Single-molecule fluorescence studies of functional biomolecule dynamics rely on the ability to provide biologically relevant experimental conditions. Long measurement times on single molecules require their immobilization, which might modify their dynamics through interactions with the trapping medium, e.g., a glass surface or a polymer gel. In an effort to overcome this problem we have devised a new immobilization technique, based on the confinement of single biomolecules inside 100 nm surface-tethered lipid vesicles. The number of molecules in each vesicle can be accurately determined from fluorescence time traces; under our experimental conditions the number distribution of encapsulated molecules obeys a Poisson distribution with an average occupancy of 0.65 molecules per vesicle. It is further shown that the distribution of fluorescence polarization values of trapped molecules can serve as a sensitive probe for their freedom of motion and thus for the environment they sample inside the liposomes. Polarization distributions are obtained for two vesicleentrapped labeled proteins, bovine serum albumin and adenylate kinase, and compared with distributions measured for the same proteins directly adsorbed on glass. From the significant relative narrowing of the distributions for encapsulated molecules, it is concluded that their motion within the vesicles is quite similar to free solution.

We study the phase sensitivity of collisional phase diffusion between weakly coupled Bose-Einstein condensates, using a semiclassical picture of the two-mode Bose-Hubbard model. When weak coupling is allowed, zero relative phase locking is attained in the Josephson-Fock transition regime, whereas a pi relative phase is only locked in Rabi-Josephson point. Our analytic semiclassical estimates agree well with the numerical results.

Thermodynamics of a three-level maser was studied in the pioneering work of Scovil-Schulz-DuBois [Phys. Rev. Lett. 2, 262 (1959)10.1103/PhysRevLett.2.262]. In this Letter we consider the same three-level model, but we give a full thermodynamic analysis based on Hamiltonian and dissipative Lindblad superoperators. The first law of thermodynamics is obtained using a recently developed alternative [Phys. Rev. A 74, 063823 (2006)10.1103/PhysRevA.74.063823] to Alicki's definitions for heat flux and power [J. Phys. A 12, L103 (1979)10.1088/0305-4470/12/5/007]. Using a novel variation on Spohn's entropy production function [J. Math. Phys. (N.Y.) 19, 1227 (1978)10.1063/1.523789], we obtain Carnot's efficiency inequality and the Scovil-Schulz-DuBois maser efficiency formula when the three-level system is operated as a heat engine (amplifier). Finally, we show that the three-level system has two other modes of operation--a refrigerator mode and a squanderer mode--both of which attenuate the electric field.

Thermodynamics of a three-level maser was studied in the pioneering work of Scovil and SchulzDuBois [Phys. Rev. Lett. 2, 262 (1959)]. In this work we consider the same three-level model, but treat both the matter and light quantum mechanically. Specifically, we analyze an extended (three-level) dissipative Jaynes-Cummings model (ED-JCM) within the framework of a quantum heat engine, using novel formulas for heat flux and power in bipartite systems introduced in our previous work [E. Boukobza and D. J. Tannor, PRA (in press)]. Amplification of the selected cavity mode occurs even in this simple model, as seen by a positive steady state power. However, initial field coherence is lost, as seen by the decaying off-diagonal field density matrix elements, and by the Husimi-Kano Q function. We show that after an initial transient time the field's entropy rises linearly during the operation of the engine, which we attribute to the dissipative nature of the evolution and not to matter-field entanglement. We show that the second law of thermodynamics is satisfied in two formulations (Clausius, Carnot) and that the efficiency of the ED-JCM heat engine agrees with that defined intuitively by Scovil and Schulz-DuBois. Finally, we compare the steady state heat flux and power of the fully quantum model with the semiclassical counterpart of the ED-JCM, and derive the engine efficiency formula of Scovil and Schulz-DuBois analytically from fundamental thermodynamic fluxes.

The Jaynes-Cummings model is the simplest fully quantum model that describes the interaction between light and matter. We extend a previous analysis by Phoenix and Knight (S. J. D. Phoenix, P. L. Knight, Annals of Physics 186, 381). of the JCM by considering mixed states of both the light and matter. We present examples of qualitatively different entropic correlations. In particular, we explore the regime of entropy exchange between light and matter, i.e. where the rate of change of the two are anti-correlated. This behavior contrasts with the case of pure light-matter states in which the rate of change of the two entropies are positively correlated and in fact identical. We give an analytical derivation of the anti-correlation phenomenon and discuss the regime of its validity. Finally, we show a strong correlation between the region of the Bloch sphere characterized by entropy exchange and that characterized by minimal entanglement as measured by the negative eigenvalues of the partially transposed density matrix.Comment: 8 pages, 5 figure