Energy transfer efficiency distributions in polymers in solution during folding and unfolding

Distribution of fluorescence resonance energy transfer (FRET) efficiency between the two ends of a Lennard-Jones polymer chain both at equilibrium and during folding and unfolding has been calculated, for the first time, by Brownian dynamics simulations. The distribution of FRET efficiency becomes bimodal during folding of the extended state subsequent to a temperature quench, with the width of the distribution for the extended state broader than that for the folded state. The reverse process of unfolding subsequent to a upward temperature jump shows different characteristics. The distributions show significant viscosity dependence which can be tested against experiments.

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.

Fracture energy and softening behavior of high-strength concrete

An experimental investigation on the fracture properties of high-strength concrete (HSC) is reported. Three-point bend beam specimens of size 100 x 100 x 500 mm were used as per RILEM-FMC 50 recommendations. The influence of maximum size of coarse aggregate on fracture energy, fracture toughness, and characteristic length of concrete has been studied. The compressive strength of concrete ranged between 40 and 75 MPa. Relatively brittle fracture behavior was observed with the increase in compressive strength. The load-CMOD relationship is linear in the ascending portion and gradually drops off after the peak value in the descending portion. The length of the tail end portion of the softening curve increases as the size of coarse aggregate increases. The fracture energy increases as the maximum size of coarse aggregate and compressive strength of concrete increase. The characteristic length of concrete increases with the maximum size of coarse aggregate and decreases as the compressive strength increases, (C) 2002 Elsevier Science Ltd. All rights reserved.

Ratchet for energy transport between identical reservoirs

A one-dimensional periodic array of elastically colliding hard points, with a noncentrosymmetric unit cell, connected at its two ends to identical but nonthermal energy reservoirs, is shown to carry a sustained unidirectional energy current.

A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands

Angiogenin is a protein belonging to the superfamily of RNase A. The RNase activity of this protein is essential for its angiogenic activity. Although members of the RNase A family carry out RNase activity, they differ markedly in their strength and specificity. In this paper, we address the problem of higher specificity of angiogenin towards cytosine against uracil in the first base binding position. We have carried out extensive nano-second level molecular dynamics(MD) computer simulations on the native bovine angiogenin and on the CMP and UMP complexes of this protein in aqueous medium with explicit molecular solvent. The structures thus generated were subjected to a rigorous free energy component analysis to arrive at a plausible molecular thermodynamic explanation for the substrate specificity of angiogenin.

Effect of orientational motion of mobile chromophores on the dynamics of Forster energy transfer in polymers

Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientational motion of the donor-acceptor (D-A) chromophore pair on the Forster energy transfer between the D-A pair embedded in a polymer chain in solution. It is found that the usually employed orientational averaging (that is, replacing the orientational factor, kappa, by kappa (2) = 2/3) may lead to an error in the estimation of the rate of the reaction by about 20%. In the limit of slow orientational relaxation, the preaveraging of the orientational factor leads to an overestimation of the rate, while in the opposite limit of very fast orientational relaxation, the usual scheme underestimates the rate. The latter results from an interesting interplay between reaction and diffusion. On the other hand, when one of the chromophores is fixed, the preaveraged rate is found to be fairly reliable if the rotational relaxation of the chromophore is sufficiently fast. The present study also reveals a power law dependence of the FRET rate on the chain length (rate proportional to N- alpha, with alpha approximate to 2.6).

Electronic structure of ${\rm Ca}_{1-x}{\rm Sr}_x{\rm VO}_3$: A tale of two energy scales

We investigate the electronic structure of Ca1-xSrxVO3 using photoemission spectroscopy. Core level spectra establish an electronic phase separation at the surface, leading to a distinctly different surface electronic structure compared to the bulk. Analysis of the photoemission spectra of this system allowed us to separate the surface and bulk contributions. These results help us to understand properties related to two vastly differing energy scales, namely the low-energy scale of thermal excitations ( $\sim\!k_{\rm B}T$) and the high-energy scale related to Coulomb and other electronic interactions.