In this paper, we describe the way to set up the floppy-box Monte Carlo (FBMC) method [L. Filion, M. Marechal, B. van Oorschot, D. Pelt, F. Smallenburg, and M. Dijkstra, Phys. Rev. Lett. 103, 188302 (2009)] to predict crystal-structure candidates for colloidal particles. The algorithm is explained in detail to ensure that it can be straightforwardly implemented on the basis of this text. The ha...

To investigate conformational properties of an isolated n-octadecane chain solvated in water-acetonitrile mixtures, configurational-bias Monte Carlo simulations in the isobaric-isothermal ensemble were performed at T = 323 K and p = 10 atm. The united-atom version of the transferable potentials for phase equilibria force field was used to represent n-octadecane and acetonitrile, and the TIP-4P ...

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can ...

Supercoiled DNA polymer models for which the torsional energy depends on the total twist of molecules (Tw) are a priori well suited for thermodynamic analysis of long molecules. So far, nevertheless, the exact determination of Tw in these models has been based on a computation of the writhe of the molecules (Wr) by exploiting the conservation of the linking number, Lk=Tw+Wr, which reflects topo...

BACKGROUND Intradermal testing (IDT) in cats has potential limitations; this has led to an interest in novel testing methods. A pilot study demonstrated that healthy cats produced reliable percutaneous glycerinated (PG) histamine wheals, whereas percutaneously applied glycerosaline did not lead to wheal formation. HYPOTHESIS/OBJECTIVE The purpose of this study was to determine if percutaneous...

Since, landfill areas are still the most widely used solid waste disposal method across the world, leachate generated from landfills should be given importance. Leachate of landfills exerts environmental risks mostly on surface and groundwater with its high pollutant content, which may cause unbearable water quality. This leads to the obligation for decontamination and remediation program to be...

Research on the systems side of Computer Science straddles the line between science and engineering. Both aspects are important, so neither side should be ignored in favor of the other. In my research, I have sought to discover the underlying nature of the mechanisms responsible for a given behavior. Using this understanding, I could create a simple model of the process whose underlying science...