Biomedical subjects

Hsiao-Ping Hsu

Publications and source records attributed to Hsiao-Ping Hsu.

6 recordsLinked to original sources

PubMed2004

Metropolis simulations of Met-Enkephalin with solvent-accessible area parametrizations.

We investigate the solvent-accessible area method by means of Metropolis simulations of the brain peptide Met-Enkephalin at 300 K. For the energy function ECEPP/2 nine atomic solvation parameter (ASP) sets are studied. The simulations are compared with one another, with simulations with a distance dependent electrostatic permittivity epsilon(r), and with vacuum simulations (epsilon=2). Parallel tempering and the biased Metropolis techniques RM1 are employed and their performance is evaluated. The measured observables include energy and dihedral probability densities, integrated autocorrelation times, and acceptance rates. Two of the ASP sets turn out to be unsuitable for these simulations. For all other systems selected configurations are minimized in the search for global energy minima, which are found for vacuum and the epsilon(r) system, but for none of the ASP models. Other observables show a remarkable dependence on the ASPs. In particular, we find three ASP sets for which the autocorrelations at 300 K are considerably smaller than those for vacuum simulations.

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PubMed2004

Polymers confined between two parallel plane walls.

Single three-dimensional polymers confined to a slab, i.e., to the region between two parallel plane walls, are studied by Monte Carlo simulations. They are described by N-step walks on a simple cubic lattice confined to the region 1< or = z < or = D. The simulations cover both regions D< >RF (where RF approximately Nnu is the Flory radius, with nu approximately 0.587), as well as the cross-over region in between. Chain lengths are up to N=80 000, slab widths up to D=120. In order to test the analysis program and to check for finite size corrections, we actually studied three different models: (a) ordinary random walks (mimicking Theta polymers); (b) self-avoiding walks; and (c) Domb-Joyce walks with the self-repulsion tuned to the point where finite size corrections for free (unrestricted) chains are minimal. For the simulations we employ the pruned-enriched-Rosenbluth method with Markovian anticipation. In addition to the partition sum (which gives us a direct estimate of the forces exerted onto the walls), we measure the density profiles of monomers and of end points transverse to the slab, and the radial extent of the chain parallel to the walls. All scaling laws and some of the universal amplitude ratios are compared to theoretical predictions.

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PubMed2003

Structure optimization in an off-lattice protein model.

We study an off-lattice protein toy model with two species of monomers interacting through modified Lennard-Jones interactions. Low energy configurations are optimized using the pruned-enriched-Rosenbluth method (PERM), hitherto employed to native state searches only for off-lattice models. For two dimensions we found states with lower energy than previously proposed putative ground states for all chain lengths >/=13. This indicates that PERM has the potential to produce native states also for more realistic protein models. For d=3, where no published ground states exist, we present some putative lowest energy states for future comparison with other methods.

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PubMed2003

Growth-based optimization algorithm for lattice heteropolymers.

An improved version of the pruned-enriched-Rosenbluth method (PERM) is proposed and tested on finding lowest energy states in simple models of lattice heteropolymers. It is found to outperform not only the previous version of PERM, but also all other fully blind general purpose stochastic algorithms which have been employed on this problem. In many cases, it found new lowest energy states missed in previous papers. Limitations are discussed.

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PubMed2003

Early hyperbaric oxygen therapy attenuates disease severity in lupus-prone autoimmune (NZB x NZW) F1 mice.

The effects of hyperbaric oxygen (HBO(2)) therapy on the immune system are reported including potential changes to the CD4/CD8 ratio and a decreased proliferation of lymphocytes during exposure. The immunosuppressive effect of HBO(2) had been suggested to be applicable for the treatment of certain autoimmune diseases. (NZB x NZW) F1 hybrid mice, the unique lupus-prone mice, have been used for elucidating the pathogenesis of SLE. To investigate the effect of HBO(2) on NZB/W F1 lupus-prone mice, 32 female mice were divided into four groups. Three groups of mice were treated with HBO(2) (2.5 atm abs (ATA) for 90 min daily over 2 weeks) starting at (A) 3 months, (B) 6 months, or (C) 8 months of age, while the remaining group (D) served as control. Animals were followed until 11 months of age. Experimental parameters included life span, proteinuria, peripheral lymphocytes, anti-dsDNA antibody titers, and renal histopathology. HBO(2) treatment resulted in increased survival, decreased proteinuria, alterations in lymphocyte-subset redistribution, reduced anti-dsDNA antibody titers, and amelioration of immune-complex deposition in groups A and B. Our data demonstrated that HBO(2) therapy attenuated disease severity in NZB/W F1 mice. HBO(2) treatment may be of use in the clinical treatment of lupus patients and would benefit from further study.

Age Factors↗

PubMed2002

Stretched polymers in a poor solvent.

Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest-neighbor attraction. The bias corresponds to opposite forces applied to the first and last monomers. We show that both in d=2 and d=3 a phase transition occurs as this force is increased beyond a critical value, where the polymer changes from a collapsed globule to a stretched configuration. This transition is second order in d=2 and first order in d=3. For d=2 we predict the transition point quantitatively from properties of the unstretched polymer. This is not possible in d=3, but even there we can estimate the transition point precisely, and we can study the scaling at temperatures slightly below the collapse temperature of the unstretched polymer. We find very large finite size corrections that would make very difficult the estimate of the transition point from straightforward simulations.

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