Quantum Chemistry

The biochemistry of geotropism in plants and gravisensing in e.g. cyanobacteria or paramacia is still not well understood today [1]. Perhaps there are more ways than one for organisms to sense gravity. The two best known relatively old explanations for gravity sensing are sensing through the redistribution of cellular starch statoliths and sensing through redistribution of auxin. The starch containing statoliths in a gravity field produce pressure on the endoplasmic reticulum of the cell. This enables the cell to sense direction. (...) Alternatively, there is the redistribution of auxin under the action of gravity. This is known as the Cholodny-Went hypothesis [2], [3]. The latter redistribution coincides with a redistribution of electrical charge in the cell. With the present study the aim is to add a mathematical unified field explanation to gravisensing. (shrink)

Science frequently gives us multiple, compatible ways of solving the same problem or formulating the same theory. These compatible formulations change our understanding of the world, despite providing the same explanations. According to what I call "conceptualism," reformulations change our understanding by clarifying the epistemic structure of theories. I illustrate conceptualism by analyzing a typical example of symmetry-based reformulation in chemical physics. This case study poses a problem for "explanationism," the rival thesis that differences in understanding require ontic explanatory differences. (...) To defend conceptualism, I consider how prominent accounts of explanation might accommodate this case study. I argue that either they do not succeed, or they generate a skeptical challenge. (shrink)

Computational reproducibility possesses its own dynamics and narratives of crisis. Alongside the difficulties of computing as an ubiquitous yet complex scientific activity, computational reproducibility suffers from a naive expectancy of total reproducibility and a moral imperative to embrace the principles of free software as a non-negotiable epistemic virtue. We argue that the epistemic issues at stake in actual practices of computational reproducibility are best unveiled by focusing on software as a pivotal concept, one that is surprisingly often overlooked in accounts (...) of reproducibility issues. Software is not only about designing and coding but also about maintaining, supporting, distributing, licensing, and governance; it is not only about developers but also about users. We focus on openness debates among computational chemists involved in molecular modeling software packages as empirical grounding for our argument. We then identify and analyse four epistemic characteristics as key to the role of software in computational reproducibility. (shrink)

The thesis is: the “periodic table” of “dark matter” is equivalent to the standard periodic table of the visible matter being entangled. Thus, it is to consist of all possible entangled states of the atoms of chemical elements as quantum systems. In other words, an atom of any chemical element and as a quantum system, i.e. as a wave function, should be represented as a non-orthogonal in general (i.e. entangled) subspace of the separable complex Hilbert space relevant to the system (...) to which the atom at issue is related as a true part of it. The paper follows previous publications of mine stating that “dark matter” and “dark energy” are projections of arbitrarily entangled states on the cognitive “screen” of Einstein’s “Mach’s principle” in general relativity postulating that gravitational field can be generated only by mass or energy. (shrink)

Arthur Clark and Michael Kube–McDowell (“The Triger”, 2000) suggested the sci-fi idea about the direct transformation from a chemical substance to another by the action of a newly physical, “Trigger” field. Karl Brohier, a Nobel Prize winner, who is a dramatic persona in the novel, elaborates a new theory, re-reading and re-writing Pauling’s “The Nature of the Chemical Bond”; according to Brohier: “Information organizes and differentiates energy. It regularizes and stabilizes matter. Information propagates through matter-energy and mediates the interactions of (...) matter-energy.” Dr Horton, his collaborator in the novel replies: “If the universe consists of energy and information, then the Trigger somehow alters the information envelope of certain substances –“. “Alters it, scrambles it, overwhelms it, destabilizes it” Brohier adds. There is a scientific debate whether or how far chemistry is fundamentally reducible to quantum mechanics. Nevertheless, the fact that many essential chemical properties and reactions are at least partly representable in terms of quantum mechanics is doubtless. For the quantum mechanics itself has been reformulated as a theory of a special kind of information, quantum information, chemistry might be in turn interpreted in the same terms. Wave function, the fundamental concept of quantum mechanics, can be equivalently defined as a series of qubits, eventually infinite. A qubit, being defined as the normed superposition of the two orthogonal subspaces of the complex Hilbert space, can be interpreted as a generalization of the standard bit of information as to infinite sets or series. All “forces” in the Standard model, which are furthermore essential for chemical transformations, are groups [U(1),SU(2),SU(3)] of the transformations of the complex Hilbert space and thus, of series of qubits. One can suggest that any chemical substances and changes are fundamentally representable as quantum information and its transformations. If entanglement is interpreted as a physical field, though any group above seems to be unattachable to it, it might be identified as the “Triger field”. It might cause a direct transformation of any chemical substance by from a remote distance. Is this possible in principle? (shrink)

To this day, a hundred and fifty years after Mendeleev's discovery, the overal structure of the periodic system remains unaccounted for in quantum-mechanical terms. Given this dire situation, a handful of scientists in the 1970s embarked on a quest for the symmetries that lie hidden in the periodic table. Their goal was to explain the table's structure in group-theoretical terms. We argue that this symmetry program required an important paradigm shift in the understanding of the nature of chemical elements. The (...) idea, in essence, consisted of treating the chemical elements, not as particles, but as states of a superparticle. We show that the inspiration for this came from elementary particle physics, and in particular from Heisenberg's suggestion to treat the proton and neutron as different states of the nucleon. We provide a careful study of Heisenberg's last paper on the nature of elementary particles, and explain why the Democritean picture of matter no longer applied in modern physics and a Platonic symmetry-based picture was called for instead. We show how Heisenberg's Platonic philosophy came to dominate the field of elementary particle physics, and how it found its culmination point in Gell-Mann's classification of the hadrons in the eightfold way. We argue that it was the success of Heisenberg's approach in elementary particle physics that sparked the group-theoretical approach to the periodic table. We explain how it was applied to the set of chemical elements via a critical examination of the work of the Russian mathematician Abram Ilyich Fet the Turkish-American physicist Asim Orhan Barut, before giving some final reflections. (shrink)

Computational chemistry grew in a new era of “desktop modeling,” which coincided with a growing demand for modeling software, especially from the pharmaceutical industry. Parameterization of models in computational chemistry is an arduous enterprise, and we argue that this activity leads, in this specific context, to tensions among scientists regarding the epistemic opacity transparency of parameterized methods and the software implementing them. We relate one flame war from the Computational Chemistry mailing List in order to assess in detail the relationships (...) between modeling methods, parameterization, software and the various forms of their enclosure or disclosure. Our claim is that parameterization issues are an important and often neglected source of epistemic opacity and that this opacity is entangled in methods and software alike. Models and software must be addressed together to understand the epistemological tensions at stake. (shrink)

In this paper we investigate with a case study from chemistry under what conditions a simulation can serve as a surrogate for an experiment. The case-study concerns a simulation of H2-formation in outer space. We find that in this case the simulation can act as a surrogate for an experiment, because there exists comprehensive theoretical background knowledge in form of quantum mechanics about the range of phenomena to which the investigated process belongs and because any particular modelling assumptions as can (...) be justified. If these requirements are met then direct empirical validation may even be dispensable. We conjecture that this is not the case in the absence of comprehensive theoretical background knowledge. (shrink)