Probing the kinetic landscape of transient peptide-protein interactions by use of peptide (15)n NMR relaxation dispersion spectroscopy: binding of an antithrombin peptide to human prothrombin

Protein-ligand interactions may lead to the formation of multiple molecular complexes in dynamic exchange, affecting the kinetic and thermodynamic characteristics of the binding equilibrium. We followed the dissociation kinetics of the transient and specific complex of an antithrombotic peptide N-acetyl-Asp(55)-Phe-Glu-Glu-Ile-Pro(60)-Glu-Glu-Tyr-Leu-Gln(65) with human prothrombin by use of (15)N NMR relaxation dispersion spectroscopy of the peptide. Every one of the five (15)N-labeled adjacent residues of the peptide exhibited apparently different kinetic exchange and relaxation behaviors, which were especially evident at different concentrations of prothrombin. Binding-induced (15)N relaxation dispersion of residues Phe(56), Glu(57), Glu(58), and Ile(59) can be fitted phenomenologically to a two-site on-and-off exchange mechanism with physically feasible relaxation and kinetic parameters obtained for residues Phe(56), Glu(58), and Ile(59), independent of the prothrombin concentration. The apparent kinetic parameters of Glu(57) show some dependence on the concentration of prothrombin and the extracted transverse relaxation rate for Glu(57) in the bound state was severalfold higher than that expected for a protein-peptide complex with a size of approximately 72 kDa. In addition, the equilibrium population of the bound peptide obtained for Glu(57) was inconsistent with those for Phe(56), Glu(58), and Ile(59) and with the prothrombin/peptide ratios used in the experiments. These discrepancies can be explained by the presence of two conformations for the peptide-protein complex exchanging at a rate of approximately 100 s(-)(1). In all, our study shows that fast dissociation of protein-peptide complexes can be studied quantitatively using peptide (15)N NMR relaxation dispersion measurements without a precise knowledge of the peptide and protein concentrations. In addition, protein titration was found to improve the accuracy of quantitative analysis and may make it possible to determine the rate of conformational changes within the protein-peptide complex.     

Counting statistics and detector properties of quantum point contacts

Quantum detector properties of the quantum point contact (QPC) are analyzed for an arbitrary electron transparency and coupling strength to the measured system and are shown to be determined by the electron counting statistics. Conditions of the quantum-limited operation of the QPC detector, which prevent information loss through the scattering time and scattering phases, are found for arbitrary coupling. We show that the phase information can be restored and used for the quantum-limited detection by inclusion of the QPC detector in the electronic Mach-Zehnder interferometer.     

New Plasmon Waveguides Composed of Twin Metal Wedges with a Nano Gap

We have numerically shown the existence of coupled wedge plasmons (CWPs) which propagates along a nano gap of a twin metal wedge. The CWPs are formed by wedge plasmons which can interact with each other. The dispersion relations of the wavenumber, propagation distance, and beam area of CWPs, are described and show that the characteristics of CWPs are similar to those of wedge plasmons and of gap plasmons. We also propose a new plasmon waveguide composed of twin metal wedges with a nano gap.     

Optical tailoring of electron spin coherence in quantum dots

We address the precession of an ensemble of electron spins, each confined in a (In, Ga)As/GaAs self-assembled quantum dot. The quantum dot inhomogeneity is directly reflected in the precession of the optically oriented electron spins about an external magnetic field, which is subject to fast dephasing on a nanoseconds time scale. Proper periodic laser excitation allows synchronization of the electron spin precessions with the excitation cycle. The experimental conditions can be tailored such that eventually all (about a million) electron spins that are excited by the laser precess with a single frequency. In this regime the ensemble can be exploited during the single electron spin coherence times being in the microseconds range.     

Higher spin $${{\mathfrak {s}}}{{\mathfrak {l}}}_2$$ s l 2 R-matrix from equivariant (co)homology

Letters in Mathematical Physics - We compute the rational $${{\mathfrak {s}}}{{\mathfrak {l}}}_2$$ R-matrix acting in the product of two spin- $$\ell \over 2$$ ( $${\ell \in {\mathbb {N}}}$$ )...     

From Quantum Probabilities to Quantum Amplitudes

The task of reconstructing the system’s state from the measurements results, known as the Pauli problem, usually requires repetition of two successive steps. Preparation in an initial state to be determined is followed by an accurate measurement of one of the several chosen operators in order to provide the necessary “Pauli data”. We consider a similar yet more general problem of recovering Feynman’s transition (path) amplitudes from the results of at least three consecutive measurements. The three-step histories of a pre- and post-selected quantum system are subjected to a type of interference not available to their two-step counterparts. We show that this interference can be exploited, and if the intermediate measurement is “fuzzy”, the path amplitudes can be successfully recovered. The simplest case of a two-level system is analysed in detail. The “weak measurement” limit and the usefulness of the path amplitudes are also discussed.     

Observation of size-dependent thermalization in CdSe nanocrystals using time-resolved photoluminescence spectroscopy

We report heat dissipation times in semiconductor nanocrystals of CdSe. Specifically, a previously unresolved, subnanosecond decay component in the low-temperature photoluminescence decay dynamics exhibits longer decay lifetimes (tens to hundreds of picoseconds) for larger nanocrystals as well as a size-independent, ~25-meV spectral shift. We attribute the fast relaxation to transient phonon-mediated relaxation arising from nonequilibrium acoustic phonons. Following acoustic phonon dissipation, the dark exciton state recombines more slowly via LO-phonon assistance resulting in the observed spectral shift. The measured relaxation time scales agree with classical calculations of thermal diffusion, indicating that interfacial thermal conductivity does not limit thermal transport in these semiconductor nanocrystal dispersions.     

Collective Tunnelling of Strongly Interacting Cold Atoms in a Double-Well Potential

It is known that under resonance conditions, a group of strongly interacting bosonic atoms, trapped in a double-well potential, mimics a single particle, performing Rabi oscillations between the wells. By implication, all atoms need to tunnel at roughly the same time, even though the Bose–Hubbard Hamiltonian accounts only for one-atom-at-a-time transfers. The mechanism of this collective behavior is analyzed, the Rabi frequencies in the process are evaluated, and the limitation of this simple picture is discussed. In particular, it is shown that the small rapid oscillations superimposed on the slow Rabi cycle result from splitting the transferred cluster at the sudden onset of tunnelling, and disappear if tunnelling is turned on gradually.     

Effect of Fe on the glass-forming ability,structure and devitrification behavior of Zr–Cu–Al bulk glass-forming alloys

We report on the glass-forming ability and devitrification behavior of Zr₆₀Cu₃₀Al₁₀, Zr₆₀Cu₂₅Al₁₀Fe₅ and Zr_62.5Cu_22.5Al₁₀Fe₅ bulk glass-forming alloys on heating. The effect of Fe addition on the structure of Zr–Al–Cu alloys is also discussed. Crystallization kinetics and structural changes in the glassy alloys were studied using X-ray diffraction, transmission electron microscopy, differential scanning and isothermal calorimetry methods. The results indicate that good glass-formers, such as Zr_62.5Cu_22.5Al₁₀Fe₅, are located somewhat beyond the equilibrium eutectic point. Possible phase separation in the supercooled liquid on heating and electron beam-induced in situ crystallization are observed and discussed.