Thermodynamic Analysis of Interacting Nucleic Acid Strands

Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. This expression can be evaluated explicitly for small numbers of strands, allowing the calculation of the equilibrium population distribution for each species of complex. Alternatively, for large systems (e.g., a test tube), we show that the unique complex concentrations corresponding to thermodynamic equilibrium can be obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality

Kaolin shear thickening fluid reinforced UHMWPE composites for protective clothing

This study reports the designing and reinforcing of impact resistant textile composites using kaolin based shear thickening colloidal dispersions as the filler material. The reinforced fabric is targeted for the chest protection of cricketers. A shear thickening fluid (STF) has been prepared using kaolin and glycerol, at kaolin volume fractions of 34% and 38%. A combination of mixing techniques including mechanical blending and ultra-sonication are used to prepare the colloidal dispersions. Ultra high molecular weight polyethylene (UHMWPE) woven fabric structures are reinforced with the STF. The fabric coated with STF are then measured for their flexibility, and impact resistance using Shirley stiffness tester and a series of modified drop tower tests respectively. Kaolin STF at 38% volume fraction shows best results in impregnated fabric samples. STF reinforced fabrics provide better impact resistance with improved moisture absorption and flexibility in comparison to the conventional chest guard material

Evidence for a Noachian-Aged Ephemeral Lake in Gusev Crater, Mars

Gusev crater was selected as the landing site for the Spirit rover because of the likelihood that it contained an ancient lake. Although outcrops rich in Mg-Fe carbonate dubbed Comanche were discovered in the Noachian-aged Columbia Hills, they were inferred to result from volcanic hydrothermal activity. Spirit encountered other mineral and chemical indicators of aqueous activity, but none was recognized as definitive evidence for a former lake in part because none was associated with obvious lacustrine sedimentary deposits. However, water discharge into Martian crater basins like Gusev may have been episodic, producing only small amounts of sediment and shallow ephemeral lakes. Evaporative precipitation from such water bodies has been suggested as a way of producing the Mg- and Fe-rich carbonates found in ALH84001 and carbonates and salts in some nakhlites a hypothesis we examine for the Comanche carbonate

Developing Freight Analysis Zones at a State Level: A Cluster Analysis Approach

The ability to forecast freight to support transportation infrastructure decisions is limited by data availability at a level of detail meaningful to the transportation planner. The Freight Analysis Framework Version 2 is a national, comprehensive public freight database. The difficulty that transportation planners encounter when using this data is due to extensive aggregation. In this paper, the authors develop a methodology for creating freight analysis zones (FAZs) at a sub-state level by partitioning a state into meaningful zones that support freight transportation planning and analysis. The authors conc

Reconciling the Differences between the Measurements of CO2 Isotopes by the Phoenix and MSL Landers

Precise stable isotope measurements of the CO2 in the martian atmosphere have the potential to provide important constraints for our understanding of the history of volatiles, the carbon cycle, current atmospheric processes, and the degree of water/rock interaction on Mars. There have been several different measurements by landers and Earth based systems performed in recent years that have not been in agreement. In particular, measurements of the isotopic composition of martian atmospheric CO2 by the Thermal and Evolved Gas Analyzer (TEGA) instrument on the Mars Phoenix Lander and the Sample Analysis at Mars (SAM) instrument on the Mars Science Laboratory (MSL) are in stark disagreement. This work attempts to use measurements of mass 45 and mass 46 of martian atmospheric CO2 by the SAM and TEGA instruments to search for agreement as a first step towards reaching a consensus measurement that might be supported by data from both instruments

Topological constraints in nucleic acid hybridization kinetics

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex