Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast

A combined multidimensional chromatography-mass spectrometry approach known as "MudPIT" enables rapid identification of proteins that interact with a tagged bait while bypassing some of the problems associated with analysis of polypeptides excised from SDS-polyacrylamide gels. However, the reproducibility, success rate, and applicability of MudPIT to the rapid characterization of dozens of proteins have not been reported. We show here that MudPIT reproducibly identified bona fide partners for budding yeast Gcn5p. Additionally, we successfully applied MudPIT to rapidly screen through a collection of tagged polypeptides to identify new protein interactions. Twenty-five proteins involved in transcription and progression through mitosis were modified with a new tandem affinity purification (TAP) tag. TAP-MudPIT analysis of 22 yeast strains that expressed these tagged proteins uncovered known or likely interacting partners for 21 of the baits, a figure that compares favorably with traditional approaches. The proteins identified here comprised 102 previously known and 279 potential physical interactions. Even for the intensively studied Swi2p/Snf2p, the catalytic subunit of the Swi/Snf chromatin remodeling complex, our analysis uncovered a new interacting protein, Rtt102p. Reciprocal tagging and TAP-MudPIT analysis of Rtt102p revealed subunits of both the Swi/Snf and RSC complexes, identifying Rtt102p as a common interactor with, and possible integral component of, these chromatin remodeling machines. Our experience indicates it is feasible for an investigator working with a single ion trap instrument in a conventional molecular/cellular biology laboratory to carry out proteomic characterization of a pathway, organelle, or process (i.e. "pathway proteomics") by systematic application of TAP-MudPIT

Charting the protein complexome in yeast by mass spectrometry

It has become evident over the past few years that many complex cellular processes, including control of the cell cycle and ubiquitin-dependent proteolysis, are carried out by sophisticated multisubunit protein machines that are dynamic in abundance, post-translational modification state, and composition. To understand better the nature of the macromolecular assemblages that carry out the cell cycle and ubiquitin-dependent proteolysis, we have used mass spectrometry extensively over the past few years to characterize both the composition of various protein complexes and the modification states of their subunits. In this article we review some of our recent efforts, and describe a promising new approach for using mass spectrometry to dissect protein interaction networks

Measuring Temperature Gradients over Nanometer Length Scales

When a quantum dot is subjected to a thermal gradient, the temperature of electrons entering the dot can be determined from the dot's thermocurrent if the conductance spectrum and background temperature are known. We demonstrate this technique by measuring the temperature difference across a 15 nm quantum dot embedded in a nanowire. This technique can be used when the dot's energy states are separated by many kT and will enable future quantitative investigations of electron-phonon interaction, nonlinear thermoelectric effects, and the effciency of thermoelectric energy conversion in quantum dots.Comment: 6 pages, 5 figure

New insights into electron spin dynamics in the presence of correlated noise

The changes of the spin depolarization length in zinc-blende semiconductors when an external component of correlated noise is added to a static driving electric field are analyzed for different values of field strength, noise amplitude and correlation time. Electron dynamics is simulated by a Monte Carlo procedure which keeps into account all the possible scattering phenomena of the hot electrons in the medium and includes the evolution of spin polarization. Spin depolarization is studied by examinating the decay of the initial spin polarization of the conduction electrons through the D'yakonov-Perel process, the only relevant relaxation mechanism in III-V crystals. Our results show that, for electric field amplitude lower than the Gunn field, the dephasing length shortens with the increasing of the noise intensity. Moreover, a nonmonotonic behavior of spin depolarization length with the noise correlation time is found, characterized by a maximum variation for values of noise correlation time comparable with the dephasing time. Instead, in high field conditions, we find that, critically depending on the noise correlation time, external fluctuations can positively affect the relaxation length. The influence of the inclusion of the electron-electron scattering mechanism is also shown and discussed.Comment: Published on "Journal of Physics: Condensed Matter" as "Fast Track Communications", 11 pages, 9 figure

Study of Thermal Properties of Graphene-Based Structures Using the Force Constant Method

