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At least 1,495 records · Page 83Linked to original sources
PubMed2004

Quantum models of the mind: are they compatible with environment decoherence?

Quantum models of the mind associate consciousness with coherent superposition of states in the brain. Some authors consider consciousness to be the result of a kind of internal quantum measurement process in the brain. In this paper we discuss the ideas of Hameroff-Penrose and Tegmark and their calculation for an estimate of decoherence time. We criticize the Hameroff-Penrose model in the context of a quantum brain model by gravitational collapse orchestrated objective reduction (OOR), assumed by Penrose, and we propose instead that the decoherence process is caused by interaction with the environment. We consider it useful to exploit this possibility because of the growing importance of the decoherence theory in quantum measurement, and also because quantum mechanics can be applied to brain study independently of the Hameroff-Penrose model for mind and consciousness. Our conclusion is that the Hameroff-Penrose model is not compatible with decoherence, but nevertheless the quantum brain can still be considered if we replace gravitational collapse OOR with decoherence. However, our result does not agree with Tegmark's conclusion of refuting not only the Hameroff-Penrose gravitational collapse but also the quantum brain, based on decoherence time calculations in specific cases in the brain. In spite of this fact we also disagree with some points of the response to Tegmark's article given by Hagan, Hameroff, and Tuszynski.

Adaptation, Physiological↗
PubMed2004

Quantum Monte Carlo for electronic excitations of free-base porphyrin.

Accurate calculations of allowed and nonallowed transitions in porphyrin are reported. Using the quantum Monte Carlo method in the diffusion Monte Carlo variant, the vertical transition between the ground state singlet and the second excited state singlet as well as the adiabatic transition between the ground state and the lowest triplet state have been computed for this 162-electron system. The present theoretical results are compared to experiment and to results of other theoretical methods. The diffusion Monte Carlo energy differences are found to be in excellent agreement with experiment.

Computer Simulation↗
PubMed2003

A three dimensional (3-D) physical model of DNA polymerase movement in DNA replication.

In this study, we propose new concepts of Active Potential Energy Well, Specificity and Non-Specificity of the wells. We perform these concepts to establish a 3-D physical model and to elucidate how a complete functional DNA polymerase traps a deoxyribonucleoside triphosphate, and how it moves along a DNA template strand in the elongation of a DNA replication. In our model, we first introduce concepts of reduced mass and relative coordinates of a two objects system. Then we simplify a DNA polymerase movement in DNA replication. We also introduce concepts of active objects and active controls in this study. Our model is based on quantum mechanics, thermal dynamics and published biochemical data.

Computer Simulation↗
PubMed2000

Fast algorithm for finding the eigenvalue distribution of very large matrices

A theoretical analysis is given of the equation of motion method, due to Alben et al. [Phys. Rev. B 12, 4090 (1975)], to compute the eigenvalue distribution (density of states) of very large matrices. The salient feature of this method is that for matrices of the kind encountered in quantum physics the memory and CPU requirements of this method scale linearly with the dimension of the matrix. We derive a rigorous estimate of the statistical error, supporting earlier observations that the computational efficiency of this approach increases with the matrix size. We use this method and an imaginary-time version of it to compute the energy and specific heat of three different, exactly solvable, spin-1/2 models, and compare with the exact results to study the dependence of the statistical errors on sample and matrix size.

Journal Article↗
PubMed1996

On the value of clinical information. Is there a bridge between quantum theory and medical diagnosis?

This paper discusses the problems in assigning a precise value to an item (or group of items) of clinical information. Historical viewpoints are reviewed; the paper illustrates how determinist descriptive thinking has been overtaken by concepts of uncertainty and probability. Four equations are proposed outlining the factors which affect the value of clinical information. The validation of these equations and their implications is discussed. Parallels are drawn between the situation in theoretical physics a century ago and medical diagnostics today; and the central theme of uncertainty in both is emphasised. Finally, the need for further radical thinking is stressed.

