Entropy involved in fidelity of DNA replication

Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. We introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorporation of the nucleotides. The copied strand is, to first order of approximation, a state of independent and non-indentically distributed random variables for which the nucleotide that is incorporated by the polymerase at each step is dictated by the template strand, and to second order of approximation, a state of non-uniformly distributed random variables with nearest-neighbor interactions for which the recognition of secondary structure by the polymerase in the resultant double-stranded polymer determines the entropy of the replicated strand. Two incorporation mechanisms arise naturally and their biological meanings are explained. It is known that replication occurs far from equilibrium and therefore the Shannon entropy here derived represents an upper bound for replication to take place. Likewise, this entropy sets a universal lower bound for the copying fidelity in replication.Comment: 25 pages, 5 figure

Noncyclic geometric phase for neutrino oscillation

We provide explicit formulae for the noncyclic geometric phases or Pancharatnam phases of neutrino oscillations. Since Pancharatnam phase is a generalization of the Berry phase, our results generalize the previous findings for Berry phase in a recent paper [Phys. Lett. B, 466 (1999) 262]. Unlike the Berry phase, the noncyclic geometric phase offers distinctive advantage in terms of measurement and prediction. In particular, for three-flavor mixing, our explicit formula offers an alternative means of determining the CP-violating phase. Our results can also be extended easily to explore geometric phase associated with neutron-antineutron oscillations

European sea bass show behavioural resilience to near-future ocean acidification

Ocean acidification (OA)—caused by rising concentrations of carbon dioxide (CO₂)—is thought to be a major threat to marine ecosystems and has been shown to induce behavioural alterations in fish. Here we show behavioural resilience to near-future OA in a commercially important and migratory marine finfish, the Sea bass (Dicentrarchus labrax). Sea bass were raised from eggs at 19°C in ambient or near-future OA (1000 µatm pCO₂) conditions and n = 270 fish were observed 59–68 days post-hatch using automated tracking from video. Fish reared under ambient conditions, OA conditions, and fish reared in ambient conditions but tested in OA water showed statistically similar movement patterns, and reacted to their environment and interacted with each other in comparable ways. Thus our findings indicate behavioural resilience to near-future OA in juvenile sea bass. Moreover, simulated agent-based models indicate that our analysis methods are sensitive to subtle changes in fish behaviour. It is now important to determine whether the absences of any differences persist under more ecologically relevant circumstances and in contexts which have a more direct bearing on individual fitness

Non-Abelian Geometric Phase, Floquet Theory, and Periodic Dynamical Invariants

For a periodic Hamiltonian, periodic dynamical invariants may be used to obtain non-degenerate cyclic states. This observation is generalized to the degenerate cyclic states, and the relation between the periodic dynamical invariants and the Floquet decompositions of the time-evolution operator is elucidated. In particular, a necessary condition for the occurrence of cyclic non-adiabatic non-Abelian geometrical phase is derived. Degenerate cyclic states are obtained for a magnetic dipole interacting with a precessing magnetic field.Comment: Plain LaTeX, 13 pages, accepted for publication in J. Phys. A: Math. Ge

Geometric phases and hidden local gauge symmetry

The analysis of geometric phases associated with level crossing is reduced to the familiar diagonalization of the Hamiltonian in the second quantized formulation. A hidden local gauge symmetry, which is associated with the arbitrariness of the phase choice of a complete orthonormal basis set, becomes explicit in this formulation (in particular, in the adiabatic approximation) and specifies physical observables. The choice of a basis set which specifies the coordinate in the functional space is arbitrary in the second quantization, and a sub-class of coordinate transformations, which keeps the form of the action invariant, is recognized as the gauge symmetry. We discuss the implications of this hidden local gauge symmetry in detail by analyzing geometric phases for cyclic and noncyclic evolutions. It is shown that the hidden local symmetry provides a basic concept alternative to the notion of holonomy to analyze geometric phases and that the analysis based on the hidden local gauge symmetry leads to results consistent with the general prescription of Pancharatnam. We however note an important difference between the geometric phases for cyclic and noncyclic evolutions. We also explain a basic difference between our hidden local gauge symmetry and a gauge symmetry (or equivalence class) used by Aharonov and Anandan in their definition of generalized geometric phases.Comment: 25 pages, 1 figure. Some typos have been corrected. To be published in Phys. Rev.

Beyond the First Recurrence in Scar Phenomena

The scarring effect of short unstable periodic orbits up to times of the order of the first recurrence is well understood. Much less is known, however, about what happens past this short-time limit. By considering the evolution of a dynamically averaged wave packet, we show that the dynamics for longer times is controlled by only a few related short periodic orbits and their interplay.Comment: 4 pages, 4 Postscript figures, submitted to Phys. Rev. Let

Noncyclic geometric phase and its non-Abelian generalization

We use the theory of dynamical invariants to yield a simple derivation of noncyclic analogues of the Abelian and non-Abelian geometric phases. This derivation relies only on the principle of gauge invariance and elucidates the existing definitions of the Abelian noncyclic geometric phase. We also discuss the adiabatic limit of the noncyclic geometric phase and compute the adiabatic non-Abelian noncyclic geometric phase for a spin 1 magnetic (or electric) quadrupole interacting with a precessing magnetic (electric) field.Comment: Plain Latex, accepted for publication in J. Phys. A: Math. Ge

Perturbative Calculation of the Adiabatic Geometric Phase and Particle in a Well with Moving Walls

We use the Rayleigh-Schr\"odinger perturbation theory to calculate the corrections to the adiabatic geometric phase due to a perturbation of the Hamiltonian. We show that these corrections are at least of second order in the perturbation parameter. As an application of our general results we address the problem of the adiabatic geometric phase for a one-dimensional particle which is confined to an infinite square well with moving walls.Comment: Plain Latex, accepted for publication in J. Phys. A: Math. Ge