DNA-Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.

First, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.

Using low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.

For effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 μL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.

With the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.

As differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.

Mercados financieros: análisis fundamental y técnico

Explicación de conceptos claves relacionados con los mercados financieros desde una perspectiva simple y dirigida a personas sin grandes conocimientos de la materia.

Fundamental aspects of the feeding of the amphipod Gammarus (R.) balcanicus (Crustacea, Amphipoda). [Translation from: Nauchn.Dokl.vyssh.Shkoly (Biol.Nauk) 1970(7) 12-16, 1970]

The amphipods are major food items for many commercial fishes, and they are used as protein food for agricultural animals. In the present paper are presented the results of four-year observations on the feeding of Gammarus balcanicus in nature and in an aquarium. Among the studied aspects were the dependence of daily food ration on sex and physiological state (with and without eggs) and feeding on different kinds of plant food. The study concludes that Gammarus balcanicus willingly feed on soft half-decayed plant residues; into their ration also enters food of animal origin. In contrast to other amphipods, G. balcanicus eats representatives of its own species very rarely, and only dead or immobile ones.

Continuous stochastic processes

A general review of stochastic processes is given in the introduction; definitions, properties and a rough classification are presented together with the position and scope of the author's work as it fits into the general scheme.

The first section presents a brief summary of the pertinent analytical properties of continuous stochastic processes and their probability-theoretic foundations which are used in the sequel.

The remaining two sections (II and III), comprising the body of the work, are the author's contribution to the theory. It turns out that a very inclusive class of continuous stochastic processes are characterized by a fundamental partial differential equation and its adjoint (the Fokker-Planck equations). The coefficients appearing in those equations assimilate, in a most concise way, all the salient properties of the process, freed from boundary value considerations. The writer’s work consists in characterizing the processes through these coefficients without recourse to solving the partial differential equations.

First, a class of coefficients leading to a unique, continuous process is presented, and several facts are proven to show why this class is restricted. Then, in terms of the coefficients, the unconditional statistics are deduced, these being the mean, variance and covariance. The most general class of coefficients leading to the Gaussian distribution is deduced, and a complete characterization of these processes is presented. By specializing the coefficients, all the known stochastic processes may be readily studied, and some examples of these are presented; viz. the Einstein process, Bachelier process, Ornstein-Uhlenbeck process, etc. The calculations are effectively reduced down to ordinary first order differential equations, and in addition to giving a comprehensive characterization, the derivations are materially simplified over the solution to the original partial differential equations.

In the last section the properties of the integral process are presented. After an expository section on the definition, meaning, and importance of the integral process, a particular example is carried through starting from basic definition. This illustrates the fundamental properties, and an inherent paradox. Next the basic coefficients of the integral process are studied in terms of the original coefficients, and the integral process is uniquely characterized. It is shown that the integral process, with a slight modification, is a continuous Markoff process.

The elementary statistics of the integral process are deduced: means, variances, and covariances, in terms of the original coefficients. It is shown that an integral process is never temporally homogeneous in a non-degenerate process.

Finally, in terms of the original class of admissible coefficients, the statistics of the integral process are explicitly presented, and the integral process of all known continuous processes are specified.

I. Numerical solution of exact pair equations. II. Numerical solution of first-order pair equations

Part I

Numerical solutions to the S-limit equations for the helium ground state and excited triplet state and the hydride ion ground state are obtained with the second and fourth difference approximations. The results for the ground states are superior to previously reported values. The coupled equations resulting from the partial wave expansion of the exact helium atom wavefunction were solved giving accurate S-, P-, D-, F-, and G-limits. The G-limit is -2.90351 a.u. compared to the exact value of the energy of -2.90372 a.u.

Part II

The pair functions which determine the exact first-order wavefunction for the ground state of the three-electron atom are found with the matrix finite difference method. The second- and third-order energies for the (1s1s)¹S, (1s2s)³S, and (1s2s)¹S states of the two-electron atom are presented along with contour and perspective plots of the pair functions. The total energy for the three-electron atom with a nuclear charge Z is found to be E(Z) = -1.125•Z² +1.022805•Z-0.408138-0.025515•(1/Z)+O(1/Z²)a.u.

Co-incineração de pneus com resíduos sólidos urbanos

O aumento da população, o crescimento das grandes cidades, da industrialização e do consumo, tem trazido preocupação com relação a sustentabilidade quanto à disponibilidade energética e quanto à destinação dos resíduos sólidos urbanos gerados. Dessa forma, é fundamental realizarem-se os estudos visando novas formas de reutilização dos resíduos gerados pelas atividades industriais. Os resíduos sólidos urbanos e os pneus inservíveis gerados trazem conseqüências ao meio ambiente e às populações quando destinados inadequadamente. A destinação final dos resíduos sólidos urbanos é complexa, sendo sempre um grande desafio para as administrações públicas. Com a Política Nacional de Resíduos Sólidos (instituída pela Lei n 12.305/2010), tem-se um marco da preservação ambiental, coma a gestão e gerenciamento de resíduos sólidos, com a ordem de prioridade: não geração, redução, reutilização, reciclagem, tratamento dos resíduos sólidos e disposição final ambientalmente adequada dos rejeitos e prevê, de forma inteligente, a atribuição aos fabricantes de responsabilidade pelo retorno de produtos descartados pelos consumidores. Uma alternativa para minimizar estes aspectos e impactos ambientais é o tratamento térmico com aproveitamento energético. Este processo contribui para mais uma solução de destinação dos resíduos, proporcionado uma redução das áreas a serem utilizadas nos aterros sanitários e contribuindo como uma fonte de geração de energia elétrica