Clinical Medicine↗
PubMed2001

Detective quantum efficiency of a direct-detection active matrix flat panel imager at megavoltage energies.

The use of an amorphous selenium (a-Se) based direct-detection active matrix flat-panel imager (AMFPI) is studied for megavoltage imaging. The detector consists of a 1.2 mm copper front plate and 200 microm a-Se layer, and has a 85 microm pixel pitch. The Modulation Transfer Function (MTF), Noise Power Spectrum (NPS), and Detective Quantum Efficiency (DQE) are measured for 6 and 15 MV photon beams. A theoretical expression for the DQE is derived using a recently developed formalism for nonelementary cascade stages. A comparison of theory with experiment is good for the 6 and 15 MV beams. The model is used to explore the DQE for more typical pixel sizes. The results indicate that with proper modifications, such as a larger a-Se thickness, a direct flat-panel AMFPI is a very promising detector for megavoltage imaging.

Electrons↗
PubMed2000

Interpretation of chemical shifts and coupling constants in macromolecules.

Recent developments in NMR spectroscopy, along with advances in computational techniques, have produced new approaches to the interpretation of chemical shifts and spin-spin coupling constants in biomolecules. Quantum chemical studies of useful accuracy are now becoming more routine and are increasingly being used in conjunction with experimental studies to map out expected structural patterns for peptides and oligonucleotides. Topics of recent special interest include spin couplings across hydrogen bonds and patterns of chemical shift anisotropies, in both diamagnetic and paramagnetic proteins.

Anisotropy↗
PubMed1994

Quantum optical coherence in cytoskeletal microtubules: implications for brain function.

'Laser-like,' long-range coherent quantum phenomena may occur biologically within cytoskeletal microtubules. This paper presents a theoretical prediction of the occurrence in biological media of the phenomena which we term 'superradiance' and 'self-induced transparency'. Interactions between the electric dipole field of water molecules confined within the hollow core of microtubules and the quantized electromagnetic radiation field are considered, and microtubules are theorized to play the roles of non-linear coherent optical devices. Superradiance is a specific quantum mechanical ordering phenomenon with characteristic times much shorter than those of thermal interaction. Consequently, optical signalling (and computation) in microtubules would be free from both thermal noise and loss. Superradiant optical computing in networks of microtubules and other cytoskeletal structures may provide a basis for biomolecular cognition and a substrate for consciousness.

Animals↗
PubMed2006

High-throughput pKa screening and prediction amenable for ADME profiling.

Recent technological advances have made it possible for several new pK(a) assays to be used in drug screening. In this review, a critical overview is provided of current new methodologies for high-throughput screening and prediction of pK(a). Typical applications of using pK(a )constants and charge state for absorption, distribution, metabolism and excretion (ADME) profiling and quantitative structure-activity relationship modelling complements the methodological comparisons and discussions. The experimental methods discussed include high-throughput screening of pK(a) by multiplexed capillary with ultraviolet absorbance detection on a 96-capillary format instrument, capillary electrophoresis and mass spectrometry (CEMS) based on sample pooling, determination of pK(a) by pH gradient high-performance liquid chromatography, and measurement of pK(a) by a mixed-buffer liner pH gradient system. Comparisons of the different experimental assays are made with emphasis on the newly developed CEMS method. The current status and recent progress in computational approaches to pK(a) prediction are also discussed. In particular, the accuracy limits of simple fragment-based approaches as well as quantum mechanical methods are addressed. Examples of pK(a) prediction from in-house drug candidates as well as commercially available drug molecules are shown and an outline is provided for how drug discovery companies can integrate experiments with computational approaches for increased applications for ADME profiling.

Animals↗
PubMed2002

Determination of carbon-13 chemical shielding tensor in the liquid state by combining NMR relaxation experiments and quantum chemical calculations.

