Spin-Mediated Consciousness Theory: An Approach Based On Pan-Protopsychism

As an alternative to our original dualistic approach, we present here our spin-mediated consciousness theory based on pan-protopsychism. We postulate that consciousness is intrinsically connected to quantum mechanical spin since said spin is embedded in the microscopic structure of spacetime and may be more fundamental than spacetime itself. Thus, we theorize that consciousness emerges quantum mechanically from the collective dynamics of "protopsychic" spins under the influence of spacetime dynamics. That is, spin is the "pixel" of mind. The unity of mind is achieved by quantum entanglement of the mind-pixels. Applying these ideas to the particular structures and dynamics of the brain, we postulate that the human mind works as follows: The nuclear spin ensembles ("NSE") in both neural membranes and proteins quantum mechanically process consciousness-related information such that conscious experience emerges from the collapses of entangled quantum states of NSE under the influence of the underlying spacetime dynamics. Said information is communicated to NSE through strong spin-spin couplings by biologically available unpaired electronic spins such as those carried by rapidly diffusing oxygen molecules and neural transmitter nitric oxides that extract information from their diffusing pathways in the brain. In turn, the dynamics of NSE has effects through spin chemistry on the classical neural activities such as action potentials and receptor functions thus influencing the classical neural networks of said brain. We also present supporting evidence and make important predictions. We stress that our theory is experimentally verifiable with present technologies

Foerster resonance energy transfer rate and local density of optical states are uncorrelated in any dielectric nanophotonic medium

Motivated by the ongoing debate about nanophotonic control of Foerster resonance energy transfer (FRET), notably by the local density of optical states (LDOS), we study an analytic model system wherein a pair of ideal dipole emitters - donor and acceptor - exhibit energy transfer in the vicinity of an ideal mirror. The FRET rate is controlled by the mirror up to distances comparable to the donor-acceptor distance, that is, the few-nanometer range. For vanishing distance, we find a complete inhibition or a four-fold enhancement, depending on dipole orientation. For mirror distances on the wavelength scale, where the well-known `Drexhage' modification of the spontaneous-emission rate occurs, the FRET rate is constant. Hence there is no correlation between the Foerster (or total) energy transfer rate and the LDOS. At any distance to the mirror, the total energy transfer between a closely-spaced donor and acceptor is dominated by Foerster transfer, i.e., by the static dipole-dipole interaction that yields the characteristic inverse-sixth-power donor-acceptor distance dependence in homogeneous media. Generalizing to arbitrary inhomogeneous media with weak dispersion and weak absorption in the frequency overlap range of donor and acceptor, we derive two main theoretical results. Firstly, the spatially dependent Foerster energy transfer rate does not depend on frequency, hence not on the LDOS. Secondly the FRET rate is expressed as a frequency integral of the imaginary part of the Green function. This leads to an approximate FRET rate in terms of the LDOS integrated over a huge bandwidth from zero frequency to about 10 times the donor emission frequency, corresponding to the vacuum-ultraviolet. Even then, the broadband LDOS hardly contributes to the energy transfer rates. We discuss practical consequences including quantum information processing.Comment: 17 pages, 9 figure

Self-calibrating tomography for multi-dimensional systems

We present a formalism for self-calibrating tomography of arbitrary dimensional systems. Self-calibrating quantum state tomography was first introduced in the context of qubits, and allows the reconstruction of the density matrix of an unknown quantum state despite incomplete knowledge of the unitary operations used to change the measurement basis. We show how this can be generalized to qudits, i.e. d-level systems, and provide a specific example for a V-type three-level atomic system whose transition dipole moments are not known. We show that it is always possible to retrieve the unknown state and process parameters, except for a set of zero measure in the state-parameter space.Comment: Revised version. 9 pages, 3 figure

Quantum Coherence as a Witness of Vibronically Hot Energy Transfer in Bacterial Reaction Centre

Photosynthetic proteins have evolved over billions of years so as to undergo optimal energy transfer to the sites of charge separation. Based on spectroscopically detected quantum coherences, it has been suggested that this energy transfer is partially wavelike. This conclusion critically depends on assignment of the coherences to the evolution of excitonic superpositions. Here we demonstrate for a bacterial reaction centre protein that long-lived coherent spectroscopic oscillations, which bear canonical signatures of excitonic superpositions, are essentially vibrational excited state coherences shifted to the ground state of the chromophores . We show that appearance of these coherences is brought about by release of electronic energy during the energy transfer. Our results establish how energy migrates on vibrationally hot chromophores in the reaction centre and they call for a re-examination of claims of quantum energy transfer in photosynthesis

