Quantum mechanics in complex systems

This document should be considered in its separation; there are three distinct topics contained within and three distinct chapters within the body of works. In a similar fashion, this abstract should be considered in three parts. Firstly, we explored the existence of multiply-charged atomic ions by having developed a new set of dimensional scaling equations as well as a series of relativistic augmentations to the standard dimensional scaling procedure and to the self-consistent field calculations. Secondly, we propose a novel method of predicting drug efficacy in hopes to facilitate the discovery of new small molecule therapeutics by modeling the agonist-protein system as being similar to the process of Inelastic Electron Tunneling Spectroscopy. Finally, we facilitate the instruction in basic quantum mechanical topics through the use of quantum games; this method of approach allows for the generation of exercises with the intent of conveying the fundamental concepts within a first year quantum mechanics classroom. Furthermore, no to be mentioned within the body of the text, yet presented in appendix form, certain works modeling the proliferation of cells types within the confines of man-made lattices for the purpose of facilitating artificial vascular transplants. ^ In Chapter 2, we present a theoretical framework which describes multiply-charged atomic ions, their stability within super-intense laser fields, also lay corrections to the systems due to relativistic effects. Dimensional scaling calculations with relativistic corrections for systems: H, H-, H 2-, He, He-, He2-, He3- within super-intense laser fields were completed. Also completed were three-dimensional self consistent field calculations to verify the dimensionally scaled quantities. With the aforementioned methods the system\u27s ability to stably bind \u27additional\u27 electrons through the development of multiple isolated regions of high potential energy leading to nodes of high electron density is shown. These nodes are spaced far enough from each other to minimized the electronic repulsion of the electrons, while still providing adequate enough attraction so as to bind the excess elections into orbitals. We have found that even with relativistic considerations these species are stably bound within the field. It was also found that performing the dimensional scaling calculations for systems within the confines of laser fields to be a much simpler and more cost-effective method than the supporting D=3 SCF method. The dimensional scaling method is general and can be extended to include relativistic corrections to describe the stability of simple molecular systems in super-intense laser fields.^ Chapter 3, we delineate the model, and aspects therein, of inelastic electron tunneling and map this model to the protein environment. G protein-coupled receptors (GPCRs) constitute a large family of receptors that sense molecules outside of a cell and activate signal transduction pathways inside the cell. Modeling how an agonist activates such a receptor is important for understanding a wide variety of physiological processes and it is of tremendous value for pharmacology and drug design. Inelastic electron tunneling spectroscopy (IETS) has been proposed as the mechanism by which olfactory GPCRs are activated by an encapsulated agonist. In this note we apply this notion to GPCRs within the mammalian nervous system using ab initio quantum chemical modeling. We found that non-endogenous agonists of the serotonin receptor share a singular IET spectral aspect both amongst each other and with the serotonin molecule: a peak that scales in intensity with the known agonist activities. We propose an experiential validation of this model by utilizing lysergic acid dimethylamide (DAM-57), an ergot derivative, and its isotopologues in which hydrogen atoms are replaced by deuterium. If validated our theory may provide new avenues for guided drug design and better in silico prediction of efficacies. ^ Our final chapter, explores methods which may be explored to assist in the early instruction in quantum mechanics. The learning of quantum mechanics is contingent upon an understanding of the physical significance of the mathematics that one must perform. Concepts such as normalization, superposition, interference, probability amplitude and entanglement can prove challenging for the beginning student. This paper outlines several class exercises that use a non-classical version of tic-tac-toe to instruct several topics in an undergraduate quantum mechanics course. Quantum tic-tac-toe (QTTT) is a quantum analogue of classical tic-tac-toe (CTTT) benefiting from the use of superposition in movement, qualitative (and later quantitative) displays of entanglement and state collapse due to observation. QTTT can be used for the benefit of the students understanding in several other topics with the aid of proper discussion

