General statistical-thermodynamical treatment of one-dimensional multicomponent molecular hetero-assembly in solution

A general treatment has been developed for the multicomponent one-dimensional non-covalent molec-ular hetero-assembly in solution using transfer matrix and sequence generating function approaches. The main result is set of equations, which allows one to obtain any thermodynamical quantities of the mul-ticomponent system and, in particular, experimental observable enabling one to get all equilibrium parameters of molecular interaction. The matrix form of presentation of the key equations allows their direct incorporation into matrix-oriented mathematical software, which leads to a two orders of magni-tude increase in speed of calculation of as compared to other known approache

Theoretical description of metabolism using queueing theory

A theoretical description of the process of metabolism has been developed on the basis of the Pachinkomodel (seeNicholson andWilson in Nat Rev Drug Discov 2:668–676, 2003) and the queueing theory. The suggested approach relies on the probabilistic nature of the metabolic events and the Poisson distribution of the incoming flowof substratemolecules.The main focus of thework is an output flowofmetabolites or the effectiveness of metabolism process. Two simplest models have been analyzed: short- and long-living complexes of the source molecules with a metabolizing point (Hole) without queuing. It has been concluded that the approach based on queueing theory enables a very broad range of metabolic events to be described theoretically from a single probabilistic point of vie

Quantitative correlation of the in vitro biological effect with parameters of molecular complexation in mutagen-interceptor systems

According to the theory of interceptor-protector action a quantitative link between the physico-chemical parameters of molecular complexation and in vitro biological effect in aromatic drug-interceptor systems must exist. In the present communication such link between relative change in mutagenicity of IQ-type aromatic mutagens on addition of aromatic interceptor molecules with equilibrium hetero-association constants of mutagen-interceptor complexation has been found using the published in vitro data in bacteria cell system

Energy analysis of non-covalent ligand binding to nucleic acids: Present and future

Generalization of current views on energy analysis of complex formation of biologically active compounds with nucleic acids is represented and the outlook for further developments is determine

The theory of interceptor-protector action of DNA binding drugs

The review discusses the theory of interceptor-protector action (the IPA theory) as the new selfconsistent biophysical theory establishing a quantitative interrelation between parameters measured in independent physico-chemical experiment and in vitro biological experiment for the class of DNA binding drugs. The elements of the theory provide complete algorithm of analysis, which may potentially be applied to any system of DNA targeting aromatic drugs. Such analytical schemes, apart from extension of current scientific knowledge, are important in the context of rational drug design for managing drug's response by changing the physico-chemical parameters of molecular complexatio

Entropic binding mode preference in cooperative homo-dimeric drug-DNA recognition

The present work reveals the entropic preference in the two-step binding process of small molecule DNA minor groove binders (MGBs), involving the formation of a dimer in free solution followed by the binding of that dimer to DNA, which contrasts with the sequential or simultaneous cooperative binding of two unbound MGB molecules with DNA that is implicitly assumed in the majority of reported DNA-MGB binding studies. The results are generalized for the n-mer binding case and the methodological outcomes are discussed

Space-charge region recombination in monocrystalline silicon-based barrier structures with long lifetimes and its impact on key characteristics of high-efficiency solar cells

The recombination rate in the space charge region (SCR) of a silicon-based barrier structure with long Shockley-Reed-Hall lifetime is calculated theoretically taking into account the concentration gradient of excess electron-hole pairs in the base region. The effects of the SCR lifetime and the applied voltage on the structure's ideality factor are analyzed. The ideality factor is significantly reduced by the concentration gradient of electron-hole pairs. This mechanism provides an increase of the effective lifetime compared to the case when it is insignificant, which is realized at sufficiently low pair concentrations. The theoretical results are shown to be in agreement with experimental data

General features of the energetics of complex formation between ligand and nucleic acids

The analysis of the energy contributions of various physical factors to the complex formation between biologically active compounds and nucleic acids in aqueous solution was performed. A comparison of the energy parameters was made for ligand-ligand, intercalator-DNA, MGB-DNA and ligand-RNA groups. It was shown that the energetics of these reactions is of compensatory nature. Physical factors exerting the most pronounced influence on the energy parameters were identified. Correlation of the energy contributions to MGB-DNA complex formation and its biological effect was foun

Double Entropic Stochastic Resonance

We demonstrate the appearance of a purely entropic stochastic resonance (ESR) occurring in a geometrically confined system, where the irregular boundaries cause entropic barriers. The interplay between a periodic input signal, a constant bias and intrinsic thermal noise leads to a resonant ESR-phenomenon in which feeble signals become amplified. This new phenomenon is characterized by the presence of two peaks in the spectral amplification at corresponding optimal values of the noise strength. The main peak is associated with the manifest stochastic resonance synchronization mechanism involving the inter-well noise-activated dynamics while a second peak relates to a regime of optimal sensitivity for intra-well dynamics. The nature of ESR, occurring when the origin of the barrier is entropic rather than energetic, offers new perspectives for novel investigations and potential applications. ESR by itself presents yet another case where one constructively can harvest noise in driven nonequilibrium systems.Comment: 6 pages, 7 figures ; Europhys. Lett., in press (2009