A Nonadiabatic Theory for Ultrafast Catalytic Electron Transfer: A Model for the Photosynthetic Reaction Center

A non-adiabatic theory of Electron Transfer (ET), which improves the standard theory near the inversion point and becomes equivalent to it far from the inversion point, is presented. The complex amplitudes of the electronic wavefunctions at different sites are used as Kramers variables for describing the quantum tunneling of the electron in the deformable potential generated by its environment (nonadiabaticity) which is modeled as a harmonic classical thermal bath. After exact elimination of the bath, the effective electron dynamics is described by a discrete nonlinear Schrödinger equation with norm preserving dissipative terms and a Langevin random force, with a frequency cut-off, due to the thermalized phonons. This theory reveals the existence of a specially interesting marginal case when the linear and nonlinear coefficients of a two electronic states system are appropriately tuned for forming a Coherent Electron-Phonon Oscillator (CEPO). An electron injected on one of the electronic states of a CEPO generates large amplitude charge oscillations (even at zero temperature) associated with coherent phonon oscillations and electronic level oscillations. This fluctuating electronic level may resonate with a third site which captures the electron so that Ultrafast Electron Transfer (UFET) becomes possible. Numerical results are shown where two weakly interacting sites, a donor and a catalyst, form a CEPO that triggers an UFET to an acceptor. Without a catalytic site, a very large energy barrier prevents any direct ET. This UFET is shown to have many qualitative features similar to those observed in the primary charge separation in photosynthetic reaction centers. We suggest that more generally, CEPO could be a paradigm for understanding many selective chemical reactions involving electron transfer in biosystems.     

Quantum mechanical aspects of effects of weak magnetic fields upon biological objects

Possible mechanisms of action of weak combined magnetic fields on biological systems have been discussed in terms of quantum mechanics. The approaches proposed make it possible to solve the problem of the failure to compare the energy of active factors with the energy of thermal motion (kT problem). A mechanism of action of combined magnetic fields on biosystems has been proposed.     

Is there a biology of quantum information?

This paper briefly considers the notion of a biology of quantum information from a number of complementary points of view. We begin with a very brief look at some of the biomolecular systems that are thought to exploit quantum mechanical effects and then turn to the issue of measurement in these systems and the concomitant generation of information. This leads us to look at the internalist stance and the exchange interaction of quantum particles. We suggest that exchange interaction can also be viewed using ecological ideas related to apparatus-object. This can also help develop the important notion of complementarity in biosystems in relation to the nature and generation of information at the microphysical scale.     

Quantum mechanical aspects of the effects of weak magnetic fields on biological objects

Possible mechanisms of action of weak combined magnetic fields on biological systems have been discussed in terms of quantum mechanics. The approaches proposed make it possible to solve the problem of the failure to compare the energy of active factors with the energy of thermal motion (kT problem). A mechanism of action of combined magnetic fields on biosystems has been proposed.     

Biomanufacturing by in vitro biosystems containing complex enzyme mixtures

Microbial fermentation is the current predominant biomanufacturing platform. However, it suffers from low production yields, slow reaction rates, and scaling-up challenges. In vitro enzymatic biosystems are emerging to expand the traditional biotechnological mode by utilizing more than three enzymes for manufacturing the desired product from cheap substrate. In the past few years, numerous proofs of the concept of in vitro biosystems containing complex enzyme mixtures from different groups worldwide have inspired the development of these platforms for biomanufacturing, these biosystems show advantages such as near-theoretical product yields, faster reaction rates, reduced interference from toxic compounds, and unprecedented level of engineering. In this review, several examples of in vitro systems are presented to illustrate these advantages and possible solutions to overcome the remaining challenges are discussed. The continuing decrease in enzyme cost and improvements in enzyme engineering techniques will make in vitro biosystems a comparable biomanufacturing platform for microbial fermentation in the near future.     

Expression of adhesion molecules and collagen on rat chondrocyte seeded into alginate and hyaluronate based 3D biosystems. Influence of mechanical stresses

Chondrocytes use mechanical signals, via interactions with their environment, to synthesize an extracellular matrix capable to withstanding high loads. Most chondrocyte-matrix interactions are mediated via transmembrane receptors such as integrins or non-integrins receptors (i.e. annexin V and CD44). The aim of this study was to analyze, by flow cytometry, the adhesion molecules (alpha5/beta1 integrins and CD44) on rat chondrocytes seeded into 3D biosystem made of alginate and hyaluronate. These biosystems were submitted to mechanical stress by knocking the biosystems between them for 48 hours. The expression of type I and type II collagen was also evaluated. The results of the current study showed that mechanical stress induced an increase of type II collagen production and weak variations of alpha5/beta1 receptors expression no matter what biosystems. Moreover, our results indicated that hyaluronan receptor CD44 expression depends on extracellular matrix modifications. Thus, these receptors were activated by signals resulted from cell environment variations (HA addition and modifications owing to mechanical stress). It suggested that this kind of receptor play a crucial role in extracellular matrix homeostasis. Finally, on day 24, no dedifferentiation of chondrocytes was noted either in biosystems or under mechanical stress. For all biosystems, the neosynthesized matrix contained an important level of collagen, which was type II, whatever biosystems. In conclusion, it appeared that the cells, under mechanical stress, maintained their phenotype. In addition, it seems that, on rat chondrocytes, alpha5/beta1 integrins did not act as the main mechanoreceptor (as described for human chondrocytes). In return, hyaluronan receptor CD44 seems to be in relation with matrix composition.     