Aspects of emergent cyclicity in language and computation

This thesis has four parts, which correspond to the presentation and development of a theoretical framework for the study of cognitive capacities qua physical phenomena, and a case study of locality conditions over natural languages. Part I deals with computational considerations, setting the tone of the rest of the thesis, and introducing and defining critical concepts like ‘grammar’, ‘automaton’, and the relations between them . Fundamental questions concerning the place of formal language theory in linguistic inquiry, as well as the expressibility of linguistic and computational concepts in common terms, are raised in this part. Part II further explores the issues addressed in Part I with particular emphasis on how grammars are implemented by means of automata, and the properties of the formal languages that these automata generate. We will argue against the equation between effective computation and function-based computation, and introduce examples of computable procedures which are nevertheless impossible to capture using traditional function-based theories. The connection with cognition will be made in the light of dynamical frustrations: the irreconciliable tension between mutually incompatible tendencies that hold for a given dynamical system. We will provide arguments in favour of analyzing natural language as emerging from a tension between different systems (essentially, semantics and morpho-phonology) which impose orthogonal requirements over admissible outputs. The concept of level of organization or scale comes to the foreground here; and apparent contradictions and incommensurabilities between concepts and theories are revisited in a new light: that of dynamical nonlinear systems which are fundamentally frustrated. We will also characterize the computational system that emerges from such an architecture: the goal is to get a syntactic component which assigns the simplest possible structural description to sub-strings, in terms of its computational complexity. A system which can oscillate back and forth in the hierarchy of formal languages in assigning structural representations to local domains will be referred to as a computationally mixed system. Part III is where the really fun stuff starts. Field theory is introduced, and its applicability to neurocognitive phenomena is made explicit, with all due scale considerations. Physical and mathematical concepts are permanently interacting as we analyze phrase structure in terms of pseudo-fractals (in Mandelbrot’s sense) and define syntax as a (possibly unary) set of topological operations over completely Hausdorff (CH) ultrametric spaces. These operations, which makes field perturbations interfere, transform that initial completely Hausdorff ultrametric space into a metric, Hausdorff space with a weaker separation axiom. Syntax, in this proposal, is not ‘generative’ in any traditional sense –except the ‘fully explicit theory’ one-: rather, it partitions (technically, ‘parametrizes’) a topological space. Syntactic dependencies are defined as interferences between perturbations over a field, which reduce the total entropy of the system per cycles, at the cost of introducing further dimensions where attractors corresponding to interpretations for a phrase marker can be found. Part IV is a sample of what we can gain by further pursuing the physics of language approach, both in terms of empirical adequacy and theoretical elegance, not to mention the unlimited possibilities of interdisciplinary collaboration. In this section we set our focus on island phenomena as defined by Ross (1967), critically revisiting the most relevant literature on this topic, and establishing a typology of constructions that are strong islands, which cannot be violated. These constructions are particularly interesting because they limit the phase space of what is expressible via natural language, and thus reveal crucial aspects of its underlying dynamics. We will argue that a dynamically frustrated system which is characterized by displaying mixed computational dependencies can provide straightforward characterizations of cyclicity in terms of changes in dependencies in local domains

Simulation of chiral ordering process in the adsorption of chiral organic molecules on metal surfaces by Monte Carlo methods

Experimental observations have shown that haloalkane molecules, e.g. l-cWorododecane, physisorbed on Si(111)-(7 x 7) self-assemble to form dimers stable to 100° C which corral silicon adatoms. The corral size is governed by the haloalkane chain-length. Spectroscopic and theoretical evidence shows that the haloalkane dimer induces electron transfer to the corralled adatom. The enclosed silicon adatom, within a bistable dimeric corral of self-assembled chlorododecane molecules, switches its energy levels permanently (Type-II corrals) or discontinuously (Type-I corrals). Both types of corral, switching and stable, can be seen to alter the local surface charge distribution. Density Functional Theory and electron transport (STM) simulations of the switch and the stable molecular configurations can help the theoretical understanding of both phenomena in order to characterized the exact molecular conformations that produce field effects to the corralled silicon adatom and local surface charge distribution. Chiral heterogeneous catalysts are mostly fabricated from chiral molecules on a metal support. They playa crucial role in intermediate reactions in the fabrication of pharmacies, itself and important part of today's health econolPY. However, the key parameters in the fabrication of these catalysts, a requirements for their rational design, are still poorly understood despite years of experimental research. In essence, such an understanding can only come from high-level simulations. Here, we present the first predictions about the structure of such a catalyst, tartaric acid on a copper support, over the whole phase space of temperature and coverage. Interestingly, we find that molecular vibrations playa key role in the ensuing ordered structures, and that tuning the fabrication temperature should allow for a wide range of molecular separations, which can be targeted at specific molecules and reactions in chiral heterogeneous catalysis

On Musical Self-Similarity : Intersemiosis as Synecdoche and Analogy

Self-similarity, a concept borrowed from mathematics, is gradually becoming a keyword in musicology. Although a polysemic term, self-similarity often refers to the multi-scalar feature repetition in a set of relationships, and it is commonly valued as an indication for musical ‘coherence’ and ‘consistency’. In this study, Gabriel Pareyon presents a theory of musical meaning formation in the context of intersemiosis, that is, the translation of meaning from one cognitive domain to another cognitive domain (e.g. from mathematics to music, or to speech or graphic forms). From this perspective, the degree of coherence of a musical system relies on a synecdochic intersemiosis: a system of related signs within other comparable and correlated systems. The author analyzes the modalities of such correlations, exploring their general and particular traits, and their operational bounds. Accordingly, the notion of analogy is used as a rich concept through its two definitions quoted by the Classical literature—proportion and paradigm, enormously valuable in establishing measurement, likeness and affinity criteria. At the same time, original arguments by Benoît B. Mandelbrot (1924–2010) are revised, alongside a systematic critique of the literature on the subject. In fact, connecting Charles S. Peirce’s ‘synechism’ with Mandelbrot’s ‘fractality’ is one of the main developments of the present study