Direct Imaging of Protein Organization in an Intact Bacterial Organelle Using High-Resolution Atomic Force Microscopy

The function of bioenergetic membranes is strongly influenced by the spatial arrangement of their constituent membrane proteins. Atomic force microscopy (AFM) can be used to probe protein organization at high resolution, allowing individual proteins to be identified. However, previous AFM studies of biological membranes have typically required that curved membranes are ruptured and flattened during sample preparation, with the possibility of disruption of the native protein arrangement or loss of proteins. Imaging native, curved membranes requires minimal tip–sample interaction in both lateral and vertical directions. Here, long-range tip–sample interactions are reduced by optimizing the imaging buffer. Tapping mode AFM with high-resonance-frequency small and soft cantilevers, in combination with a high-speed AFM, reduces the forces due to feedback error and enables application of an average imaging force of tens of piconewtons. Using this approach, we have imaged the membrane organization of intact vesicular bacterial photosynthetic “organelles”, chromatophores. Despite the highly curved nature of the chromatophore membrane and lack of direct support, the resolution was sufficient to identify the photosystem complexes and quantify their arrangement in the native state. Successive imaging showed the proteins remain surprisingly static, with minimal rotation or translation over several-minute time scales. High-order assemblies of RC-LH1-PufX complexes are observed, and intact ATPases are successfully imaged. The methods developed here are likely to be applicable to a broad range of protein-rich vesicles or curved membrane systems, which are an almost ubiquitous feature of native organelles

From Monochrome to Technicolor: Simple Generic Approaches to Multicomponent Protein Nanopatterning Using Siloxanes with Photoremovable Protein-Resistant Protecting Groups.

We show that sequential protein deposition is possible by photodeprotection of films formed from a tetraethylene-glycol functionalized nitrophenylethoxycarbonyl-protected aminopropyltriethoxysilane (NPEOC-APTES). Exposure to near-UV irradiation removes the protein-resistant protecting group, and allows protein adsorption onto the resulting aminated surface. The protein resistance was tested using proteins with fluorescent labels and microspectroscopy of two-component structures formed by micro- and nanopatterning and deposition of yellow and green fluorescent proteins (YFP/GFP). Nonspecific adsorption onto regions where the protecting group remained intact was negligible. Multiple component patterns were also formed by near-field methods. Because reading and writing can be decoupled in a near-field microscope, it is possible to carry out sequential patterning steps at a single location involving different proteins. Up to four different proteins were formed into geometric patterns using near-field lithography. Interferometric lithography facilitates the organization of proteins over square cm areas. Two-component patterns consisting of 150 nm streptavidin dots formed within an orthogonal grid of bars of GFP at a period of ca. 500 nm could just be resolved by fluorescence microscopy

The one-dimensional Bose-Hubbard Model with nearest-neighbor interaction

We study the one-dimensional Bose-Hubbard model using the Density-Matrix Renormalization Group (DMRG).For the cases of on-site interactions and additional nearest-neighbor interactions the phase boundaries of the Mott-insulators and charge density wave phases are determined. We find a direct phase transition between the charge density wave phase and the superfluid phase, and no supersolid or normal phases. In the presence of nearest-neighbor interaction the charge density wave phase is completely surrounded by a region in which the effective interactions in the superfluid phase are repulsive. It is known from Luttinger liquid theory that a single impurity causes the system to be insulating if the effective interactions are repulsive, and that an even bigger region of the superfluid phase is driven into a Bose-glass phase by any finite quenched disorder. We determine the boundaries of both regions in the phase diagram. The ac-conductivity in the superfluid phase in the attractive and the repulsive region is calculated, and a big superfluid stiffness is found in the attractive as well as the repulsive region.Comment: 19 pages, 30 figure

Quantum corrections to the dynamics of interacting bosons: beyond the truncated Wigner approximation

We develop a consistent perturbation theory in quantum fluctuations around the classical evolution of a system of interacting bosons. The zero order approximation gives the classical Gross-Pitaevskii equations. In the next order we recover the truncated Wigner approximation, where the evolution is still classical but the initial conditions are distributed according to the Wigner transform of the initial density matrix. Further corrections can be characterized as quantum scattering events, which appear in the form of a nonlinear response of the observable to an infinitesimal displacement of the field along its classical evolution. At the end of the paper we give a few numerical examples to test the formalism.Comment: published versio

