Self-calibrated 3D differential phase contrast microscopy with optimized illumination.

3D phase imaging recovers an object's volumetric refractive index from intensity and/or holographic measurements. Partially coherent methods, such as illumination-based differential phase contrast (DPC), are particularly simple to implement in a commercial brightfield microscope. 3D DPC acquires images at multiple focus positions and with different illumination source patterns in order to reconstruct 3D refractive index.

Asymmetric temperature equilibration with heat flow from cold to hot in a quantum thermodynamic system.

A model computational quantum thermodynamic network is constructed with two variable temperature baths coupled by a linker system, with an asymmetry in the coupling of the linker to the two baths. It is found in computational simulations that the baths come to "thermal equilibrium" at different bath energies and temperatures. In a sense, heat is observed to flow from cold to hot.

Soft Mode Metal-Linker Dynamics in Carboxylate MOFs Evidenced by Variable-Temperature Infrared Spectroscopy.

Through comprehensive analysis of carboxylate-based metal-organic frameworks (MOFs), we present general evidence that challenges the common perception of MOF metal-linker bonds being static. Structural dynamics in MOFs, however, typically refers to the "breathing" behavior of cavities, where pores open and close in response to guest molecules, and to the transient binding of guest molecules, but dynamic bonding would explain important MOF phenomena in catalysis, postsynthetic exchange, negative thermal expansion, and crystal growth. Here, we demonstrate, through use of variable-temperature diffuse reflectance infrared Fourier transform spectroscopy (VT-DRIFTS) aided by ab initio plane wave density functional theory, that similar evidence for melting behavior in zeolitic imidazolate frameworks (ZIFs), i.

Simulating quantum thermodynamics of a finite system and bath with variable temperature.

We construct a finite bath with variable temperature for quantum thermodynamic simulations in which heat flows between a system S and the bath environment E in time evolution of an initial SE pure state. The bath consists of harmonic oscillators that are not necessarily identical. Baths of various numbers of oscillators are considered; a bath with five oscillators is used in the simulations.

Quantum Microcanonical Entropy, Boltzmann's Equation, and the Second Law.

A recent proposal for a quantum entropy S for a pure state of a system-environment "universe" is developed to encompass a much more realistic temperature bath. Microcanonical entropy is formulated in the context of the idea of a quantum microcanonical shell. The fundamental relation that holds for the classical microcanonical ensemble - TΔ S = Δ F is tested for the quantum entropy Δ S in numerical simulations.

Kinetic Model of Translational Autoregulation.

We investigate the dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its mRNA, known in molecular biology as translational autoregulation. We first show how linear models without feedback set the stage with a nonequilibrium steady state that constitutes the target of the regulation. However, regulation in the simple linear model is far from optimal.

Motion-resolved quantitative phase imaging.

The temporal resolution of quantitative phase imaging with Differential Phase Contrast (DPC) is limited by the requirement for multiple illumination-encoded measurements. This inhibits imaging of fast-moving samples. We present a computational approach to model and correct for non-rigid sample motion during the DPC acquisition in order to improve temporal resolution to that of a single-shot method and enable imaging of motion dynamics at the framerate of the sensor.

Node-Pore Coded Coincidence Correction: Coulter Counters, Code Design, and Sparse Deconvolution.

We present a novel method to perform individual particle (e.g. cells or viruses) coincidence correction through joint channel design and algorithmic methods.

BARKER-CODED NODE-PORE RESISTIVE PULSE SENSING WITH BUILT-IN COINCIDENCE CORRECTION.

A resistive pulse sensing device is able to extract quantities such as concentration and size distribution of particles, e.g. cells or microspheres, as they flow through the device's sensor region, i.

Time dependent quantum thermodynamics of a coupled quantum oscillator system in a small thermal environment.

Simulations are performed of a small quantum system interacting with a quantum environment. The system consists of various initial states of two harmonic oscillators coupled to give normal modes. The environment is "designed" by its level pattern to have a thermodynamic temperature.

Visualizing the zero order basis of the spectroscopic Hamiltonian.

Recent works have shown that a generalization of the spectroscopic effective Hamiltonian can describe spectra in surprising regions, such as isomerization barriers. In this work, we seek to explain why the effective Hamiltonian is successful where there was reason to doubt that it would work at all. All spectroscopic Hamiltonians have an underlying abstract zero-order basis (ZOB) which is the "ideal" basis for a given form and parameterization of the Hamiltonian.

Isotope effect in normal-to-local transition of acetylene bending modes.

The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH.

Effective Hamiltonian for femtosecond vibrational dynamics.

Time propagation of zero-order states of an effective spectroscopic Hamiltonian is tested against femtosecond time dependent dynamics of adiabatic wavepackets evolving on a model potential energy surface for two coupled modes of the radical HO(2) with multiple potential wells and above barrier motion. A generalized Hamiltonian which breaks the usual conserved polyad action by including extra resonance couplings (V(2:1) and V(3:1)) successfully describes the time evolution after the further addition of two "ultrafast" couplings. These new couplings are a nonresonant coupling a(1)a(2)+a(1)(†)a(2)(†) and a resonant coupling V(1:1) that functions as an ultrafast term because the system is far from 1:1 frequency resonance.

