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PubMed2006

Coherent exciton transport in dendrimers and continuous-time quantum walks.

We model coherent exciton transport in dendrimers by continuous-time quantum walks. For dendrimers up to the second generation the coherent transport shows perfect recurrences when the initial excitation starts at the central node. For larger dendrimers, the recurrence ceases to be perfect, a fact which resembles results for discrete quantum carpets. Moreover, depending on the initial excitation site, we find that the coherent transport to certain nodes of the dendrimer has a very low probability. When the initial excitation starts from the central node, the problem can be mapped onto a line which simplifies the computational effort. Furthermore, the long time average of the quantum mechanical transition probabilities between pairs of nodes shows characteristic patterns and allows us to classify the nodes into clusters with identical limiting probabilities. For the (space) average of the quantum mechanical probability to be still or to be again at the initial site, we obtain, based on the Cauchy-Schwarz inequality, a simple lower bound which depends only on the eigenvalue spectrum of the Hamiltonian.

Journal Article↗
PubMed2006

A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution.

An effective state specific (SS) model for the inclusion of solvent effects in time dependent density functional theory (TD-DFT) computations of excited electronic states has been developed and coded in the framework of the so-called polarizable continuum model (PCM). Different relaxation time regimes can be treated thus giving access to a number of different spectroscopic properties together with solvent relaxation energies of paramount relevance in electron transfer processes. SS and conventional linear response (LR) models have been compared for two benchmark systems (coumarin 153 and formaldehyde in different solvents) and in the limiting simple case of a dipolar solute embedded in a spherical cavity. The results point out the complementarity of LR and SS approaches and the advantages of the latter model especially for polar solvents. The favorable scaling properties of PCM-TD-DFT models in both SS and LR variants and their availability in effective quantum mechanical codes pave the route for the computation of reliable spectroscopic properties of large molecules of technological and/or biological interest in their natural environments.

Biophysics↗
PubMed2005

An application of the QM-QSAR method to predict and rationalize lipophilicity of simple monomers.

OBJECTIVES: The goal of this study is to develop a model used to predict octanol/water partition coefficients (log P(o/w)) values for a variety of potential dental materials. In this way, a primary consideration for potential toxicity and a rough estimate of solubility in various environments can be obtained. METHOD: The AM1 semiempirical quantum mechanical method (in AMPAC) was used to compute chemical data for all compounds in the study. CODESSA then imported the chemical information from AMPAC and computed a large set of informational descriptors. A quantitative structure activity relationship (QSAR) model was derived correlating experimental results from a training set of molecules with certain of the descriptors computed above. RESULTS: A training set of 92 molecules was used to derive the QSAR model and three descriptors were obtained: the molecular surface area, the total dipole moment of the molecule, and FPSA-3 (fractional atom charge weighted partial positive surface area). Various quality indicators were also computed and all fell within acceptable ranges: R(2)=0.945; adjusted R(2)=0.943; R(cv)(2)=0.940; variance inflation factors (VIF) for the descriptors above are 1.116, 1.044, and 1.162, respectively. SIGNIFICANCE: This QSAR model can be used to accurately and rapidly predict log P(o/w) values for a wide variety of small organic molecules, including potential dental monomers.

Databases, Factual↗
PubMed2006

TICT formation in para- and meta-derivatives of N-phenylpyrrole.

The photophysical properties of m- and p-cyano N-phenylpyrrole (m- and p-PBN) are compared. Both compounds show highly red-shifted and strongly forbidden emission in polar solvents, assigned to a charge transfer state. The forbidden nature is indicative of very weak coupling between the two pi-systems, and a twisted emissive structure is suggested (TICT state). Comparison to quantum chemical calculations indicates that the twisted structure possesses an antiquinoid distortion of the benzonitrile group, i.e., the central bonds in the ring are lengthened instead of shortened. m-PBN is the first meta compound which shows a CT emission assignable to a TICT state. It differs from p-PBN by a less exergonic formation of the CT state from the LE/ICT quinoid state. Consequently, it shows only single LE/ICT fluorescence in nonpolar alkane solvents, whereas p-PBN shows dual fluorescence in this solvent (LE/ICT and TICT).

Computer Simulation↗
PubMed1996

Stochastic particle formulation of the vesicle hypothesis. Relevance to short-term phenomena.

