Brian Weiner

The Mycobacterium tuberculosis regulatory network and hypoxia

We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.

Nanosphere dispersed liquid crystals for tunable negative-zero-positive index of refraction in the optical and terahertz regimes

An analysis of aligned nematic liquid crystal cells containing core-shell nanospheres shows that it is possible to devise a new type of metamaterial whose index of refraction is tunable from negative, through zero, to positive values. The design parameters for the constituents can be scaled for application in the optical as well as very long wavelength (e.g., terahertz and microwave) regions.

Tunable Frequency Selective Surfaces and Negative-Zero-Positive Index Metamaterials Based on Liquid Crystals

We utilize the properties of aligned nematic liquid crystal (LC) cells in the design of: (i) a new type of metamaterial whose index of refraction is tunable from negative, through zero, to positive values and (ii) micron-scale metallodielectric and all-dielectric tunable frequency selective surfaces (FSSs). The metamaterial is constructed by randomly doping a liquid crystal substrate with coated dielectric (non-magnetic) spheres and can be utilized over a large spectral range. FSSs with a liquid crystal superstrate are synthesized using conventional and genetic algorithm methods to exhibit broadband tunable filter characteristics at mid-infrared (mid-IR) wavelengths. These LC tunable FSS structures can be used to develop a new class of infrared/optical switches for terahertz applications.

Molecular dynamics with combined quantum and empirical potentials : C2H2 adsorption on Si(100)

Classical trajectory calculations were employed to study the reaction of acetylene with dimer sites on the Si(100) surface at 105 K. Two types of potential energy functions were combined to describe interactions for different regions of the model surface. A quantum mechanical potential based on the semiempirical AM1 Hamiltonian was used to describe interactions between C2H2 and a portion of the silicon surface, while an empirically parametrized potential was developed to extend the size of the surface and simulate the dynamics of the surrounding silicon atoms. Reactions of acetylene approaching different sites were investigated, directly above a surface dimer, and between atoms from separate dimers. In all cases, the outcome of C2H2 surface collisions was controlled by the amount of translational energy possessed by the incoming molecule. Acetylene molecules with high translational energy reacted with silicon dimers to form surface species with either one or two Si–C bonds. Those molecules with low transl...

Coherent state formulation of multiconfiguration states

The theory of vector coherent states is applied to multiconfiguration states that are given a complex parametrization, based on the underlying special linear group. Using the time‐dependent variational principle, equations of motion for such states are formulated as evolution equations in a generalized phase space. The classical Hamiltonian for these equations is given in terms of the reduced first‐ and second‐order density matrices, which can be expressed in terms of partial derivatives with respect to the group parameters of the overlap kernel. The multiconfiguration self‐consistent‐field (MCSCF) and configuration interaction (CI) equations arise as special cases of these equations. Using the coherent state formulation we obtain very compact and numerically efficient expressions for the time‐dependent quantum mechanical description of chemical reactions.

Polarization propagator calculations with an AGP reference state

A consistent approximation to the polarization propagator is developed and compared to others viz Tamm–Dancoff and random phase approximations (TDA and RPA, respectively). The role of a properly defined vacuum as the reference state for the propagator is examined. It is shown that the closest one can come to a ‘‘consistent RPA’’ is a generalized TDA which corresponds to a polarization propagator based on an energy optimized generalized antisymmetrized geminal power (GAGP) state. The theory is applied to the nitrogen molecule in a slightly simplified form and calculated excited electronic states are compared to experimentally observed ones.

Fukutome symmetry classification of the Kohn–Sham auxiliary one-matrix and its associated state or ensemble

Ž . ABSTRACT: The Kohn]Sham KS procedure for variational minimization of the Hohenberg]Kohn density functional utilizes a one-particle reduced density matrix of assumed diagonal form, hence depends implicitly on a set of auxiliary states. Originally, the auxiliary state was assumed to be a single determinant with doubly occupied spin orbitals, i.e., of the same form as in ‘‘restricted’’ Hartree]Fock theory. The pragmatic and formal extension of the KS procedure to noninteger occupation numbers requires extension to more general forms of the auxiliary state or even its replacement by an auxiliary ensemble. Though attention has been given to the symmetry properties of the KS one-matrix, its spin and time-reversal symmetries have not been classified along the lines of Fukutome’s treatment of the generalized Hartree]Fock problem. Here we show Ž . that, in the context of constrained search density functional theory DFT , Fukutome’s analysis goes through essentially unaltered. We then consider the broken symmetry consequences for the case that the KS one-matrix is restricted to a single-determinantal KS auxiliary state. Q 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 451]460, 1998

A theoretical analysis of a diamond (100)‐(2×1) dimer bond

The nature of the bonding between the carbon atoms of reconstructed dimers on a dehydrogenated (100)‐(2×1) diamond surface is examined. Utilizing a complete active space self‐consistent field (CASSCF) description and a 6‐31G** basis set it is demonstrated that such dimer units form a biradical and are not purely π bonded as has often been conjectured. The significance of these findings for growth mechanisms on diamond surfaces involving radical sites is discussed.

Near-infrared metamaterial films with reconfigurable transmissive/reflective properties.

A near-infrared metamaterial design that is reconfigurable between almost completely transmissive and reflective states is presented. The reconfiguration is enabled by tuning the anisotropic nematic liquid crystals used as a spacer layer between two silver nanoplates in a planar doubly periodic metamaterial. The design is optimized for maximum difference in transmittance between the two states by using a genetic algorithm. For a linearly polarized illumination at normal incidence, full-wave electromagnetic analysis predicts that the optimized metamaterial film can change the transmittance between 98.7% and 0.1% at a wavelength of 1.1 microm.

Coherent state approach to electron nuclear dynamics with an antisymmetrized geminal power state

A formulation of the complete dynamics of electrons and nuclei is presented. The dynamical equations are derived using the time‐dependent variational principle (TDVP). The approximate electronic state vectors are antisymmetrized geminal power (AGP) states parameterized as projected coherent states, while the nuclei are treated as classical point particles. This leads to a formulation of time‐dependent AGP theory that generalizes time‐dependent Hartree–Fock (TDHF) theory and explicitly includes the dynamics of the nuclei. The linear approximation to the evolution equations (the classical harmonic approximation) which corresponds to a generalized random phase approximation (RPA) based on an AGP electronic reference state and which explicitly includes the dynamics of the nuclei, is studied and presented in this paper. The equations are formulated in terms of the primitive nonorthogonal electronic atomic basis thus avoiding any transformation to orthonormal molecular orbitals during the evolution.