The thermal properties of graphene-based materials are theoretically investigated. The fourth-nearest neighbor force constant method for phonon properties is used in conjunction with both the Landauer ballistic and the non-equilibrium Green's function techniques for transport. Ballistic phonon transport is investigated for different structures including graphene, graphene antidot lattices, and graphene nanoribbons. We demonstrate that this particular methodology is suitable for robust and efficient investigation of phonon transport in graphene-based devices. This methodology is especially useful for investigations of thermoelectric and heat transport applications.Comment: 23 pages, 9 figures, 1 tabl

Theory of biopolymer stretching at high forces

We provide a unified theory for the high force elasticity of biopolymers solely in terms of the persistence length, $\xi_p$, and the monomer spacing, $a$. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the Worm-like Chain (WLC) is a better model. We show that $\xi_p$ can be estimated from the force extension curve (FEC) at the extension $x\approx 1/2$ (normalized by the contour length of the biopolymer). After validating the theory using simulations, we provide a quantitative analysis of the FECs for a diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and unstructured PEVK domain of titin) for $x \ge 1/2$. The success of a specific polymer model (FJC or WLC) to describe the FEC of a given biopolymer is naturally explained by the theory. Only by probing the response of biopolymers over a wide range of forces can the $f$-dependent elasticity be fully described.Comment: 20 pages, 4 figure

Negative Thermal Expansion Coefficient of Graphene Measured by Raman Spectroscopy

The thermal expansion coefficient (TEC) of single-layer graphene is estimated with temperature-dependent Raman spectroscopy in the temperature range between 200 and 400 K. It is found to be strongly dependent on temperature but remains negative in the whole temperature range, with a room temperature value of -8.0x10^{-6} K^{-1}. The strain caused by the TEC mismatch between graphene and the substrate plays a crucial role in determining the physical properties of graphene, and hence its effect must be accounted for in the interpretation of experimental data taken at cryogenic or elevated temperatures.Comment: 17 pagese, 3 figures, and supporting information (4 pages, 3 figures); Nano Letters, 201

Screening of suitable cationic dopants for solar absorber material CZTS/Se: A first principles study

The earth abundant and non-toxic solar absorber material kesterite Cu2ZnSn(S/Se)(4) has been studied to achieve high power conversion efficiency beyond various limitations, such as secondary phases, antisite defects, band gap adjustment and microstructure. To alleviate these hurdles, we employed screening based approach to find suitable cationic dopant that can promote the current density and the theoretical maximum upper limit of the energy conversion efficiency (P(%)) of CZTS/Se solar devices. For this task, the hybrid functional (Heyd, Scuseria and Ernzerhof, HSE06) were used to study the electronic and optical properties of cation (Al, Sb, Ga, Ba) doped CZTS/Se. Our in-depth investigation reveals that the Sb atom is suitable dopant of CZTS/CZTSe and also it has comparable bulk modulus as of pure material. The optical absorption coefficient of Sb doped CZTS/Se is considerably larger than the pure materials because of easy formation of visible range exciton due to the presence of defect state below the Fermi level, which leads to an increase in the current density and P(%). Our results demonstrate that the lower formation energy, preferable energy gap and excellent optical absorption of the Sb doped CZTS/Se make it potential component for relatively high efficient solar cells

Thermal Properties of Graphene, Carbon Nanotubes and Nanostructured Carbon Materials

Recent years witnessed a rapid growth of interest of scientific and engineering communities to thermal properties of materials. Carbon allotropes and derivatives occupy a unique place in terms of their ability to conduct heat. The room-temperature thermal conductivity of carbon materials span an extraordinary large range - of over five orders of magnitude - from the lowest in amorphous carbons to the highest in graphene and carbon nanotubes. I review thermal and thermoelectric properties of carbon materials focusing on recent results for graphene, carbon nanotubes and nanostructured carbon materials with different degrees of disorder. A special attention is given to the unusual size dependence of heat conduction in two-dimensional crystals and, specifically, in graphene. I also describe prospects of applications of graphene and carbon materials for thermal management of electronics.Comment: Review Paper; 37 manuscript pages; 4 figures and 2 boxe