Polaron hopping in olivine phosphates studied by nuclear resonant scattering

Valence fluctuations of Fe²⁺ and Fe³⁺ were studied in a solid solution of Li_xFePO₄ by nuclear resonant forward scattering of synchrotron x rays while the sample was heated in a diamond-anvil pressure cell. The spectra acquired at different temperatures and pressures were analyzed for the frequencies of valence changes using the Blume-Tjon model of a system with a fluctuating Hamil- tonian. These frequencies were analyzed to obtain activation energies and an activation volume for polaron hopping. There was a large suppression of hopping frequency with pressure, giving an anomalously large activation volume. This large, positive value is typical of ion diffusion, which indicates correlated motions of polarons, and Li⁺ ions that alter the dynamics of both.

In a parallel study of Na_xFePO₄, the interplay between sodium ordering and electron mobility was investigated using a combination of synchrotron x-ray diffraction and nuclear resonant scattering. Conventional Mossbauer spectra were collected while the sample was heated in a resistive furnace. An analysis of the temperature evolution of the spectral shapes was used to identify the onset of fast electron hopping and determine the polaron hopping rate. Synchrotron x-ray diffraction measurements were carried out in the same temperature range. Reitveld analysis of the diffraction patterns was used to determine the temperature of sodium redistribution on the lattice. The diffraction analysis also provides new information about the phase stability of the system. The temperature evolution of the iron site occupancies from the Mossbauer measurements, combined with the synchrotron diffraction results give strong evidence for a relationship between the onset of fast electron dynamics and the redistribution of sodium in the lattice.

Measurements of activation barriers for polaron hopping gave fundamental insights about the correlation between electronic carriers and mobile ions. This work established that polaron-ion interactions can alter the local dynamics of electron and ion transport. These types of coupled processes may be common in many materials used for battery electrodes, and new details concerning the influence of polaron-ion interactions on the charge dynamics are relevant to optimizing their electrochemical performance.

Vectorial solution of Kukhtarev equations for doubly doped crystals and optimal choice of recording directions in nonvolatile holographic storage

Vectorial Kukhtarev equations modified for the nonvolatile holographic recording in doubly doped crystals are analyzed, in which the bulk photovoltaic effect and the external electrical field are both considered. On the basis of small modulation approximation, both the analytic solution to the space-charge field with time in the recording phase and in the readout phase are deduced. The analytic solutions can be easily simplified to adapt the one-center model, and they have the same analytic expressions given those when the grating vector is along the optical axis. Based on the vectorial analyses of the band transport model an optimal recording direction is given to maximize the refractive index change in doubly doped LiNbO3:Fe: Mn crystals. (c) 2007 Optical Society of America.

Some theorems in classical elastodynamic

This investigation is concerned with various fundamental aspects of the linearized dynamical theory for mechanically homogeneous and isotropic elastic solids. First, the uniqueness and reciprocal theorems of dynamic elasticity are extended to unbounded domains with the aid of a generalized energy identity and a lemma on the prolonged quiescence of the far field, which are established for this purpose. Next, the basic singular solutions of elastodynamics are studied and used to generate systematically Love's integral identity for the displacement field, as well as an associated identity for the field of stress. These results, in conjunction with suitably defined Green's functions, are applied to the construction of integral representations for the solution of the first and second boundary-initial value problem. Finally, a uniqueness theorem for dynamic concentrated-load problems is obtained.

Fast Lattice Green's Function Methods for Viscous Incompressible Flows on Unbounded Domains

In this thesis, a collection of novel numerical techniques culminating in a fast, parallel method for the direct numerical simulation of incompressible viscous flows around surfaces immersed in unbounded fluid domains is presented. At the core of all these techniques is the use of the fundamental solutions, or lattice Green’s functions, of discrete operators to solve inhomogeneous elliptic difference equations arising in the discretization of the three-dimensional incompressible Navier-Stokes equations on unbounded regular grids. In addition to automatically enforcing the natural free-space boundary conditions, these new lattice Green’s function techniques facilitate the implementation of robust staggered-Cartesian-grid flow solvers with efficient nodal distributions and fast multipole methods. The provable conservation and stability properties of the appropriately combined discretization and solution techniques ensure robust numerical solutions. Numerical experiments on thin vortex rings, low-aspect-ratio flat plates, and spheres are used verify the accuracy, physical fidelity, and computational efficiency of the present formulations.