Electronic energy transfer in biomacromolecules

Electronic energy transfer is widely used as a molecular ruler to interrogate the structure of biomacromolecules, and performs a key task in photosynthesis by transferring collected energy through specialized pigment-protein complexes. Förster theory, introduced over 70 years ago, allows linking transfer rates to simple structural and spectroscopic properties of the energy‐transferring molecules. In biosystems, however, significant deviations from Förster behavior often arise due to breakdown of the ideal dipole approximation, dielectric screening effects due to the biological environment, or departure from the weak‐coupling regime. In this review, we provide a concise overview of advances in simulations of energy transfer in biomacromolecules that allow overcoming the main limitations of Förster theory. We first discuss advances in quantum chemical methods to compute electronic couplings, their extension to multiscale formulations to include screening effects, and strategies to treat the interplay between coupling fluctuations and energy transfer dynamics. We then examine the spectral overlap term, and how this quantity can be estimated from simulations of the spectral density of exciton-phonon coupling. Finally, we discuss rate theories that can describe energy transfers in situations where strong coupling leads to delocalized excitions, a common situation found in closely packed multichromophoric systems such as photosynthetic complexes and nucleic acids

Optimal design of adaptively sampled NMR experiments for measurement of methyl group dynamics with application to a ribosome-nascent chain complex

NMR measurements of cross-correlated nuclear spin relaxation provide powerful probes of polypeptide dynamics and rotational diffusion, free from contributions due to chemical exchange or interactions with external spins. Here, we report on the development of a sensitivity-optimized pulse sequence for the analysis of the differential relaxation of transitions within isolated 13CH3 spin systems, in order to characterise rotational diffusion and side chain order through the product S2τc. We describe the application of optimal design theory to implement a real-time ‘on-the-fly’ adaptive sampling scheme that maximizes the accuracy of the measured parameters. The increase in sensitivity obtained using this approach enables quantitative measurements of rotational diffusion within folded states of translationally-arrested ribosome–nascent chain complexes of the FLN5 filamin domain, and can be used to place strong limits on interactions between the domain and the ribosome surface

Biomolecular electrostatics with continuum models: a boundary integral implementation and applications to biosensors

The implicit-solvent model uses continuum electrostatic theory to represent the salt solution around dissolved biomolecules, leading to a coupled system of the Poisson-Boltzmann and Poisson equations. This thesis uses the implicit-solvent model to study solvation, binding and adsorption of proteins. We developed an implicit-solvent model solver that uses the boundary element method (BEM), called PyGBe. BEM numerically solves integral equations along the biomolecule-solvent interface only, therefore, it does not need to discretize the entire domain. PyGBe accelerates the BEM with a treecode algorithm and runs on graphic processing units. We performed extensive verification and validation of the code, comparing it with experimental observations, analytical solutions, and other numerical tools. Our results suggest that a BEM approach is more appropriate than volumetric based methods, like finite-difference or finite-element, for high accuracy calculations. We also discussed the effect of features like solvent-filled cavities and Stern layers in the implicit-solvent model, and realized that they become relevant in binding energy calculations. The application that drove this work was nano-scale biosensors-- devices designed to detect biomolecules. Biosensors are built with a functionalized layer of ligand molecules, to which the target molecule binds when it is detected. With our code, we performed a study of the orientation of proteins near charged surfaces, and investigated the ideal conditions for ligand molecule adsorption. Using immunoglobulin G as a test case, we found out that low salt concentration in the solvent and high positive surface charge density leads to favorable orientations of the ligand molecule for biosensing applications. We also studied the plasmonic response of localized surface plasmon resonance (LSPR) biosensors. LSPR biosensors monitor the plasmon resonance frequency of metallic nanoparticles, which shifts when a target molecule binds to a ligand molecule. Electrostatics is a valid approximation to the LSPR biosensor optical phenomenon in the long-wavelength limit, and BEM was able to reproduce the shift in the plasmon resonance frequency as proteins approach the nanoparticle

Electronic Energy Transfer in Polarizable Heterogeneous Environments:a Systematic Investigation of Different Quantum Chemical Approaches

Theoretical prediction of transport and optical properties of protein–pigment complexes is of significant importance when aiming at understanding the structure–function relationship in such systems. Electronic energy transfer (EET) couplings represent a key property in this respect since such couplings provide important insight into the strength of interaction between photoactive pigments in protein–pigment complexes. Recently, attention has been payed to how the environment modifies or even controls the electronic couplings. To enable such theoretical predictions, a fully polarizable embedding model has been suggested (Curutchet, C., et al. <i>J. Chem. Theory Comput.</i>, 2009, <i>5</i>, 1838–1848). In this work, we further develop this computational model by extending it with an ab initio derived polarizable force field including higher-order multipole moments. We use this extended model to systematically examine three different ways of obtaining EET couplings in a heterogeneous medium ranging from use of the exact transition density to a point-dipole approximation. Several interesting observations are made, for example, the explicit use of transition densities in the calculation of the electronic couplings, and also when including the explicit environment contribution, can be replaced by a much simpler transition point charge description without comprising the quality of the model predictions