Based on the vesicle hypothesis, the modes of elementary quantum-vesicle interactions have been formulated in terms of probabilities of induced and spontaneous interstate quanta transitions and generalized within the framework of the previously developed theory of the double barrier synapse. Among the three allowed states for a quantum, the transition state is a novel formulation for the fraction of immediately available quanta governed by both vesicle and presynaptic membranes. The parameters of the model were determined by fitting solutions to the experimental curves representing effects of single pulse and short train activation on transmitter release at the frog neuromuscular junction. Qualitative differences in particle physics of transmitter release found under low quantal outputs on one hand and normal transmission on the other allowed the formulation of the uncertainty hypothesis and the quantum condition of synaptic homeostasis.

Computer Simulation↗
PubMed2006

Study of molecular quantum similarity of enantiomers of amino acids.

Molecular quantum similarity is evaluated for enantiomers in the case of molecules showing conformational flexibility, using our earlier proposed Boltzmann weighted similarity index. The conformers of the enantiomers of the amino acids alanine, asparagine, cysteine, leucine, serine, and valine were examined. Next to studying global indices, the evaluation of local similarity is carried out using our earlier proposed local similarity index based on the Hirshfeld partitioning, to further illustrate Mezey's holographic electron density theorem in chiral systems and to quantify dissimilarity of enantiomers.

Amino Acids↗
PubMed2002

Interactive computer simulations of knee-replacement surgery.

OBJECTIVE: Current surgical training programs in the United States are based on an apprenticeship model. This model is outdated because it does not provide conceptual scaffolding, promote collaborative learning, or offer constructive reinforcement. Our objective was to create a more useful approach by preparing students and residents for operative cases using interactive computer simulations of surgery. Total-knee-replacement surgery (TKR) is an ideal procedure to model on the computer because there is a systematic protocol for the procedure. Also, this protocol is difficult to learn by the apprenticeship model because of the multiple instruments that must be used in a specific order. We designed an interactive computer tutorial to teach medical students and residents how to perform knee-replacement surgery. We also aimed to reinforce the specific protocol of the operative procedure. Our final goal was to provide immediate, constructive feedback. DESCRIPTION: We created a computer tutorial by generating three-dimensional wire-frame models of the surgical instruments. Next, we applied a surface to the wire-frame models using three-dimensional modeling. Finally, the three-dimensional models were animated to simulate the motions of an actual TKR. The tutorial is a step-by-step tutorial that teaches and tests the correct sequence of steps in a TKR. The student or resident must select the correct instruments in the correct order. The learner is encouraged to learn the stepwise surgical protocol through repetitive use of the computer simulation. Constructive feedback is acquired through a grading system, which rates the student's or resident's ability to perform the task in the correct order. The grading system also accounts for the time required to perform the simulated procedure. We evaluated the efficacy of this teaching technique by testing medical students who learned by the computer simulation and those who learned by reading the surgical protocol manual. Both groups then performed TKR on manufactured bone models using real instruments. Their technique was graded with the standard protocol. The students who learned on the computer simulation performed the task in a shorter time and with fewer errors than the control group. They were also more engaged in the learning process. DISCUSSION: Surgical training programs generally lack a consistent approach to preoperative education related to surgical procedures. This interactive computer tutorial has allowed us to make a quantum leap in medical student and resident teaching in our orthopedic department because the students actually participate in the entire process. Our technique provides a linear, sequential method of skill acquisition and direct feedback, which is ideally suited for learning stepwise surgical protocols. Since our initial evaluation has shown the efficacy of this program, we have implemented this teaching tool into our orthopedic curriculum. Our plans for future work with this simulator include modeling procedures involving other anatomic areas of interest, such as the hip and shoulder.

Arthroplasty, Replacement, Knee↗
PubMed2004

Quantitative structure-activity relationships for phenyl triazolinones of protoporphyrinogen oxidase inhibitors: a density functional theory study.

The equilibrium geometries, electronic structures, and electrostatic potentials of a series of substituted phenyl triazolinones of protoporphyrinogen oxidase (PPO) inhibitors have been investigated by using the density functional theory (DFT) method. The quantum chemical descriptors, highest occupied molecular orbital and lowest unoccupied molecular orbital energy gap (DeltaE), weighted electrophilic, and nucleophilic atomic frontier electron density (FAE and FAN), and net atomic charge (QA), were computed at the same DFT level. Based on these precise quantum chemical descriptors, a quantitative structure-activity relationships study has been carried out and shown that QC11, FN5E, FC10N, and DeltaE of individual molecules are most likely to be responsible for the in vitro biological activity and greenhouse preemergence activity of phenyl triazolinones. The ability to quite accurately predict the biological activity of phenyl triazolinones by using DFT-based QSAR can be expected to help facilitate the design of additional substituted phenyl triazolinones as PPO inhibitors with good biological activity.

