Nonextensive statistical mechanics applied to protein folding problem: kinetics aspects

A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein folding process, by Monte Carlo simulation. Nonextensive statistical approach is used: transition probability p i j between configurations i &#8594; j is given by p i j =[1 +(1 - q)&#916;Gi j/kB T ]1/(1-q), where q is the nonextensive (Tsallis) parameter. The system model consists of a chain of 27 beads immerse in its solvent; the beads represent the sequence of amino acids along the chain by means of a 10-letter stereo-chemical alphabet; a syntax (rule) to design the amino acid sequence for any given 3D structure is embedded in the model. The study focuses mainly kinetic aspects of the folding problem related with the protein folding time, represented in this work by the concept of first passage time (FPT). Many distinct proteins, whose native structures are represented here by compact self avoiding (CSA) configurations, were employed in our analysis, although our results are presented exclusively for one representative protein, for which a rich statistics was achieved. Our results reveal that there is a specific combinations of value for the nonextensive parameter q and temperature T, which gives the smallest estimated folding characteristic time (t). Additionally, for q = 1.1, (t) stays almost invariable in the range 0.9 < T < 1.3, slightly oscillating about its average value <img border=0 width=32 height=32 src="../../../../../../../img/revistas/bjp/v39n2a/a16txt01.gif" align=absmiddle > or = 27 ±&#963;, where &#963; = 2 is the standard deviation. This behavior is explained by comparing the distribution of the folding times for the Boltzmann statistics (q &#8594; 1), with respect to the nonextensive statistics for q = 1.1, which shows that the effect of the nonextensive parameter q is to cut off the larger folding times present in the original (q &#8594; 1) distribution. The distribution of natural logarithm of the folding times for Boltzmann statistics is a triple peaked Gaussian, while, for q = 1.1 (Tsallis), it is a double peaked Gaussian, suggesting that a log-normal process with two characteristic times replaced the original process with three characteristic times. Finally we comment on the physical meaning of the present results, as well its significance in the near future works

Role-separating ordering in social dilemmas controlled by topological frustration

"Three is a crowd" is an old proverb that applies as much to social interactions, as it does to frustrated configurations in statistical physics models. Accordingly, social relations within a triangle deserve special attention. With this motivation, we explore the impact of topological frustration on the evolutionary dynamics of the snowdrift game on a triangular lattice. This topology provides an irreconcilable frustration, which prevents anti-coordination of competing strategies that would be needed for an optimal outcome of the game. By using different strategy updating protocols, we observe complex spatial patterns in dependence on payoff values that are reminiscent to a honeycomb-like organization, which helps to minimize the negative consequence of the topological frustration. We relate the emergence of these patterns to the microscopic dynamics of the evolutionary process, both by means of mean-field approximations and Monte Carlo simulations. For comparison, we also consider the same evolutionary dynamics on the square lattice, where of course the topological frustration is absent. However, with the deletion of diagonal links of the triangular lattice, we can gradually bridge the gap to the square lattice. Interestingly, in this case the level of cooperation in the system is a direct indicator of the level of topological frustration, thus providing a method to determine frustration levels in an arbitrary interaction network.Comment: 9 two-column pages, 9 figures; accepted for publication in Physical Review

Resistance exercise load reduction and exercise-induced micro-damage

High volumes of resistance exercise increase muscle hypertrophy, independent of the extent of muscle damage. We compared volume load and markers of muscle damage after resistance exercise using two load reduction strategies versus a constant intensity. Methods: Twenty-seven trained men (age = 23.4±3.5 years, body mass = 74.5±10.7 Kg, height = 174±8 cm, 10 RM = 211±40 Kg) completed one weekly bout of 4 sets of leg press exercise under three loading schemes in a randomized, counterbalanced order over a three-week period. The loading schemes were (a) constant load for all sets (CON), (b) 5% load reduction after each set (LR5), and (c) 10% load reduction after each set (LR10). Volume load, muscle soreness (SOR), and range of motion (ROM) at the knee were assessed after each bout. Results: Volume load was significantly different amongst all conditions (CON = 6799±1583 Kg; LR5 = 8753±1789 Kg; 10896±2262 Kg; F=31,731; p<0.001). ROM and SOR were significantly different among conditions, with LR5 and LR10 producing greater preservations of ROM (p =<0.001) and less SOR (p < 0.001). These data may support the use of load reductions when training for hypertrophy

Detection of radiation pressure acting on 2009 BD

We report the direct detection of radiation pressure on the asteroid 2009 BD, one of the smallest multi-opposition near-Earth objects currently known, with H ~ 28.4. Under the purely gravitational model of NEODyS the object is currently considered a possible future impactor, with impact solutions starting in 2071. The detection of a radiation-related acceleration allows us to estimate an Area to Mass Ratio (AMR) for the object, that can be converted (under some assumptions) into a range of possible values for its average density. Our result AMR = (2.97 \pm 0.33) x 10^(-4) m^2 kg^(-1) is compatible with the object being of natural origin, and it is narrow enough to exclude a man-made nature. The possible origin of this object, its future observability, and the importance of radiation pressure in the impact monitoring process, are also discussed.Comment: To be submitted for refereed publication. Preliminary analysis based on the 2009-2010 data, published on arXiv because of the current observability window of the targe

Schwinger multichannel method: A study of a Feshbach resonance in e-H_2 collisions

We present results of the application of the Schwinger multichannel method to study the role of Feshbach resonances on the elastic and electronic excitation cross sections in e-H_2 collisions. Using a ^2Σ_g^+2 resonance associated with the a ^3Σ^+_g and E^1Σ^+_g states of H_2 as an example, we quantitatively illustrate the dramatic influence of open channels on the decay of such Feshbach resonances in electron-molecule collisions

Olive Oil Composition: Volatile Compounds

volatile composition of olive oil