HP-sequence design for lattice proteins - an exact enumeration study on diamond as well as square lattice

We present an exact enumeration algorithm for identifying the {\it native} configuration - a maximally compact self avoiding walk configuration that is also the minimum energy configuration for a given set of contact-energy schemes; the process is implicitly sequence-dependent. In particular, we show that the 25-step native configuration on a diamond lattice consists of two sheet-like structures and is the same for all the contact-energy schemes, ${(-1,0,0);(-7,-3,0); (-7,-3,-1); (-7,-3,1)}$; on a square lattice also, the 24-step native configuration is independent of the energy schemes considered. However, the designing sequence for the diamond lattice walk depends on the energy schemes used whereas that for the square lattice walk does not. We have calculated the temperature-dependent specific heat for these designed sequences and the four energy schemes using the exact density of states. These data show that the energy scheme $(-7,-3,-1)$ is preferable to the other three for both diamond and square lattice because the associated sequences give rise to a sharp low-temperature peak. We have also presented data for shorter (23-, 21- and 17-step) walks on a diamond lattice to show that this algorithm helps identify a unique minimum energy configuration by suitably taking care of the ground-state degeneracy. Interestingly, all these shorter target configurations also show sheet-like secondary structures.Comment: 19 pages, 7 figures (eps), 11 tables (latex files

Stability of flow of a thermoviscoelastic fluid between rotating coaxial circular cylinders

The stability problem of thermoviscoelastic fluid flow between rotating coaxial cylinders is investigated using nonlinear thermoviscoelastic constitutive equations due to Eringen and Koh. The velocity field is found to be identical with that of the classical viscous case and the case of the viscoelastic fluid, but the temperature and pressure fields are found to be different. By imposing some physically reasonable mechanical and geometrical restrictions on the flow, and by a suitable mathematical analysis, the problem is reduced to a characteristic value problem. The resulting problem is solved and stability criteria are obtained in terms of critical Taylor numbers. In general, it is found that thermoviscoelastic fluids are more stable than classical viscous fluids and viscoinelastic fluids under similar conditions

Automorphisms of moduli spaces of vector bundles over a curve

Let X be an irreducible smooth complex projective curve of genus g at least 4. Let M(r,\Lambda) be the moduli space of stable vector bundles over X or rank r and fixed determinant \Lambda, of degree d. We give a new proof of the fact that the automorphism group of M(r,\Lambda) is generated by automorphisms of the curve X, tensorization with suitable line bundles, and, if r divides 2d, also dualization of vector bundles.Comment: 12 page

Novel, high throughput method to study in vitro protein release from polymer nanospheres

Controlled delivery of therapeutic protein drugs using biodegradable polymer carriers is a desired characteristic that enables effective, application-specific therapy and treatment. Previous studies have focused on protein delivery from polymers using conventional one-sample-at-a- time techniques, which are time-consuming and costly. In addition, many therapeutic proteins are in limited supply and are expensive, so it is desirable to reduce sample size for design and development of delivery devices. We have developed a rapid, high throughput technique based on a highly sensitive fluorescence-based assay to detect and quantify protein released from polyanhydrides while utilizing relatively small amounts of protein (∼40 μg). These studies focused on the release of a model protein, Texas Red conjugated bovine serum albumin, from polyanhydride copolymers based on sebacic acid (SA) and 1,6-bis(p-carboxyphenoxy)hexane (CPH). The protein release profiles were assessed simultaneously to investigate the effect of polymer device geometry (nanospheres vs films), polymer chemistry, and pH of the release medium. The results indicated that the nanosphere geometry, SA-rich chemistries, and neutral pH release medium led to a more rapid release of the protein compared to the film geometry, CPH-rich chemistries, and acidic pH release medium, respectively. This high throughput fluorescence-based method can be readily extended to study release kinetics for other proteins and polymer systems

Can coarse-graining introduce long-range correlations in a symbolic sequence?

We present an exactly solvable mean-field-like theory of correlated ternary sequences which are actually systems with two independent parameters. Depending on the values of these parameters, the variance on the average number of any given symbol shows a linear or a superlinear dependence on the length of the sequence. We have shown that the available phase space of the system is made up a diffusive region surrounded by a superdiffusive region. Motivated by the fact that the diffusive portion of the phase space is larger than that for the binary, we have studied the mapping between these two. We have identified the region of the ternary phase space, particularly the diffusive part, that gets mapped into the superdiffusive regime of the binary. This exact mapping implies that long-range correlation found in a lower dimensional representative sequence may not, in general, correspond to the correlation properties of the original system.Comment: 10 pages including 1 figur