Benzene Derivatives↗
PubMed2005

Transport properties of normal liquid helium: comparison of various methodologies.

We revisit the problem of self-diffusion in normal liquid helium above the lambda transition. Several different methods are applied to compute the velocity autocorrelation function. Since it is still impossible to determine the exact result for the velocity autocorrelation function from simulation, we appeal to the computation of short-time moments to determine the accuracy of the different approaches at short times. The main conclusion reached from our study is that both the quantum mode-coupling theory and the numerical analytic continuation approach must be regarded as a viable and competitive methods for the computation of dynamical properties of quantum systems.

Journal Article↗
PubMed2000

[Clinical method of newborn's maturity evaluation according to R. Klimek's index].

The object of the study was to evaluate R. Klimek's new simple clinical method of computing newborn's maturity index (K) without having to use the computer-aided method or understand the basics of the quantum mechanics or theory of relativity, which gave rise to the modern definition of maturity. The study was based on the material of 1000 successive newborns delivered in the Clinic of Gynecology and Obstetrics of the Jagiellonian University. Their maturity was determined routinely in BK scale, and confirmed by means of computer-aided method of birth term prognosis. Posture, angle of the elbow, pulling an elbow to the middle line of the body, breast appearance, presence of lanugo and plantar creases were evaluated by means of K index with points from 0 to 2. Newborns' maturity index K was 9.2 +/- 1.9 points (range 2-12). 2.6% newborns were immature and one third of them (0.8%) were born with the gestational age < 37 weeks, 28 of which (77%) had correct K index > or = 6 points. There is a high, statistically significant correlation between maturity assessed in Ballard-Klimek scale and K index (r = 0.61, t = 24.78).

Electronic Data Processing↗
PubMed1998

Magnetocardiographic localization of arrhythmia substrates: a methodology study with accessory pathway ablation as reference.

In magnetocardiographic (MCG) localization of arrhythmia substrates, a model of the thorax as volume conductor is a crucial component of the calculations. In this study, we investigated different models of the thorax, to determine the most suitable to use in the computations. Our methods and results are as follows. We studied 11 patients with overt Wolff-Parkinson-White syndrome, scheduled for catheter ablation. The MCG registrations were made with a 37-channel "superconducting quantum interference device" system. The underlying equivalent current dipole was computed for the delta-wave. Three models of the thorax were used: the infinite halfspace, a sphere and a box. For anatomical correlation and to define the suitable sphere and box, magnetic resonance images were obtained. As reference we used the position of the tip of the catheter, at successful radio-frequency-ablation, documented by cine-fluoroscopy. Nine patients could be evaluated. The mean errors (range) when using the infinite halfspace, the sphere and the box were 96 (49-125), 21 (5-39), and 36 mm (20-58 mm), respectively (p < 0.0001). In conclusion, the sphere was significantly better suited than the other models tested in this study, but even with this model the accuracy of MCG localization must further improve to be clinically useful. More realistic models of the thorax are probably required to achieve this goal.

Adult↗
PubMed1998

Digital x-ray imaging using amorphous selenium: reduction of aliasing.

Alias reduction is analyzed with the concept of an equivalent presampling filter, and a mathematical approach is established to find the equivalent presampling filter corresponding to specific digital image processing algorithms. The effects of different sampling period T and sampling aperture tau on aliasing artifacts and on the resultant detective quantum efficiency (DQE) for a self-scanned, flat-panel, amorphous selenium detector are obtained. Different effective apertures can be obtained from the same detector by averaging signals over adjacent pixels. It is shown that adding outputs from M adjacent pixels is equivalent to introducing an equivalent presampling filter with special properties. Appropriate selection of the averaging parameters (M and weights) is shown to reduce the aliasing artifact in the resultant image. The effect of incomplete charge collection due to geometrical effects (fill factor) is examined. It is shown that a large fill factor is desirable for aliasing reduction. The relationship between a digital filter applied to the sampled signal and its equivalent presampling analog filter is also established. Analytical formulas for the sampled spectrum of white signal and for the sampled power spectrum of white noise are obtained for aperture functions with a spatially uniform response. These formulas take into accounts aliasing artifacts, signal correlation and aperture function response, and demonstrate the dependence of sampled spectra on T and tau. With these formulas the detective quantum efficiency DQE is derived. It is shown that the resultant DQE depends only on the fill factor and the size of readout electrode tau 0, but is completely independent of the degree or type of pixel averaging. That is, even though the pixel averaging method reduces aliasing it leaves DQE (omega) unchanged. When significant amplifier noise is present the DQE obtained with the pixel averaging method can be better than those obtained with an analog presampling filter. Finally, it is pointed out that the requirement of reducing aliasing artifacts conflicts with other requirements for a detector such as maximizing modulation transfer function (MTF). A careful and practical compromise has to be made by a detector designer in choosing the extent to which the aliasing artifacts are eliminated.