Detailed analysis of polyad-breaking spectroscopic Hamiltonians for multiple minima with above barrier motion: isomerization in HO2.

We present a two-dimensional model for isomerization in the hydroperoxyl radical (HO(2)). We then show that spectroscopic fitting Hamiltonians are capable of reproducing large scale vibrational structure above isomerization barriers. Two resonances, the 2:1 and 3:1, are necessary to describe the pertinent physical features of the system and, hence, a polyad-breaking Hamiltonian is required.

Communication: Effective spectroscopic Hamiltonian for multiple minima with above barrier motion: Isomerization in HO(2).

We present a two-dimensional potential surface for the isomerization in the hydroperoxyl radical HO(2) and calculate the vibrational spectrum. We then show that a simple effective spectroscopic fitting Hamiltonian is capable of reproducing large scale vibrational spectral structure above the isomerization barrier. Polyad breaking with multiple resonances is necessary to adequately describe the spectral features of the system.

Bifurcation phase diagram for C(2)H(2) bending dynamics has a tetracritical point with spectral patterns.

Critical points and bifurcations are considered for the acetylene effective Hamiltonian in the polyad space of total bend and vibrational angular momentum quantum numbers [N(b), [Formula: see text]]. A "phase diagram" is constructed for the surface of minimum energy critical points. The phases denote vibrational modes of different character, including new types of anharmonic modes born in bifurcations from the ordinary normal modes.

Critical points bifurcation analysis of high-l bending dynamics in acetylene.

The bending dynamics of acetylene with pure vibrational angular momentum excitation and quantum number l not = 0 are analyzed through the method of critical points analysis, used previously [V. Tyng and M. E.

Spectral intensity patterns and vibrational phase space structure.

We examine patterns of absorption intensity in two-mode systems with a 2:1 Fermi resonance in an intensity model based on the effective fitting Hamiltonian. We relate these patterns to the Fermi resonance phase space structure and catastrophe map. Each of the four zones of the catastrophe map has a phase sphere structure with a certain number of distinct regions.

Catastrophe map and the role of individual resonances in C2H2 bending dynamics.

A catastrophe map analysis is presented of the birth of new modes in bifurcations of the normal modes of the acetylene pure bending system using a spectroscopic fitting Hamiltonian that is nonseparable with multiple resonances. The map splits into two independent maps for subspaces defined by the resonance frequency conditions. Nonetheless, both resonance couplings act on each of the resonance subspaces, since the system is nonseparable.

Effective Hamiltonian for chaotic coupled oscillators.

A generalized effective fitting Hamiltonian is tested against a model system of highly excited coupled Morse oscillators. At energies approaching dissociation, a very few resonance couplings in addition to the standard 1:1 and 2:2 couplings of the Darling-Dennison Hamiltonian suffice to fit the spectrum and match the large-scale features of the mixed regular and chaotic phase spaces, consisting of resonance zones organized around periodic orbits of low order that break the total polyad action.

Moment of inertia, backbending, and molecular bifurcation.

We predict an anomaly in highly excited bending spectra of acetylene with high vibrational angular momentum. We interpret this in terms of a vibrational shape effect with moment of inertia backbending, induced by a sequence of bifurcations with a transition from "local" to "orthogonal" modes.

The dance of molecules: new dynamical perspectives on highly excited molecular vibrations.

At low energies, molecular vibrational motion is described by the normal modes model. This model breaks down at higher energy, with strong coupling between normal modes and onset of chaotic dynamics. New anharmonic modes are born in bifurcations, or branchings of the normal modes.

Bending dynamics of acetylene: new modes born in bifurcations of normal modes.

Semiclassical techniques are used to analyze highly excited pure bending vibrational dynamics from spectra of C2H2. An analytic bifurcation approach is developed, based on critical points of a classical version of the quantum fitting Hamiltonian. At high energy four new types of anharmonic modes are born in bifurcations of the normal modes: local, orthogonal, precessional, and counter-rotator.

Short-course rifamycin and pyrazinamide treatment for latent tuberculosis infection in patients with HIV infection: the 2-year experience of a comprehensive community-based program in Broward County, Florida.

Objectives: To determine the completion rate and tolerability of short-course rifamycin and pyrazinamide treatment of latent tuberculosis infection (LTBI) in HIV-infected patients through a comprehensive community-based program.

Design: Prospective cohort, with comparison to a historical control group.

Patients: Of 3,118 patients with HIV infection screened for LTBI between February 1999 and March 2001, 135 patients were placed on rifamycin/pyrazinamide for 2 months under directly observed therapy and were compared to a historical group comprised of 93 HIV-infected patients who were placed on self-administered treatment of isoniazid for 12 months between 1996 and 1998.

Quantum calculation of highly excited vibrational energy levels of CS2(X) on a new empirical potential energy surface and semiclassical analysis of 1:2 Fermi resonance.

We report a refined potential energy function for the ground electronic state of CS2 based on a least-squares fitting to several low-lying experimental vibrational frequencies. Energy levels up to 20,000 cm(-1) have been obtained on this empirical potential using the Lanczos algorithm and potential optimized discrete variable representation. Among them, 329 levels below 10,000 cm(-1) are assigned with approximate normal mode quantum numbers (n1, n(0)2, n3), based on expectation values of one-dimensional (1D) reference Hamiltonians.