DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base...

Scorpion primers can be used to detect PCR products in homogeneous solution. Their structure promotes a unimolecular probing mechanism. We compare their performance with that of the same probe sequence forced to act in a bimolecular manner. The data suggest that Scorpions indeed probe by a unimolecular mechanism which is faster and more efficient than the bimolecular mechanism. This mechanism i...

The kinetic stability of non-covalent macromolecular complexes controls many biological phenomena. Here we find that physical models of complex dissociation predict that competitor molecules will, in general, accelerate the breakdown of isolated bimolecular complexes by occluding rapid rebinding of the two binding partners. This prediction is largely independent of molecular details. We confirm...

Abstract We address the question of which small, bimolecular, mass action chemical reaction networks (CRNs) are capable Andronov–Hopf bifurcation (from here on abbreviated to ‘Hopf bifurcation’). It is easily shown that any such network must have at least three species and four irreversible reactions, one example a with exactly reactions was previously known due Wilhelm. In this paper, we devel...

1. A single-celled, elongating sporangiophore of Phycomyces responds to a sufficient increase in intensity of illumination by a brief increase in growth rate. This is the "light-growth response" of Blaauw. 2. The reaction time is compound, consisting of an exposure period and a latent period (this comprising both the true latent period resulting from photochemical action and any "action time" n...

We have studied ultrafast dynamics of photoexcited carriers in mc-Si:H by pump and probe laser spectroscopy. We have found that the dynamics of photoexcited carriers in mc-Si:H depend on the crystallinity of the material: in the samples with low crystalline fraction, the dynamics have a fast decay and resemble those in a-Si:H, while in the samples with high crystallinity the dynamics are slower...

In the crystal of the title compound, C6H9N3·C6H8O2, the 2-amino-4,6-di-methyl-pyrimidine and sorbic acid mol-ecules are linked through N-H⋯O and O-H⋯N hydrogen bonds, which generate a cyclic bimolecular heterosynthon with an R 2 (2)(8) graph-set motif. Further, two inversion-related pyrimidine mol-ecules are base-paired via a pair of N-H⋯N hydrogen bonds, forming a cyclic bimolecular homosynth...

Several stochastic simulation algorithms (SSAs) have recently been proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice model described by the reaction-diffusion master equation. The second SSA is an off-lattice model based on the simulation of Brownian motion of individual molecu...

When sufficiently small amounts of excitability-inducing material (EIM) are added to a bimolecular lipid membrane, the conductance is limited to a few discrete levels and changes abruptly from one level to another. From our study of these fluctuations, we have concluded that the EIM-doped bilayer contains ion-conducting channels capable of undergoing transitions between two states of different ...

The mechanism by which the peptide exchange factor HLA-DM catalyzes peptide loading onto structurally homologous class II MHC proteins is an outstanding problem in antigen presentation. The peptide-loading reaction of class II MHC proteins is complex and includes conformational changes in both empty and peptide-bound forms in addition to a bimolecular binding step. By using a fluorescence energ...