Microscopic Theory of Protein Folding Rates.I: Fine Structure of the Free Energy Profile and Folding Routes from a Variational Approach

A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G. Wolynes, Phys. Rev. Lett. {\bf 81}, 5237 (1998)]. We choose the $\lambda$-repressor protein as an illustrative example and focus on how the polymer chain statistics influence free energy profiles and partially ordered ensembles of structures. In particular, we investigate the role of chain stiffness on the free energy profile and folding routes. We evaluate the applicability of simpler approximations in which the conformations of the protein molecule along the folding route are restricted to have residues that are either entirely folded or unfolded in contiguous stretches. We find that the folding routes obtained from only one contiguous folded region corresponds to a chain with a much greater persistence length than appropriate for natural protein chains, while the folding route obtained from two contiguous folded regions is able to capture the relatively folded regions calculated within the variational approach. The free energy profiles obtained from the contiguous sequence approximations have larger barriers than the more microscopic variational theory which is understood as a consequence of partial ordering.Comment: 16 pages, 11 figure

Game Based Learning for Safety and Security Education

Safety and security education are important part of technology related education, because of recent number of increase in safety and security related incidents. Game based learning is an emerging and rapidly advancing forms of computer-assisted instruction. Game based learning for safety and security education enables students to learn concepts and skills without the risk of physical injury and security breach. In this paper, a pedestal grinder safety game and physical security game have been developed using industrial standard modeling and game development software. The average score of the knowledge test of grinder safety game was 82%, which is higher than traditional lecture only instruction method. In addition, the survey of physical security game shows 84% average satisfaction ratio from high school students who played the game during the summer camp. The results of these studies indicated that game based learning method can enhance students' learning without potential harm to the students

Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics

The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction coordinates are identified as collective growth modes of the unstable fluctuations about the saddle-points in the free energy surface. The description of the chain dynamics incorporates internal friction (independent of the solvent viscosity) arising from the elementary isomerizations of the backbone dihedral angles. We find that the folding rate depends linearly on the solvent friction for high viscosity, but saturates at low viscosity because of internal friction. For $\lambda$-repressor, the calculated folding rate prefactor, along with the free energy barrier from the variational theory, gives a folding rate that agrees well with the experimentally determined rate under highly stabilizing conditions, but the theory predicts too large a folding rate at the transition midpoint. This discrepancy obtained using a fairly complete quantitative theory inspires a new set of questions about chain dynamics, specifically detailed motions in individual contact formation.Comment: 18 pages, 8 figure

Drag force on an oscillating object in quantum turbulence

This paper reports results of the computation of the drag force exerted on an oscillating object in quantum turbulence in superfluid $^4$He. The drag force is calculated on the basis of numerical simulations of quantum turbulent flow about the object. The drag force is proportional to the square of the magnitude of the oscillation velocity, which is similar to that in classical turbulence at high Reynolds number. The drag coefficient is also calculated, and its value is found to be of the same order as that observed in previous experiments. The correspondence between quantum and classical turbulences is further clarified by examining the turbulence created by oscillating objects.Comment: 7 pages, 5 figures, 1 tabl

Parametrizations of triaxial deformation and E2 transitions of the wobbling band

By the very definition the triaxial deformation parameter $\gamma$ is related to the expectation values of the K=0 and K=2 components of the intrinsic quadrupole tensor operator. On the other hand, using the same symbol "$\gamma$", various different parametrizations of triaxial deformation have been employed, which are suitable for various types of the mean-field potentials. It is pointed out that the values of various "$\gamma$" are quite different for the same actual triaxial deformation, especially for the large deformation; for example, the difference can be almost a factor two for the case of the triaxial superdeformed bands recently observed in the Hf and Lu nuclei. In our previous work, we have studied the wobbling band in Lu nuclei by using the microscopic framework of the cranked Nilsson mean-field and the random phase approximation, where the most serious problem is that the calculated B(E2) value is about factor two smaller. It is shown that the origin of this underestimation can be mainly attributed to the small triaxial deformation; if is used the same triaxial deformation as in the analysis of the particle-rotor model, the calculated B(E2) increases and gives correct magnitude compared with the experimental data.Comment: 10 pages, 9 figure

Competing Ground States of a Peierls-Hubbard Nanotube

Motivated by iodo platinum complexes assembled within a quadratic-prism lattice, [Pt(C$_2$H$_8$N$_2$)(C$_{10}$H$_8$N$_2$)I]$_4$(NO$_3$)$_8$, we investigate the ground-state properties of a Peierls-Hubbard four-legged tube. Making a group-theoretical analysis, we systematically reveal a variety of valence arrangements, including half-metallic charge-density-wave states. Quantum and thermal phase competition is numerically demonstrated with particular emphasis on doping-induced successive insulator-to-metal transitions with conductivity increasing stepwise.Comment: 6 pages, 4 figures. to be published in Europhys. Lett. 87 (2009) 1700

Length-weight relationship and relative condition factor of Stolephorus commersonii (Lacepede, 1803) exploited along Kerala coast

The length-weight relationship and relative condition factor of Stolephorus commersonii was calculated to assess the significance of allometric factor and the well being. The study was carried out by using the data collected from ring seine and purse seine catches during the year 2010-2011. The length of species in catches ranged from 5 to 14.6 cm with a mean length of 9.24 ± 1.83 cm and the weight ranged from 1 to 25g with an average weight of 6.64 ± 3.96 g. Length-weight relationship calculated for male, female and pooled are W = 0.0070 L3.02, W = 0. 00756 L2.99 and W = 0. 0073 L3.006 respectively. The relative condition factor (Kn) estimated separately for male and female showed monthly fluctuation. The highest Kn values were observed in February and August and the lowest in June for both the sexes

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Atomistic study on the pressure dependence of the melting point of NdFe12

We investigated, using molecular dynamics, how pressure affects the melting point of the recently theorised and epitaxially grown structure NdFe12. We modified Morse potentials using experimental constants and a genetic algorithm code, before running two-phase solid-liquid coexistence simulations of NdFe12 at various temperatures and pressures. The refitting of the Morse potentials allowed us to significantly improve the accuracy in predicting the melting temperature of the constituent elements