Analytical description of finite size effects for RNA secondary structures

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.Comment: 10 pages, 13 figures, published in Phys. Rev.

Highly Designable Protein Structures and Inter Monomer Interactions

By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the interaction potential becomes larger than a critical value, the degree of designability of structures will depend on the parameters of potential. We also show that the existence of a unique ground state is highly sensitive to mutation in certain sites.Comment: 14 pages, Latex file, 3 latex and 6 eps figures are include

Failure to meet aerobic fitness standards among urban elementary students

The aim of this study was to explore the relationship of aerobic fitness with the elementary school environment and student characteristics among 4th and 5th grade children attending urban public schools in St. Louis, MO, USA. This cross-sectional study was conducted during 2012–2015 and included 2381 children (mean age 10.5 y) who completed the FITNESSGRAM® 20-m Progressive Aerobic Cardiovascular Endurance Run. Healthy Fitness Zone (HFZ) was defined according to FITNESSGRAM® aerobic capacity criteria. Other student-level variables included age, race, National School Lunch Program eligibility, BMI z-score, weight status, and daily pedometer steps. School environment variables included playground features and playground safety, physical education and recess practices, and school census tract data on vacant houses and median household income. Bivariate analyses with sex stratification were used to identify student-level and school-level predictors of failure to achieve the aerobic HFZ; predictors were then included in a multivariable logistic regression model. Failure to meet the aerobic HFZ was observed among 33% of boys and 57% of girls. School environment was not predictive, but higher age and fewer daily steps were: each additional year of age was associated with 41% higher odds of failing to meet the aerobic HFZ among boys and 100% higher odds among girls. Conversely, each additional 1000 daily steps was associated with 15% (boys) and 13% (girls) lower odds of failure. Obesity posed a 60% higher risk of failure to meet HFZ among girls. These results highlight the importance of childhood physical activity opportunities, especially for girls residing in low-resource areas. Keywords: Aerobic fitness, School, Environment, Student, Child, Urban, Low-resourc

Design of Copolymeric Materials

We devise a method for designing materials that will have some desired structural characteristics. We apply it to multiblock copolymers that have two different types of monomers, A and B. We show how to determine what sequence of A's and B's should be synthesised in order to give a particular structure and morphology. %For example in a melt of such %polymers, one may wish to engineer a body-centered %cubic structure. Using this method in conjunction with the theory of microphase separation developed by Leibler, we show it is possible to efficiently search for a desired morphology. The method is quite general and can be extended to design isolated heteropolymers, such as proteins, with desired structural characteristics. We show that by making certain approximations to the exact algorithm, a method recently proposed by Shakhnovich and Gutin is obtained. The problems with this method are discussed and we propose an improved approximate algorithm that is computationally efficient.Comment: 15 pages latex 2.09 and psfig, 1 postscript figure

Heteropolymer Sequence Design and Preferential Solvation of Hydrophilic Monomers: One More Application of Random Energy Model

In this paper, we study the role of surface of the globule and the role of interactions with the solvent for designed sequence heteropolymers using random energy model (REM). We investigate the ground state energy and surface monomer composition distribution. By comparing the freezing transition in random and designed sequence heteropolymers, we discuss the effects of design. Based on our results, we are able to show under which conditions solvation effect improves the quality of sequence design. Finally, we study sequence space entropy and discuss the number of available sequences as a function of imposed requirements for the design quality

Exact enumeration of Hamiltonian circuits, walks, and chains in two and three dimensions

We present an algorithm for enumerating exactly the number of Hamiltonian chains on regular lattices in low dimensions. By definition, these are sets of k disjoint paths whose union visits each lattice vertex exactly once. The well-known Hamiltonian circuits and walks appear as the special cases k=0 and k=1 respectively. In two dimensions, we enumerate chains on L x L square lattices up to L=12, walks up to L=17, and circuits up to L=20. Some results for three dimensions are also given. Using our data we extract several quantities of physical interest

Kramers rate theory of ionization and dissociation of bound states

Calculating the microscopic dissociation rate of a bound state, such as a classical diatomic molecule, has been difficult so far. The problem was that standard theories require an energy barrier over which the bound particle (or state) escapes into the preferred low-energy state. This is not the case when the long-range repulsion responsible for the barrier is either absent or screened (as in Cooper pairs, ionized plasma, or biomolecular complexes). We solve this classical problem by accounting for entropic memory at the microscopic level. The theory predicts dissociation rates for arbitrary potentials and is successfully tested on the example of plasma, where it yields an estimate of ionization in the core of Sun in excellent agreement with experiments. In biology, the new theory accounts for crowding in receptor-ligand kinetics and protein aggregation

An Approach to Web-Scale Named-Entity Disambiguation

We present a multi-pass clustering approach to large scale. wide-scope named-entity disambiguation (NED) oil collections of web pages. Our approach Uses name co-occurrence information to cluster and hence disambiguate entities. and is designed to handle NED on the entire web. We show that on web collections, NED becomes increasing), difficult as the corpus size increases, not only because of the challenge of scaling the NED algorithm, but also because new and surprising facets of entities become visible in the data. This effect limits the potential benefits for data-driven approaches of processing larger data-sets, and suggests that efficient clustering-based disambiguation methods for the web will require extracting more specialized information front documents

Viscosity Dependence of the Folding Rates of Proteins

The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is given by the Langevin equation we show that the folding rates increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and have a maximum at intermediate values. The Kramers theory of barrier crossing provides a quantitative fit of the numerical results. By mapping the simulation results to real proteins we estimate that for optimized sequences the time scale for forming a four turn \alpha-helix topology is about 500 nanoseconds, whereas the time scale for forming a beta-sheet topology is about 10 microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical Review Letter

Timed Parity Games: Complexity and Robustness

We consider two-player games played in real time on game structures with clocks where the objectives of players are described using parity conditions. The games are \emph{concurrent} in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to play strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to \emph{turn-based} (i.e., not concurrent) \emph{finite-state} (i.e., untimed) parity games. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. The states of the resulting game are based on clock regions of the original game, and the state space of the finite game is linear in the size of the region graph. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, \emph{limit-robust} and \emph{bounded-robust} winning strategies. Using a limit-robust winning strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust winning. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust winning strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers