Replica-Exchange Method in van der Waals Radius Space: Overcoming Steric Restrictions for Biomolecules

We present a new type of the Hamiltonian replica-exchange method, in which not temperatures but the van der Waals radius parameter is exchanged. By decreasing the van der Waals radii that control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum free-energy states and realizes effective sampling in the conformational space. We applied this method to an alanine dipeptide in aqueous solution and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical method.Comment: 14 pages, (Revtex4), 11 figure

Formation of Kaonic Atoms and Kaonic Nuclei by In-flight (K−,pK^-,p) reactions

We study the kaonic atom and kaonic nucleus formation by the in-flight ($K^-, p$) reactions for C, O, Si and Ca target cases theoretically. Deeply bound kaonic atoms were predicted to exist as quasi-stable states and were expected to be observed in some proper experimental methods. Kaonic nuclear states are also expected to exist with large decay widths. We evaluate the formation cross sections of the kaonic atoms and kaonic nuclei using an effective number approach. We show that the indications of the kaonic bound states can be observed in the outgoing proton energy spectra.Comment: 17 pages, 11 figures: Minor corrections made. Results and Conclusion do not chang

Monte Carlo Simulations in Multibaric-Multithermal Ensemble

We propose a new generalized-ensemble algorithm, which we refer to as the multibaric-multithermal Monte Carlo method. The multibaric-multithermal Monte Carlo simulations perform random walks widely both in volume space and in potential energy space. From only one simulation run, one can calculate isobaric-isothermal-ensemble averages at any pressure and any temperature. We test the effectiveness of this algorithm by applying it to the Lennard-Jones 12-6 potential system with 500 particles. It is found that a single simulation of the new method indeed gives accurate average quantities in isobaric-isothermal ensemble for a wide range of pressure and temperature.Comment: 8 pages, (RevTeX), 5 figure

Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions

We present the second version of Melina, a web-based tool for promoter analysis. Melina II shows potential DNA motifs in promoter regions with a combination of several available programs, Consensus, MEME, Gibbs sampler, MDscan and Weeder, as well as several parameter settings. It allows running a maximum of four programs simultaneously, and comparing their results with graphical representations. In addition, users can build a weight matrix from a predicted motif and apply it to upstream sequences of several typical genomes (human, mouse, S. cerevisiae, E. coli, B. subtilis or A. thaliana) or to public motif databases (JASPAR or DBTBS) in order to find similar motifs. Melina II is a client/server system developed by using Adobe (Macromedia) Flash and is accessible over the web at http://melina.hgc.jp

Imaginary agents exist perceptually for children but not for adults

Mental imagery refers to representations and the accompanying experience of sensory information in the absence of appropriate sensory input. Little is known about children’s social imagery, imagery about an agent. It is possible that children’s social imagery may qualitatively differ from that of adults by involving more perceptual characteristics. We conducted three experiments to investigate the perceptual existence of social imagery when induced by verbal cues. Experiment 1 was a precondition for Experiments 2 and 3, and we examined whether children’s and adults’ predictive eye movements were disrupted by the presence of a real person’s face. Preschool children (n = 20) and adults (n = 20) watched a video where a woman, with/without her face shown, placed balls into a bucket. Participants’ gazes were less predictive of the woman’s actions in ‘Face’ versus ‘No-Face’ videos, indirectly indicating the perceptual presence of agents. Next, we examined whether adults’ and children’s predictive eye movements were affected by imagining a person. In Experiment 2, adult participants were presented with a video where the balls moved automatically and were asked to either watch the video (Ball condition, n = 20) or imagine that an invisible person moved the balls (Imagination condition, n = 20). Adult gazes did not differ between conditions. However, in Experiment 3, preschool children’s gazes were less predictive when imagining an invisible person’s actions (Invisible condition, n = 20) than when not imagining anything (Ball condition, n = 20) or when imagining an object (Fan condition, n = 20). The results suggest that children experience realistic social imagery induced by verbal cues

Thrombin Stimulates Synthesis of Macrophage Colony-Stimulating Factor, Granulocyte-Macrophage Colony-Stimulating Factor and Granulocyte Colony-Stimulating Factor by Human Proximal Tubular Epithelial Cells in Culture

Background/Aims: Colony-stimulating factors (CSFs) are well-known hematopoietic growth factors. Although recent studies revealed that CSFs are involved in many inflammatory conditions, the local production of CSFs and its regulation in the kidney is not well elucidated. Therefore, using cultured human proximal tubular epithelial cells (PTEC), we examined the effect of thrombin on CSFs production, since thrombin has been suggested to play an important role in tubulointerstitial injury. Methods: PTEC were incubated with thrombin (0.5–5.0 U/ml) and the effects on the production of macrophage CSF (M-CSF), granulocyte-macrophage CSF (GM-CSF) and granulocyte CSF (G-CSF) were measured in the cell supernatant by enzyme-linked immunosorbent assay, and the expressions of mRNA were analyzed by quantitative real-time reverse transcription polymerase chain reaction. Using argatroban, a direct thrombin inhibitor, we also examined the specific effect of thrombin. Results: Thrombin 5.0 U/ml significantly stimulated the production of M-CSF (p Conclusion: We demonstrated that thrombin significantly increased the production of CSFs by PTEC. These data suggest that the local production of CSFs in the tubulointerstitium may affect tubulointerstitial lesions in kidney injury