Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions

Several stochastic simulation algorithms (SSAs) have been recently 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 molecules and their reactive collisions. In both cases, it is shown that the commonly used implementation of bimolecular reactions (i.e. the reactions of the form A + B -> C, or A + A -> C) might lead to incorrect results. Improvements of both SSAs are suggested which overcome the difficulties highlighted. In particular, a formula is presented for the smallest possible compartment size (lattice spacing) which can be correctly implemented in the first model. This implementation uses a new formula for the rate of bimolecular reactions per compartment (lattice site).Comment: 33 pages, submitted to Physical Biolog

Linking the Character of the Metal-Ligand Bond to the Ligand NMR Shielding in Transition-Metal Complexes: NMR Contributions from Spin-Orbit Coupling

Relativistic effects significantly affect various spectroscopic properties of compounds containing heavy elements. Particularly in Nuclear Magnetic Resonance (NMR) spectroscopy, the heavy atoms strongly influence the NMR shielding constants of neighboring light atoms. In this account we analyze paramagnetic contributions to NMR shielding constants and their modulation by relativistic spin-orbit effects in a series of transition-metal complexes of Pt(II), Au(I), Au(III), and Hg(II). We show how the paramagnetic NMR shielding and spin-orbit effects relate to the character of the metal-ligand (M-L) bond. A correlation between the (back)-donation character of the M-L bond in d10 Au(I) complexes and the propagation of the spin-orbit (SO) effects from M to L through the M-L bond influencing the ligand NMR shielding via the Fermi-contact mechanism is found and rationalized by using third-order perturbation theory. The SO effects on the ligand NMR shielding are demonstrated to be driven by both the electronic structure of M and the nature of the trans ligand, sharing the σ-bonding metal orbital with the NMR spectator atom L. The deshielding paramagnetic contribution is linked to the σ-type M-L bonding orbitals, which are notably affected by the trans ligand. The SO deshielding role of σ-type orbitals is enhanced in d10 Hg(II) complexes with the Hg 6p atomic orbital involved in the M-L bonding. In contrast, in d8 Pt(II) complexes, occupied π-type orbitals play a dominant role in the SO-altered magnetic couplings due to the accessibility of vacant antibonding σ-type MOs in formally open 5d-shell (d8). This results in a significant SO shielding at the light atom. The energy- and composition-modulation of σ- vs π-type orbitals by spin-orbit coupling is rationalized and supported by visualizing the SO-induced changes in the electron density around the metal and light atoms (spin-orbit electron deformation density, SO-EDD). © 2017 American Chemical Society.Czech Science Foundation [16-05961S, 15-09381S]; Ministry of Education, Youth and Sports of the Czech Republic [LQ1601, LO1504]; multilateral cooperation project [8X17009]; SASPRO Program [1563/03/02]; European Union; Slovak Academy of Sciences; Grant Agency of the Ministry of Education of the Slovak Republic; Slovak Academy of Sciences VEGA [2/0116/17]; Research Council of Norway [179568]; Norwegian supercomputing program NOTUR [NN4654K

Noise control for molecular computing

Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement of strand-displacement DNA computing, a large class of abstract biochemical networks may be physically realized using DNA molecules. Methods for systematic design of the abstract systems with prescribed behaviors have been predominantly developed at the (less-detailed) deterministic level. However, stochastic effects, neglected at the deterministic level, are increasingly found to play an important role in biochemistry. In such circumstances, methods for controlling the intrinsic noise in the system are necessary for a successful network design at the (more-detailed) stochastic level. To bridge the gap, the noise-control algorithm for designing biochemical networks is developed in this paper. The algorithm structurally modifies any given reaction network under mass-action kinetics, in such a way that (i) controllable state-dependent noise is introduced into the stochastic dynamics, while (ii) the deterministic dynamics are preserved. The capabilities of the algorithm are demonstrated on a production-decay reaction system, and on an exotic system displaying bistability. For the production-decay system, it is shown that the algorithm may be used to redesign the network to achieve noise-induced multistability. For the exotic system, the algorithm is used to redesign the network to control the stochastic switching, and achieve noise-induced oscillations

Defensive behavior is linked to altered surface chemistry following infection in a termite society

The care-kill response determines whether a sick individual will be treated or eliminated from an insect society, but little is known about the physiological underpinnings of this process. We exploited the stepwise infection dynamics of an entomopathogenic fungus in a termite to explore how care-kill transitions occur, and identify the chemical cues behind these shifts. We found collective responses towards pathogen-injected individuals to vary according to severity and timing of pathogen challenge, with elimination, via cannibalism, occurring sooner in response to a severe active infection. However, injection with inactivated fungal blastospores also resulted in increased albeit delayed cannibalism, even though it did not universally cause host death. This indicates that the decision to eliminate an individual is triggered before pathogen viability or terminal disease status has been established. We then compared the surface chemistry of differently challenged individuals, finding increased amounts of long-chained methyl-branched alkanes with similar branching patterns in individuals injected with both dead and viable fungal blastospores, with the latter showing the largest increase. This coincided with the highest amounts of observed cannibalism as well as signs of severe moribundity. Our study provides new mechanistic insight into the emergent collective behaviors involved in the disease defense of a termite society

Antimicrobial Potential of Plastic Films Incorporated with Sage Extract on Chicken Meat

The function of packaging is crucial in the maintenance of fresh meat product quality. This study aimed to assess the efficiency of six films added with coatings 2379L/220 and 2379L/221 (containing sage extracts) to inhibit Salmonella typhimurium, Staphylococcus aureus, and Escherichia coli, which showed that two of the six films had a significant effect. Additionally, the effects of the films on refrigerated skinless chicken breast meat were evaluated based on microbiological content, colour, weight loss, texture and pH. Four of the six films were examined could extend the storability of refrigerated chicken breast fillets for up to seven days. All six treated films improved the pH, colour stability, weight loss, and texture of the chicken fillets. Therefore, these findings suggested that the coatings containing sage extracts having different viscosities (2379L/220 and 2379L/221) were effective as antimicrobial adhesives in food packaging films and can be commercially applied in prolonging the storage of chicken breast meat without affecting their quality