Teaching old NCATs new tricks: using non-canonical amino acid tagging to study neuronal plasticity

The non-canonical amino acid labeling techniques BONCAT (bioorthogonal non-canonical amino acid tagging) and FUNCAT (fluorescent non-canonical amino acid tagging) enable the specific identification and visualization of newly synthesized proteins. Recently, these techniques have been applied to neuronal systems to elucidate protein synthesis dynamics during plasticity, identify stimulation-induced proteomes and subproteomes and to investigate local protein synthesis in specific subcellular compartments. The next generation of tools and applications, reviewed here, includes the development of new tags, the quantitative identification of newly synthesized proteins, the application of NCAT to whole animals, and the ability to genetically restrict NCAT labeling. These techniques will enable not only improved detection but also allow new scientific questions to be tackled

Acoustic radiation controls friction: Evidence from a spring-block experiment

Brittle failures of materials and earthquakes generate acoustic/seismic waves which lead to radiation damping feedbacks that should be introduced in the dynamical equations of crack motion. We present direct experimental evidence of the importance of this feedback on the acoustic noise spectrum of well-controlled spring-block sliding experiments performed on a variety of smooth surfaces. The full noise spectrum is quantitatively explained by a simple noisy harmonic oscillator equation with a radiation damping force proportional to the derivative of the acceleration, added to a standard viscous term.Comment: 4 pages including 3 figures. Replaced with version accepted in PR

Kinetics in one-dimensional lattice gas and Ising models from time-dependent density functional theory

Time-dependent density functional theory, proposed recently in the context of atomic diffusion and non-equilibrium processes in solids, is tested against Monte Carlo simulation. In order to assess the basic approximation of that theory, the representation of non-equilibrium states by a local equilibrium distribution function, we focus on one-dimensional lattice models, where all equilibrium properties can be worked exactly from the known free energy as a functional of the density. This functional determines the thermodynamic driving forces away from equilibrium. In our studies of the interfacial kinetics of atomic hopping and spin relaxation, we find excellent agreement with simulations, suggesting that the method is useful also for treating more complex problems.Comment: 8 pages, 5 figures, submitted to Phys. Rev.

Optimal protocols for Hamiltonian and Schr\"odinger dynamics

For systems in an externally controllable time-dependent potential, the optimal protocol minimizes the mean work spent in a finite-time transition between given initial and final values of a control parameter. For an initially thermalized ensemble, we consider both Hamiltonian evolution for classical systems and Schr\"odinger evolution for quantum systems. In both cases, we show that for harmonic potentials, the optimal work is given by the adiabatic work even in the limit of short transition times. This result is counter-intuitive because the adiabatic work is substantially smaller than the work for an instantaneous jump. We also perform numerical calculations of the optimal protocol for Hamiltonian dynamics in an anharmonic quartic potential. For a two-level spin system, we give examples where the adiabatic work can be reached in either a finite or an arbitrarily short transition time depending on the allowed parameter space.Comment: submitted to J. Stat. Mech.: Theor. Exp

Consistent Anisotropic Repulsions for Simple Molecules

We extract atom-atom potentials from the effective spherical potentials that suc cessfully model Hugoniot experiments on molecular fluids, e.g., $O_2$ and $N_2$. In the case of $O_2$ the resulting potentials compare very well with the atom-atom potentials used in studies of solid-state propertie s, while for $N_2$ they are considerably softer at short distances. Ground state (T=0K) and room temperatu re calculations performed with the new $N-N$ potential resolve the previous discrepancy between experimental and theoretical results.Comment: RevTeX, 5 figure

Cleavable Biotin Probes for Labeling of Biomolecules via Azide−Alkyne Cycloaddition

The azide−alkyne cycloaddition provides a powerful tool for bio-orthogonal labeling of proteins, nucleic acids, glycans, and lipids. In some labeling experiments, e.g., in proteomic studies involving affinity purification and mass spectrometry, it is convenient to use cleavable probes that allow release of labeled biomolecules under mild conditions. Five cleavable biotin probes are described for use in labeling of proteins and other biomolecules via azide−alkyne cycloaddition. Subsequent to conjugation with metabolically labeled protein, these probes are subject to cleavage with either 50 mM Na_2S_2O_4, 2% HOCH_2CH_2SH, 10% HCO_2H, 95% CF_3CO_2H, or irradiation at 365 nm. Most strikingly, a probe constructed around a dialkoxydiphenylsilane (DADPS) linker was found to be cleaved efficiently when treated with 10% HCO_2H for 0.5 h. A model green fluorescent protein was used to demonstrate that the DADPS probe undergoes highly selective conjugation and leaves a small (143 Da) mass tag on the labeled protein after cleavage. These features make the DADPS probe especially attractive for use in biomolecular labeling and proteomic studies