Based on multifield NMR relaxation measurements and quantum chemistry calculations, a strategy aiming at the determination of the chemical shielding tensor (CST) in the liquid state is described. Brownian motions in the liquid state restrict the direct observation of CST to a third of its trace (isotropic shift), and even if CST can be probed indirectly through some spin relaxation rates (specific longitudinal relaxation rates, dipolar chemical shift anisotropy (CSA) cross-correlation rates), an insufficient number of experimental parameters prevents its complete determination. This lack of information can be compensated by using quantum chemical calculations so as to obtain the molecular CST orientation even if a relatively modest level of computation is used. As relaxation parameters involve a dynamic part, a prerequisite is the determination of the molecular anisotropic reorientation which can be obtained independently from dipolar cross-relaxation rates. A polycyclic molecule exhibiting a well-characterized anisotropic reorientation serves as an example for such a study, and some (but not all) carbon-13 chemical shielding tensors can be accurately determined. A comparison with solid-state NMR data and numerous chemical quantum calculations are presented.

Journal Article↗
PubMed2005

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

The accuracy of biological simulations depends, in large part, on the treatment of electrostatics. Due to the availability of accurate experimental values, calculation of pKa provides stringent evaluation of computational methods. The generalized solvent boundary potential (GSBP) and Ewald summation electrostatic treatments were recently implemented for combined quantum mechanical and molecular mechanics (QM/MM) simulations by our group. These approaches were tested by calculating pKa shifts due to differences in electronic structure and electrostatic environment; the shifts were determined for a series of small molecules in solution, using various electrostatic treatments, and two residues (His 31, Lys 102) in the M102K T4-lysozyme mutant with large pKa shifts, using the GSBP approach. The calculations utilized a free energy perturbation scheme with the QM/MM potential function involving the self-consistent charge density functional tight binding (SCC-DFTB) and CHARMM as the QM and MM methods, respectively. The study of small molecules demonstrated that inconsistent electrostatic models produced results that were difficult to correct in a robust manner; by contrast, extended electrostatics, GSBP, and Ewald simulations produced consistent results once a bulk solvation contribution was carefully chosen. In addition to the electrostatic treatment, the pKa shifts were also sensitive to the level of the QM method and the scheme of treating QM/MM Coulombic interactions; however, simple perturbative corrections based on SCC-DFTB/CHARMM trajectories and higher level single point energy calculations were found to give satisfactory results. Combining all factors gave a root-mean-square difference of 0.7 pKa units for the relative pKa values of the small molecules compared to experiment. For the residues in the lysozyme, an accurate pKa shift was obtained for His 31 with multiple nanosecond simulations. For Lys 102, however, the pKa shift was estimated to be too large, even after more than 10 nanosecond simulations for each lambda window; the difficulty was due to the significant, but slow, reorganization of the protein and water structure when Lys 102 was protonated. The simulations support that Lys 102 is deprotonated in the X-ray structure and the protein is highly destabilized when this residue is protonated.

Algorithms↗
PubMed1995

Theoretical calculations of heavy-atom isotope effects.

An overview of calculations of isotope effects on biochemical and chemical reactions using quantum chemistry methods is presented. Usefulness of different levels of theoretical scrutiny for such calculations is critically discussed.

Computer Simulation↗
PubMed2005

Combined quantum mechanical/molecular mechanical study on the pentacoordinated ferric and ferrous cytochrome P450cam complexes.

The pentacoordinated ferric and ferrous cytochrome P450(cam) complexes have been investigated by combined quantum mechanical/molecular mechanical (QM/MM) calculations in the presence of a protein/solvent environment and by QM calculations on the isolated QM regions with use of density functional theory. The B3LYP functional has been found more reliable than the BLYP and BHLYP functionals for estimating the relative state energies. The B3LYP/CHARMM calculations with an all-electron basis set for iron give high-spin ground states for the title complexes, in agreement with experiment. The comparison of the B3LYP/CHARMM results of the entire protein system with the B3LYP calculations on the naked QM regions shows that the amount of stabilization by the protein environment is largest for the intermediate-spin states, followed by the high-spin states of the complexes. The calculation of Mössbauer parameters in the presence of the enzyme environment confirms the double occupation of the d(xz) orbital in the quintet spin state of the ferrous complex, consistent with the computed QM/MM energies in the enzyme environment, while the d(x)2(-)(y)2 orbital is doubly occupied in the gas-phase quintet state.