Phase Diagram of Bosonic Atoms in Two-Color Superlattices

We investigate the zero temperature phase diagram of a gas of bosonic atoms in one- and two-color standing-wave lattices in the framework of the Bose-Hubbard model. We first introduce some relevant physical quantities; superfluid fraction, condensate fraction, quasimomentum distribution, and matter-wave interference pattern. We then discuss the relationships between them on the formal level and show that the superfluid fraction, which is the relevant order parameter for the superfluid to Mott-insulator transition, cannot be probed directly via the matter wave interference patterns. The formal considerations are supported by exact numerical solutions of the Bose-Hubbard model for uniform one-dimensional systems. We then map out the phase diagram of bosons in non-uniform lattices. The emphasis is on optical two-color superlattices which exhibit a sinusoidal modulation of the well depth and can be easily realized experimentally. From the study of the superfluid fraction, the energy gap, and other quantities we identify new zero-temperature phases, including a localized and a quasi Bose-glass phase, and discuss prospects for their experimental observation.Comment: 18 pages, 17 figures, using REVTEX

Microfluidic and Nanofluidic Cavities for Quantum Fluids Experiments

The union of quantum fluids research with nanoscience is rich with opportunities for new physics. The relevant length scales in quantum fluids, 3He in particular, are comparable to those possible using microfluidic and nanofluidic devices. In this article, we will briefly review how the physics of quantum fluids depends strongly on confinement on the microscale and nanoscale. Then we present devices fabricated specifically for quantum fluids research, with cavity sizes ranging from 30 nm to 11 microns deep, and the characterization of these devices for low temperature quantum fluids experiments.Comment: 12 pages, 3 figures, Accepted to Journal of Low Temperature Physic

Probing Sub-Micron Forces by Interferometry of Bose-Einstein Condensed Atoms

We propose a technique, using interferometry of Bose-Einstein condensed alkali atoms, for the detection of sub-micron-range forces. It may extend present searches at 1 micron by 6 to 9 orders of magnitude, deep into the theoretically interesting regime of 1000 times gravity. We give several examples of both four-dimensional particles (moduli), as well as higher-dimensional particles -- vectors and scalars in a large bulk-- that could mediate forces accessible by this technique.Comment: 32 pages, 5 figures, RevTeX4, expanded discussion of interactions, references added, to appear in PR

Spin squeezing and pairwise entanglement for symmetric multiqubit states

We show that spin squeezing implies pairwise entanglement for arbitrary symmetric multiqubit states. If the squeezing parameter is less than or equal to 1, we demonstrate a quantitative relation between the squeezing parameter and the concurrence for the even and odd states. We prove that the even states generated from the initial state with all qubits being spin down, via the one-axis twisting Hamiltonian, are spin squeezed if and only if they are pairwise entangled. For the states generated via the one-axis twisting Hamiltonian with an external transverse field for any number of qubits greater than 1 or via the two-axis counter-twisting Hamiltonian for any even number of qubits, the numerical results suggest that such states are spin squeezed if and only if they are pairwise entangled.Comment: 6 pages. Version 3: Small corrections were mad

Ginzburg-Landau theory of vortices in a multi-gap superconductor

The Ginzburg-Landau functional for a two-gap superconductor is derived within the weak-coupling BCS model. The two-gap Ginzburg-Landau theory is, then, applied to investigate various magnetic properties of MgB2 including an upturn temperature dependence of the transverse upper critical field and a core structure of an isolated vortex. Orientation of vortex lattice relative to crystallographic axes is studied for magnetic fields parallel to the c-axis. A peculiar 30-degree rotation of the vortex lattice with increasing strength of an applied field observed by neutron scattering is attributed to the multi-gap nature of superconductivity in MgB2.Comment: 11 page

Brownian motion of a charged particle in electromagnetic fluctuations at finite temperature

The fluctuation-dissipation theorem is a central theorem in nonequilibrium statistical mechanics by which the evolution of velocity fluctuations of the Brownian particle under a fluctuating environment is intimately related to its dissipative behavior. This can be illuminated in particular by an example of Brownian motion in an ohmic environment where the dissipative effect can be accounted for by the first-order time derivative of the position. Here we explore the dynamics of the Brownian particle coupled to a supraohmic environment by considering the motion of a charged particle interacting with the electromagnetic fluctuations at finite temperature. We also derive particle's equation of motion, the Langevin equation, by minimizing the corresponding stochastic effective action, which is obtained with the method of Feynman-Vernon influence functional. The fluctuation-dissipation theorem is established from first principles. The backreaction on the charge is known in terms of electromagnetic self-force given by a third-order time derivative of the position, leading to the supraohmic dynamics. This self-force can be argued to be insignificant throughout the evolution when the charge barely moves. The stochastic force arising from the supraohmic environment is found to have both positive and negative correlations, and it drives the charge into a fluctuating motion. Although positive force correlations give rise to the growth of the velocity dispersion initially, its growth slows down when correlation turns negative, and finally halts, thus leading to the saturation of the velocity dispersion. The saturation mechanism in a suparohmic environment is found to be distinctly different from that in an ohmic environment. The comparison is discussed.Comment: accepter by Foundation of Physics, for IARD 6, 200