I. Fundamental limitations in microelectronics. II. Power Schottky diode design and comparison with the junction diode. III. Permittivity of strontium titanate

Part I

The physical phenomena which will ultimately limit the packing density of planar bipolar and MOS integrated circuits are examined. The maximum packing density is obtained by minimizing the supply voltage and the size of the devices. The minimum size of a bipolar transistor is determined by junction breakdown, punch-through and doping fluctuations. The minimum size of a MOS transistor is determined by gate oxide breakdown and drain-source punch-through. The packing density of fully active bipolar or static non-complementary MOS circuits becomes limited by power dissipation. The packing density of circuits which are not fully active such as read-only memories, becomes limited by the area occupied by the devices, and the frequency is limited by the circuit time constants and by metal migration. The packing density of fully active dynamic or complementary MOS circuits is limited by the area occupied by the devices, and the frequency is limited by power dissipation and metal migration. It is concluded that read-only memories will reach approximately the same performance and packing density with MOS and bipolar technologies, while fully active circuits will reach the highest levels of integration with dynamic MOS or complementary MOS technologies.

Part II

Because the Schottky diode is a one-carrier device, it has both advantages and disadvantages with respect to the junction diode which is a two-carrier device. The advantage is that there are practically no excess minority carriers which must be swept out before the diode blocks current in the reverse direction, i.e. a much faster recovery time. The disadvantage of the Schottky diode is that for a high voltage device it is not possible to use conductivity modulation as in the p i n diode; since charge carriers are of one sign, no charge cancellation can occur and current becomes space charge limited. The Schottky diode design is developed in Section 2 and the characteristics of an optimally designed silicon Schottky diode are summarized in Fig. 9. Design criteria and quantitative comparison of junction and Schottky diodes is given in Table 1 and Fig. 10. Although somewhat approximate, the treatment allows a systematic quantitative comparison of the devices for any given application.

Part III

We interpret measurements of permittivity of perovskite strontium titanate as a function of orientation, temperature, electric field and frequency performed by Dr. Richard Neville. The free energy of the crystal is calculated as a function of polarization. The Curie-Weiss law and the LST relation are verified. A generalized LST relation is used to calculate the permittivity of strontium titanate from zero to optic frequencies. Two active optic modes are important. The lower frequency mode is attributed mainly to motion of the strontium ions with respect to the rest of the lattice, while the higher frequency active mode is attributed to motion of the titanium ions with respect to the oxygen lattice. An anomalous resonance which multi-domain strontium titanate crystals exhibit below 65°K is described and a plausible mechanism which explains the phenomenon is presented.

Solar flare particle propagation--comparison of a new analytic solution with spacecraft measurements

A new analytic solution has been obtained to the complete Fokker-Planck equation for solar flare particle propagation including the effects of convection, energy-change, corotation, and diffusion with ĸ_r = constant and ĸ_Ɵ ∝ r². It is assumed that the particles are injected impulsively at a single point in space, and that a boundary exists beyond which the particles are free to escape. Several solar flare particle events have been observed with the Caltech Solar and Galactic Cosmic Ray Experiment aboard OGO-6. Detailed comparisons of the predictions of the new solution with these observations of 1-70 MeV protons show that the model adequately describes both the rise and decay times, indicating that ĸ_r = constant is a better description of conditions inside 1 AU than is ĸ_r ∝ r. With an outer boundary at 2.7 AU, a solar wind velocity of 400 km/sec, and a radial diffusion coefficient ĸ_r ≈ 2-8 x 10²⁰ cm²/sec, the model gives reasonable fits to the time-profile of 1-10 MeV protons from "classical" flare-associated events. It is not necessary to invoke a scatter-free region near the sun in order to reproduce the fast rise times observed for directly-connected events. The new solution also yields a time-evolution for the vector anisotropy which agrees well with previously reported observations.

In addition, the new solution predicts that, during the decay phase, a typical convex spectral feature initially at energy T_o will move to lower energies at an exponential rate given by T_KINK = T_oexp(-t/Ƭ_KINK). Assuming adiabatic deceleration and a boundary at 2.7 AU, the solution yields Ƭ_KINK ≈ 100h, which is faster than the measured ~200h time constant and slower than the adiabatic rate of ~78h at 1 AU. Two possible explanations are that the boundary is at ~5 AU or that some other energy-change process is operative.

Approximate analytical description for fundamental-mode fields of graded-index fibers: Beyond the Gaussian approximation

An approximate analytical description for fundamental-mode fields of graded-index fibers is explicitly presented by use of the power-series expansion method, the maximum-value condition at the fiber axis, the decay properties of fundamental-mode fields at large distance from the fiber axis, and the approximate modal parameters U obtained from the Gaussian approximation. This analytical description is much more accurate than the Gaussian approximation and at the same time keep the simplicity of the latter. As two special examples, we present the approximate analytical formulas for the fundamental-mode fields of a step profile fiber and a Gaussian profile fiber, and we find that they are both highly accurate in the single-mode range by comparing them with the corresponding exact solutions.