Camphor 5-Monooxygenase↗
PubMed2004

Converged quantum calculations of HO2 bound states and resonances for J=6 and 10.

Bound and resonance states of HO(2) are calculated quantum mechanically using both the Lanczos homogeneous filter diagonalization method and the real Chebyshev filter diagonalization method for nonzero total angular momentum J=6 and 10, using a parallel computing strategy. For bound states, agreement between the two methods is quite satisfactory; for resonances, while the energies are in good agreement, the widths are in general agreement. The quantum nonzero-J specific unimolecular dissociation rates for HO(2) are also calculated.

Journal Article↗
PubMed2004

Information transport and computation in nanometre-scale structures.

We discuss two examples of novel information-transport and processing mechanisms in nanometre-scale structures. The local modulation and detection of a quantum state can be used for information transport at the nanometre length-scale, an effect we call a 'quantum mirage'. We demonstrate that, unlike conventional electronic information transport using wires, the quantum mirage can be used to pass multiple channels of information through the same volume of a solid. We discuss a new class of nanometre-scale structures called 'molecule cascades', and show how they may be used to implement a general-purpose binary-logic computer in which all of the circuitry is at the nanometre length-scale.

Journal Article↗
PubMed2002

Computational challenges in atomic, molecular and optical physics.

Six challenges are discussed. These are the laser-driven helium atom; the laser-driven hydrogen molecule and hydrogen molecular ion; electron scattering (with ionization) from one-electron atoms; the vibrational and rotational structure of molecules such as H(3)(+) and water at their dissociation limits; laser-heated clusters; and quantum degeneracy and Bose-Einstein condensation. The first four concern fundamental few-body systems where use of high-performance computing (HPC) is currently making possible accurate modelling from first principles. This leads to reliable predictions and support for laboratory experiment as well as true understanding of the dynamics. Important aspects of these challenges addressable only via a terascale facility are set out. Such a facility makes the last two challenges in the above list meaningfully accessible for the first time, and the scientific interest together with the prospective role for HPC in these is emphasized.

Computer Simulation↗
PubMed1995

Modelling endplate currents: dependence on quantum secretion probability and decay of miniature current.

Quantification of the time course and amplitude of endplate currents (EPC) was made with respect to dispersion of quanta secretion and to changes in the exponential decay of miniature endplate currents (tau mepc). The relationship between RPC amplitude and tau mepc follows a double-exponential curve with tau1 = 0.3 ms and tau2 = 6 ms. If the amplitude of fully synchronised EPC is taken as 100%, then the loss of EPC amplitude is already 42% with "physiological" parameters of dispersion (the half-rise and decay constant of distribution of secretion probability = 0.5 ms, taumepc = 1 ms). This loss is even more substantial if secretion is more dispersed or miniature endplate currents decay faster.

Acetylcholine↗
PubMed2004

A simple method for the preparation of pseudopure states in nuclear magnetic resonance quantum information processing.

The use of nuclear magnetic resonance (NMR) to carry out quantum information processing (QIP) often requires the preparation, transformation, and detection of pseudopure states. In our previous work, it was shown that the use of pairs of pseudopure states (POPS) as a basis for QIP is very convenient because of the simplicity in experimental execution. It is now further demonstrated that the product of the NMR spectra corresponding to two sets of POPS that share a common pseudopure state has the same peak frequencies as those of the common (single) pseudopure state. Examples of applying two different quantum logic gates to a 5-qubit system are given.

Algorithms↗