arXiv subjects

James F. Glazebrook

Publications and source records attributed to James F. Glazebrook.

30 records · Page 2Linked to original sources

arXiv2019

Quantum tunneling of Davydov solitons through massive barriers

Protein clamps provide the cell with effective mechanisms for sensing of environmental changes and triggering adaptations that maintain homeostasis. The general physical mechanism behind protein clamping action, however, is poorly understood. Here, we explore the Davydov model for quantum transport of amide I energy, which is self-trapped in soliton states that propagate along the protein α-helix spines and preserve their shape upon reflection from the α-helix ends. We study computationally whether the Davydov solitons are able to reflect from massive barriers that model the presence of external protein clamps acting on a portion of the α-helix, and characterize the range of barrier conditions for which the Davydov solitons are capable of tunneling through the barrier. The simulations showed that the variability of amino acid masses in proteins has a negligible effect on Davydov soliton dynamics, but a massive barrier that is a hundred times the mass of a single amino acid presents an obstacle for the soliton propagation. The greater width of Davydov solitons stabilizes the soliton upon reflection from such a massive barrier and increases the probability of tunneling through it, whereas the greater isotropy of the exciton-lattice coupling suppresses the tunneling efficiency by increasing the interaction time between the Davydov soliton and the barrier, thereby prolonging the tunneling time through the barrier and enhancing the probability for reflection from the latter. The results as presented, demonstrate the feasibility of Davydov solitons reflecting from or tunneling through massive barriers, and suggest a general physical mechanism underlying the action of protein clamps through local enhancement of an effective protein α-helix mass.

physics.bio-ph↗

arXiv2018

On the quantum dynamics of Davydov solitons in protein $α$-helices

The transport of energy inside protein $α$-helices is studied by deriving a system of quantum equations of motion from the Davydov Hamiltonian with the use of the Schrödinger equation and the generalized Ehrenfest theorem. Numerically solving the system of quantum equations of motion for different initial distributions of the amide I energy over the peptide groups confirmed the generation of both moving or stationary Davydov solitons. In this simulation the soliton generation, propagation, and stability were found to be dependent on the symmetry of the exciton-phonon interaction Hamiltonian and the initial site of application of the exciton energy.

cond-mat.soft↗

arXiv2018

A mosaic of Chu spaces and Channel Theory with applications to Object Identification and Mereological Complexity

Chu Spaces and Channel Theory are well established areas of investigation in the general context of category theory. We review a range of examples and applications of these methods in logic and computer science, including Formal Concept Analysis, distributed systems and ontology development. We then employ these methods to describe human object perception, beginning with the construction of uncategorized object files and proceeding through categorization, individual object identification and the tracking of object identity through time. We investigate the relationship between abstraction and mereological categorization, particularly as these affect object identity tracking. This we accomplish in terms of information flow that is semantically structured in terms of local logics, while at the same time this framework also provides an inferential mechanism towards identification and perception. We show how a mereotopology naturally emerges from the representation of classifications by simplicial complexes, and briefly explore the emergence of geometric relations and interactions between objects.

cs.AI↗

arXiv2017

Homology theory formulas for generalized Riemann-Hurwitz and generalized monoidal transformations

In the context of orientable circuits and subcomplexes of these as representing certain singular spaces, we consider characteristic class formulas generalizing those classical results as seen for the Riemann-Hurwitz formula for regulating the topology of branched covering maps and that for monoidal transformations which include the standard blowing-up process. Here the results are presented as cap product pairings, which will be elements of a suitable homology theory, rather than characteristic numbers as would be the case when taking Kronecker products once Poincaré duality is defined. We further consider possible applications and examples including branched covering maps, singular varieties involving virtual tangent bundles, the Chern-Schwartz-MacPherson class, the homology L-class, generalized signature, and the cohomology signature class.

math.AT↗

arXiv2016

Rational and iterated maps, degeneracy loci, and the generalized Riemann-Hurwitz formula

We consider a generalized Riemann-Hurwitz formula as it may be applied to rational maps between projective varieties having an indeterminacy set and fold-like singularities. The case of a holomorphic branched covering map is recalled. Then we see how the formula can be applied to iterated maps having branch-like singularities. Separately, we consider a further application involving the Chern classes of determinantal varieties when the latter are realized as the degeneracy loci of certain vector bundle morphisms.

math.AT↗

arXiv2011

Differential algebras with Banach-algebra coefficients I: From C*-algebras to the K-theory of the spectral curve

We present an operator-coefficient version of Sato's infinite-dimensional Grassmann manifold, and tau-function. In this context, the Burchnall-Chaundy ring of commuting differential operators becomes a C*-algebra, to which we apply the Brown-Douglas-Fillmore theory, and topological invariants of the spectral ring become readily available. We construct KK classes of the spectral curve of the ring and, motivated by the fact that all isospectral Burchnall-Chaundy rings make up the Jacobian of the curve, we compare the (degree-1) K-homology of the curve with that of its Jacobian. We show how the Burchnall-Chaundy C*-algebra extension of the compact operators provides a family of operator-valued tau-functions.

math.OA↗

arXiv2011

Differential algebras with Banach-algebra coefficients II: The operator cross-ratio tau-function and the Schwarzian derivative

