogeneous silica/surfactant/solvent solution into a highly ordered surfactant-templated mesostructure. Using CTAB (cetyltrimethylammonium bromide) as the structure-directing surfactant, a two-dimensional (2-D) hexagonal thin-film mesophase (p6mm) with cylinder axes oriented parallel to the substrate surface forms from an incipient lamellar mesophase through a correlated micellar intermediate. Comparison with the corresponding CTAB/water/alcohol system (prepared without silica) shows that, for acidic conditions in which the siloxane condensation rate is minimized, the hydrophilic and nonvolatile silicic acid components replace water maintaining a fluidlike state that avoids kinetic barriers to self-assembly.