A search for quantum mechanical methods suitable for the conformational analysis of models related to some inverse agonists of the benzodiazepine receptor

The target of this work consists in a search, among several methods of quantum mechanical calculations, for the most suitable one (both with regard to accuracy and speed) for doing conformational analysis on models related to molecules belonging to a group of indol-3-yl glyoxylyl derivatives, many of which behave as ligands of the benzodiazepine receptor (BzR). Among the wide variety of ligands of the BzR, -carboline derivatives are included, many of which show a pharmacological profile similar to the one exhibited by compounds of interest to us. A structure analogy between our compounds and -carboline derivatives could be hypothesized, depending upon the preferred arrangement of the investigated molecules with respect to the dihedral angles of the indol glyoxylyl moiety. Therefore a potential energy surface scan has been carried out on selected models either by the quantum mechanical semiempirical methods MNDO, AM1, PM3 (by using the programs included in themopac package) or by a quantum mechanical SCFab initio method (by using thegaussian-80 program), both in order to find support for the choice of the more suitable semiempirical method, and in order to verify a structural analogy between our compounds and the -carboline ring. The results showed that AM1 and PM3, unlike MNDO, seem to be suitable semiempirical methods for doing potential energy surface scans on this kind of molecule. The preferred arrangement showed by the models with respect to the indol glyoxylyl moiety appeared to support the hypothesis about the structure analogy between the investigated ligands and -carboline derivatives.     

Thermodynamics and biological evolution

The author of the present paper hopes that the thermodynamic nature of biological evolution will be perceived in the nearest future. He suggests a macrothermodynamic model that takes into account the fact that in the course of ontogenesis, philogenesis and the appropriate stages of the general biological evolution the biosystems are enriched by energy-intensive chemical substances, which force water out of these systems. Moreover, macrothermodynamics helps one to understand adaptive changes in the composition and structure of the biosystems.     

A critical assessment of the information processing capabilities of neuronal microtubules using coherent excitations

Evidence for signaling, communication, and conductivity in microtubules (MTs) has been shown through both direct and indirect means, and theoretical models predict their potential use in both classical and quantum information processing in neurons. The notion of quantum information processing within neurons has been implicated in the phenomena of consciousness, although controversies have arisen in regards to adverse physiological temperature effects on these capabilities. To investigate the possibility of quantum processes in relation to information processing in MTs, a biophysical MT model is used based on the electrostatic interior of the tubulin protein. The interior is taken to constitute a double-well potential structure within which a mobile electron is considered capable of occupying at least two distinct quantum states. These excitonic states together with MT lattice vibrations determine the state space of individual tubulin dimers within the MT lattice. Tubulin dimers are taken as quantum well structures containing an electron that can exist in either its ground state or first excited state. Following previous models involving the mechanisms of exciton energy propagation, we estimate the strength of exciton and phonon interactions and their effect on the formation and dynamics of coherent exciton domains within MTs. Also, estimates of energy and timescales for excitons, phonons, their interactions, and thermal effects are presented. Our conclusions cast doubt on the possibility of sufficiently long-lived coherent exciton/phonon structures existing at physiological temperatures in the absence of thermal isolation mechanisms. These results are discussed in comparison with previous models based on quantum effects in non-polar hydrophobic regions, which have yet to be disproved.     

Another side of genomics: synthetic biology as a means for the exploitation of whole-genome sequence information

The successful completion of the Human Genome Project and other sequencing projects opened the door for another quantum jump in science advancement. The most important public sequence databases are doubling in size every 18 months. By revealing the genetic program of many organisms, these efforts endow biologists with the ability to study the basic information of life in toto as an initial step toward a comprehensive understanding of the complexity of entire organisms. We review the area of synthetic biology, defined as the making and use of biosystems founded on the chemical synthesis of the coding DNA (and potentially RNA). The recent developments discussed here introduce a rich source of oligonucleotides to the field: in situ synthesised microarrays, which in fact represent nothing else but matrix nucleic acid synthesisers. With this new way of producing the oligonucleotides used in the making of synthetic genes in a very cost-effective manner, the field of synthetic biology can be expected to change dramatically in the next decade. Synthetic genes will then be the tools of choice to obtain any sequence at any time in any laboratory.     

Quantum Theory of Surface Plasmon Polaritons: Planar and Spherical Geometries

A quantum theory of retarded surface plasmons on a metal–vacuum interface is formulated, by analogy with the well-known and widely exploited theory of exciton-polaritons. The Hamiltonian for mutually interacting instantaneous surface plasmons and transverse electromagnetic modes is diagonalized with recourse to a Hopfield–Bogoljubov transformation, in order to obtain a new family of modes, to be identified with retarded plasmons. The interaction with nearby dipolar emitters is treated with a full quantum formalism based on a general definition of modal effective volumes. The illustrative cases of a planar surface and of a spherical nanoparticle are considered in detail. In the ideal situation of absence of dissipation, as an effect of the conservation of in-plane wavevector, retarded plasmons on a planar surface represent true stationary states (which are usually called surface plasmon polaritons), whereas retarded plasmons in a spherical nanoparticle, characterized by frequencies that overlap with the transverse electromagnetic continuum, become resonances with a finite radiative broadening. The theory presented constitutes a suitable full quantum framework for the study of nonperturbative and nonlinear effects in plasmonic nanosystems.