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## Full-Text Articles in Physics

Modeling Correlated Main-Chain Motions In Proteins For Flexible Molecular Recognition., Maria Zavodsky, Ming Lei, M. Thorpe, Anthony Day, Leslie Kuhn

#### Modeling Correlated Main-Chain Motions In Proteins For Flexible Molecular Recognition., Maria Zavodsky, Ming Lei, M. Thorpe, Anthony Day, Leslie Kuhn

*Anthony Roy Day*

We describe a new method for modeling protein and ligand main-chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational space, including large-scale motions that typically cannot be reached in molecular dynamics simulations due to the computational intensity, as well as conformations that have not been observed yet by crystallography or NMR. A secondary goal is to assess the degree of flexibility consistent with protein–ligand recognition. Flexibility analysis of the target protein is performed using the graph-theoretic algorithm FIRST, which also identifies coupled networks of covalent and noncovalent bonds within ...

Spectral Representation Of The Electrical Properties Of Layered Materials., Anthony Day, A. Mcgurn, D. Bergman, M. Thorpe

#### Spectral Representation Of The Electrical Properties Of Layered Materials., Anthony Day, A. Mcgurn, D. Bergman, M. Thorpe

*Anthony Roy Day*

We present a spectral representation for the effective conductivity of two homogeneous layers joined at a rough interface. This spectral representation is closely related to the Bergman-Milton spectral representation for bulk composites, and is easily extended to multilayered materials. By comparing the layered system to a reference layered system that has a flat interface, we form a surface spectral density that captures all the effects of surface structure on the effective conductivity of the layered sample, and is independent of the conductivities of the two layers. Because of the anisotropy of the layered system there are two surface spectral densities ...

The Spectral Function Of A Composite From Reflectance Data., Anthony Day, M. Thorpe, A. Grant, A. Sievers

#### The Spectral Function Of A Composite From Reflectance Data., Anthony Day, M. Thorpe, A. Grant, A. Sievers

*Anthony Roy Day*

In the Bergman-Milton spectral representation for the effective dielectric constant of a composite all relevant geometric information is captured in a spectral function that is independent of material properties. We present numerical simulations of the reflectance of a model two component composite, where both components have temperature-dependant dielectric resonances, and show that the spectral function can be extracted from the data. The same spectral function is obtained from simulation data corresponding to different temperatures but the resolution depends on the width of the resonance line and is greatest at low-temperatures.

The Spectral Function Of Composites: The Inverse Problem, Anthony Day, M. Thorpe

#### The Spectral Function Of Composites: The Inverse Problem, Anthony Day, M. Thorpe

*Anthony Roy Day*

No abstract provided.

Small Scale Electronic Transport In Diamond Microcrystals., M. Jaeger, S. Hyun, Anthony Day, M. Thorpe, B. Golding

#### Small Scale Electronic Transport In Diamond Microcrystals., M. Jaeger, S. Hyun, Anthony Day, M. Thorpe, B. Golding

*Anthony Roy Day*

The interpretation of electronic transport in polycrystalline diamond has proven difficult as a result of the disorder arising from physical and chemical inhomogeneities. We describe experimental methods, based on electron beam lithography, for studying transport in single crystallites grown by CVD on Si substrates. The electrical contacting process utilizes the flexibility of the scanning electron microscope to write metallic contacts to individual crystallites with lateral dimensions of a few μm. A detailed analysis of the current distribution in the crystals allows us to extract the electronic conductivity from arbitrarily shaped, faceted crystals.

The Elastic Moduli Of Random Networks: Calculations, Anthony Day

#### The Elastic Moduli Of Random Networks: Calculations, Anthony Day

*Anthony Roy Day*

No abstract provided.

The Spectral Function Of Random Resistor Networks, Anthony Day, M. Thorpe

#### The Spectral Function Of Random Resistor Networks, Anthony Day, M. Thorpe

*Anthony Roy Day*

The effective complex conductivity [...] of a two-component material can be conveniently expressed as an integral transformation of a spectral function. The spectral function depends only on the geometry of the material, and can be used to calculate [...] for any particular choice of component conductivities. This is a very useful feature if the component conductivities can be varied (by changing the temperature or frequency, for example) at a fixed geometry. We present a derivation of the spectral function that identifies it as a density of states. We have made direct numerical calculations of the spectral function of two-dimensional random resistor networks ...

The Elastic Moduli Of A Sheet Containing Circular Holes, Anthony Day, K. Snyder, E. Garboczi, M. Thorpe

#### The Elastic Moduli Of A Sheet Containing Circular Holes, Anthony Day, K. Snyder, E. Garboczi, M. Thorpe

*Anthony Roy Day*

We apply computer simulation techniques to obtain the clastic moduli of a matrix containing circular holes. As the area fraction of holes increases, the Young's modulus of the composite decreases from E0 until it eventually vanishes at the percolation threshold. We study three distinct geometries: (a) periodically centered circular holes on a honeycomb lattice, (b) periodically centered circular holes on a triangular lattice, and (c) randomly centered circular holes. All three cases have the same dilute limit that can be calculated exactly. By examining the narrow necks between adjacent circles, we have calculated the critical behavior for the regular ...

Rigidity Percolation, Anthony Day, M. Thorpe, W. Xia

#### Rigidity Percolation, Anthony Day, M. Thorpe, W. Xia

*Anthony Roy Day*

No abstract provided.

Spectral Properties Of Percolating Central Force Elastic Networks, Anthony Day, R. Tremblay, A.-M. Tremblay

#### Spectral Properties Of Percolating Central Force Elastic Networks, Anthony Day, R. Tremblay, A.-M. Tremblay

*Anthony Roy Day*

The exponent describing the low frequency spectrum of vibrations for the central force universality class is computed with both the Coherent Potential Approximation and numerical simulations. The results of both calculations agree surprisingly well.