Several features of an analytic (infinite-dimensional) Grassmannian of (commensurable) subspaces of a Hilbert space were developed in the context of integrable PDEs (KP hierarchy). We extended some of those features when polarized separable Hilbert spaces are generalized to a class of polarized Hilbert modules, in particular the Baker and tau-functions, which become operator-valued. Following from Part I we produce a pre-determinant structure for a class of tau-functions defined in the setting of the similarity class of projections of a certain Banach *-algebra. This structure is explicitly derived from the transition map of a corresponding principal bundle. The determinant of this map gives a generalized, operator-valued tau-function that takes values in a commutative C*-algebra. We extend to this setting the operator cross-ratio which had been used to produce the scalar-valued tau-function, as well as the associated notion of a Schwarzian derivative along curves inside the space of similarity classes. We link directly this cross-ratio with Fay's trisecant identity for the tau-function (equivalent to the KP hierarchy). By restriction to the image of the Krichever map, we use the Schwarzian to introduce the notion of operator-valued projective structure on a compact Riemann surface: this allows a deformation inside the Grassmannian (as it varies its complex structure). Lastly, we use our identification of the Jacobian of the Riemann surface in terms of extensions of the Burchnall-Chaundy C*-algebra (Part I) to describe the KP hierarchy.

math.OA↗

arXiv2011

Rate distortion coevolutionary dynamics and the flow nature of cognitive epigenetic systems

We outline a model for a cognitive epigenetic system based on elements of the Shannon theory of information and the statistical physics of the generalized Onsager relations. Particular attention is paid to the concept of the rate distortion function and from another direction as motivated by the thermodynamics of computing, the fundamental homology with the free energy density of a physical system. A unifying aspect of the dynamic framework involves the concept of a groupoid and of a groupoid atlas. From a stochastic differential equation we postulate a multidimensional Ito process for an epigenetic system from which a stochastic flow may permeate through components of this atlas.

q-bio.OT↗

arXiv2009

Algebraic Topology Foundations of Supersymmetry and Symmetry Breaking in Quantum Field Theory and Quantum Gravity: A Review

A novel algebraic topology approach to supersymmetry (SUSY) and symmetry breaking in quantum field and quantum gravity theories is presented with a view to developing a wide range of physical applications. These include: controlled nuclear fusion and other nuclear reaction studies in quantum chromodynamics, nonlinear physics at high energy densities, dynamic Jahn-Teller effects, superfluidity, high temperature superconductors, multiple scattering by molecular systems, molecular or atomic paracrystal structures, nanomaterials, ferromagnetism in glassy materials, spin glasses, quantum phase transitions and supergravity. This approach requires a unified conceptual framework that utilizes extended symmetries and quantum groupoid, algebroid and functorial representations of non-Abelian higher dimensional structures pertinent to quantized spacetime topology and state space geometry of quantum operator algebras. Fourier transforms, generalized Fourier-Stieltjes transforms, and duality relations link, respectively, the quantum groups and quantum groupoids with their dual algebraic structures; quantum double constructions are also discussed in this context in relation to quasi-triangular, quasi-Hopf algebras, bialgebroids, Grassmann-Hopf algebras and higher dimensional algebra. On the one hand, this quantum algebraic approach is known to provide solutions to the quantum Yang-Baxter equation. On the other hand, our novel approach to extended quantum symmetries and their associated representations is shown to be relevant to locally covariant general relativity theories that are consistent with either nonlocal quantum field theories or local bosonic (spin) models with the extended quantum symmetry of entangled, 'string-net condensed' (ground) states.

hep-th↗

arXiv2004

Dimensional reduction of the perturbed Hermitian-Einstein equation

Given a Kaehlerian holomorphic fiber bundle whose fiber is a compact homogeneous Kaehler manifold, we describe the perturbed Hermitian-Einstein equations relative to certain holomorphic vector bundles. With respect to special metrics on the holomorphic bundles, there is a dimensional reduction procedure which reduces these equations to a system of equations on the base, known as the twisted coupled vortex equations.

math.DG↗

arXiv2004

A Fourier-Mukai transform for real torus bundles

We construct a Fourier--Mukai transform for smooth complex vector bundles $E$ over a torus bundle $π:M \to B,$ the vector bundles being endowed with various structures of increasing complexity. At a minimum, we consider vector bundles $E$ with a flat partial unitary connection, that is families or deformations of flat vector bundles (or unitary local systems) on the torus $T.$ This leads to a correspondence between such objects on $M$ and relative skyscraper sheaves $\cS$ supported on a spectral covering $Σ\hra \what M,$ where $\hatπ:\what{M} \to B$ is the flat dual fiber bundle. Additional structures on $(E,\nabla)$ (flatness, anti-self-duality) will be reflected by corresponding data on the transform $(\cS, Σ).$ Several variations of this construction will be presented, emphasizing the aspects of foliation theory which enter into this picture

math.DG↗

arXiv2002

Connections, local subgroupoids,and a holonomy Lie groupoid of a line bundle gerbe

Our main aim is to associate a holonomy Lie groupoid to the connective structure of an abelian gerbe. The construction has analogies with a procedure for the holonomy Lie groupoid of a foliation, in using a locally Lie groupoid and a globalisation procedure. We show that path connections and 2-holonomy on line bundles may be formulated using the notion of a connection pair on a double category, due to Brown-Spencer, but now formulated in terms of double groupoids using the thin fundamental groupoids introduced by Caetano-Mackaay-Picken. To obtain a locally Lie groupoid to which globalisation applies, we use methods of local subgroupoids as developed by Brown-$\dot{\rm I}$çen-Mucuk.

math.DG↗