Multidimensional replica-exchange method for free-energy calculations

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.Comment: 13 pages, (ReVTeX), 9 figures. J. Chem. Phys. 113 (2000), in pres

Generalized-ensemble simulations of spin systems and protein systems

In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the generalized-ensemble algorithms in order to overcome this multiple-minima problem. Three well-known generalized-ensemble algorithms, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described. We then present three new generalized-ensemble algorithms based on the combinations of the three methods. Effectiveness of the new methods are tested with a Potts model and protein systems.Comment: 12 pages, (LaTeX2e), 6 figures, Computer Physics Communications, in pres

Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical weight factor. In this method a short replica-exchange simulation is performed and the multicanonical weight factor is obtained by the multiple-histogram reweighting techniques. The second one is a further extension of the first in which a replica-exchange multicanonical simulation is performed with a small number of replicas. These new algorithms are particularly useful for studying the protein folding problem.Comment: 9 pages, (ReVTeX), 7 figures. Chem. Phys. Lett. (2000), in pres

Liposarcoma Arising in the Foot: A Case Report

Liposarcoma is categorized as a soft tissue sarcoma and most commonly appears in the lower extremities and rarely in the foot during adulthood. We present a very rare case report of a primary well-differentiated liposarcoma arising in the foot on a 60-year-old female. Marginal resection of the tumor with metatarsal ray amputation was eventually performed. The patient's postoperative course was uneventful without recurrence 5 years after the original operation. The authors review the literature and also report on the low incidence of this tumor arising in the foot

Proposal for Global Standard Maneuvering Orders for Tugboats

The use of “Standard Maneuvering Orders” for tugboats, vocabulary and phrases mutually pre-agreed between ships and tugboats, is essential for the former to provide clear direction for the latter when berthing or un-berthing safely. Tugboats will need time to change their posture before they take actions in response to orders from persons responsible for ships’ maneuvering. Therefore, when giving directions to change tugboats’ posture, persons who handle their ships are required to send out tug orders, with regard to “delay time,” a gap be-tween the orders from ships and the actions taken by tugboats. “Tug Orders” standardized and used in Japan are composed of the following three factors concerning towage work: tugboat’s motion, direction and engine power, but the author’s research shows that there are “Non-standard” special maneuvering orders other than those “standardized,” which causes such problems as a gap in perception between pilots and tugboat’s opera-tors, etc. The purpose of this paper is to research the delay time between orders for and actions by tugboats and consider the appropriate and safe timing of providing instructions to them, and then to propose globally-authorized “Standard Maneuvering Orders for tugboats”, discussing a problem involved in the use of the special orders used in Japan, and the way in which tug orders are used in other countries

Mite-antigen Stimulates MAL Expression in Peripheral Blood T Cells of Mite-sensitive Subjects

ABSTRACTBackgroundDifferential gene expression in CD3+ T cells from allergic patients stimulated with allergen will provide important information on the responses of T cells.MethodsAfter stimulation of peripheral blood mononuclear cells (PBMCs) with mite extracts, levels of gene transcription were examined in CD3+ T cells from allergic patients.ResultsStimulation of PBMCs from mite specific IgE positive subjects resulted in specific upregulation of MAL transcription levels that was mediated by IL-4 secretion. The MAL protein in IL-4 stimulated primary T cells preferentially localized in glycolipid-enriched membrane (GEM) microdomains. When MAL was exogenously expressed in primary T cells, CD3ζ was concomitantly enriched, along with the expression of MAL, in GEM microdomains.ConclusionsGEMs are important for the formation and stabilization of TCR signaling complexes. Therefore, MAL may play a role in the formation of GEMs in activated T cells and the high expression of MAL may contribute to Th2 immune response