Theory of phase segregation in DNA assemblies containing two different base pair sequence types

Spontaneous pairing of homologous DNA sequences – a challenging subject in molecular biophysics, often referred to as ‘homology recognition’ – ha s been observed in vitro for several DNA system s a . One of th e se experiments involved liquid crystalline quasi - columnar phases formed by a mixture of two kinds of oligo mer of double stranded DNA . Both oligomer types were of the same length and identical stoichiometric base - pair composition , but the base - pairs followed a different order . Phase segregation of the two DNA types was observed in the experiments , wit h the formation of boundaries between domai ns rich in molecules of one type (order) of base pair sequence . We formulate here a modified ‘ X - Y model ’ for phase segregation in such assemblies , obtain approximate solutions of the model , compare analytical results to Monte Carlo simulations, and rationalize past experimental observations . This study, furthermore , reveals the factors that affect the degree of segregat ion . Such information c ould be used in planning new versions of similar segregation experiments , needed for deepen i ng our understanding of forces that might be involved , e.g., in gene - gene recognition

Dynamics of the formation of a hydrogel by a pathogenic amyloid peptide: islet amyloid polypeptide

Many chronic degenerative diseases result from aggregation of misfolded polypeptides to form amyloids. Many amyloidogenic polypeptides are surfactants and their assembly can be catalysed by hydrophobic-hydrophilic interfaces (an air-water interface in-vitro or membranes in-vivo). We recently demonstrated the specificity of surface-induced amyloidogenesis but the mechanisms of amyloidogenesis and more specifically of adsorption at hydrophobic-hydrophilic interfaces remain poorly understood. Thus, it is critical to determine how amyloidogenic polypeptides behave at interfaces. Here we used surface tensiometry, rheology and electron microscopy to demonstrate the complex dynamics of gelation by full-length human islet amyloid polypeptide (involved in type II diabetes) both in the bulk solution and at hydrophobic-hydrophilic interfaces (air-water interface and phospholipids). We show that the hydrogel consists of a 3D supramolecular network of fibrils. We also assessed the role of solvation and dissected the evolution over time of the assembly processes. Amyloid gelation could have important pathological consequences for membrane integrity and cellular functions

Associations between Moderate-to-Vigorous Physical Activity and Neighbourhood Recreational Facilities: The Features of the Facilities Matter

published_or_final_versio

Kondo Insulator description of spin state transition in FeSb2

The thermal expansion and heat capacity of FeSb2 at ambient pressure agrees with a picture of a temperature induced spin state transition within the Fe t_{2g} multiplet. However, high pressure powder diffraction data show no sign of a structural phase transition up to 7GPa. A bulk modulus B=84(3)GPa has been extracted and the temperature dependence of the Gruneisen parameter has been determined. We discuss here the relevance of a Kondo insulator description for this material.Comment: Physical Review B in press (2005

A large-aperture strip-grid beam splitter for partially combined two millimeter-wave diagnostics on Korea Superconducting Tokamak Advanced Research

A large-aperture beam splitter has been developed for simultaneous operation of two millimeter-wave diagnostics employing different probe beams in the frequency and polarization, microwave imaging reflectometer (???85 GHz X-mode), and collective scattering system (300 GHz O-mode), on the Korea Superconducting Tokamak Advanced Research device. The beam splitter was designed based on a polarizer concept (i.e., grid of metal strips on a thin dielectric sheet), and this can be an optimal solution for these two diagnostics. Fabrication of the strips with uniform sub-millimeter width and spacing on a large dielectric sheet was achieved with an etching technique, and the laboratory test results on the reflection and transmission ratio are in good agreement with design values

Josephson effects in MgB2 meta masked ion damage junctions

Ion beam damage combined with nanoscale focused ion beam direct milling was used to create manufacturable SNS type Josephson junctions in 100 nm thick MgB$_{2}$ with T$_{C}$ of 38 K. The junctions show non-hysteretic current - voltage characteristics between 36 and 4.2 K. Experimental evidence for the dc and ac Josephson effects in MgB$_{2}$ metal masked ion damage junctions are presented. This technique is particularly useful for prototyping devices due to its simplicity and flexibility of fabrication and has a great potential for high-density integration.Comment: 12 pages, 4 figures, RevTeX4, submitted to AP

A Special Homotopy Continuation Method For A Class of Polynomial Systems

A special homotopy continuation method, as a combination of the polyhedral homotopy and the linear product homotopy, is proposed for computing all the isolated solutions to a special class of polynomial systems. The root number bound of this method is between the total degree bound and the mixed volume bound and can be easily computed. The new algorithm has been implemented as a program called LPH using C++. Our experiments show its efficiency compared to the polyhedral or other homotopies on such systems. As an application, the algorithm can be used to find witness points on each connected component of a real variety