Algorithms↗
PubMed2005

The coordination of uranyl in water: a combined quantum chemical and molecular simulation study.

The coordination environment of uranyl in water has been studied using a combined quantum mechanical and molecular dynamics approach. Multiconfigurational wave function calculations have been performed to generate pair potentials between uranyl and water. The quantum chemically determined energies have been used to fit parameters in a polarizable force field with an added charge transfer term. Molecular dynamics simulations have been performed for the uranyl ion and up to 400 water molecules. The results show a uranyl ion with five water molecules coordinated in the equatorial plane. The U-O(H(2)O) distance is 2.40 A, which is close to the experimental estimates. A second coordination shell starts at about 4.7 A from the uranium atom. No hydrogen bonding is found between the uranyl oxygens and water. Exchange of waters between the first and second solvation shell is found to occur through a path intermediate between association and interchange. This is the first fully ab initio determination of the solvation of the uranyl ion in water.

Computer Simulation↗
PubMed2006

Quantized time correlation function approach to nonadiabatic decay rates in condensed phase: application to solvated electrons in water and methanol.

A new, alternative form of the golden rule formula defining the nonadiabatic transition rate between two quantum states in condensed phase is presented. The formula involves the quantum time correlation function of the energy gap, of the nonadiabatic coupling, and their cross terms. Those quantities can be inferred from their classical counterparts, determined via molecular dynamics simulations. The formalism is applied to the problem of the nonadiabatic p-->s relaxation of an equilibrated p-electron in water and methanol. We find that, in both solvents, the relaxation is induced by the coupling to the vibrational modes and the quantum effects modify the rate by a factor of 2-10 depending on the quantization procedure applied. The resulting p-state lifetime for a hypothetical equilibrium excited state appears extremely short, in the sub-100 fs regime. Although this result is in contrast with all previous theoretical predictions, we also illustrate that the lifetimes computed here are very sensitive to the simulated electronic quantum gap and to the strongly correlated nonadiabatic coupling.

Journal Article↗
PubMed2001

Multichannel pseudogap Kondo model: large-N solution and quantum-critical dynamics.

We discuss a multichannel SU(N) Kondo model which displays nontrivial zero-temperature phase transitions due to a conduction electron density of states vanishing with a power law at the Fermi level. In a particular large- N limit, the system is described by coupled integral equations corresponding to a dynamic saddle point. We exactly determine the universal low-energy behavior of spectral densities at the scale-invariant fixed points, obtain anomalous exponents, and compute scaling functions describing the crossover near the quantum-critical points. We argue that our findings are relevant to recent experiments on impurity-doped d-wave superconductors.

Journal Article↗
PubMed2003

Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity.

An overview of the combined quantum mechanical/molecular mechanical (QM/MM) approach and its application to studies of biotransformation enzymes and drug metabolism is given. Theoretical methods to simulate enzymatic reactions have rapidly developed during the last decade. In particular, QM/MM methods provide detailed insights into enzyme catalyzed reactions, which can be extremely valuable in complementing experimental research. QM/MM methods allow the reacting groups in the active site of an enzyme to be studied at a quantum mechanical level, while the surrounding protein and solvent is included at a classical (and computationally less expensive) molecular mechanical level. Existing QM/MM implementations vary in the level of interaction between the QM and MM regions and in the way the partitioning into QM and MM regions is setup. Some general considerations concerning reaction modeling are discussed and a number of QM/MM studies related to drug metabolism are described. These studies illustrate that theoretical modeling of important metabolic reactions provides detailed insights into mechanisms of reaction and specific catalytic effects of enzyme residues as well as explaining variation in rates of conversion of different metabolites. Such information is essential in the development of methods to predict metabolism of drugs and to understand metabolic effects of genetic polymorphism in biotransformation enzymes.

Animals↗
PubMed2006

Automated quantification of quantum-dot-labelled epidermal growth factor receptor internalization via multiscale image segmentation.

The ability to monitor epidermal growth factor receptor (EGFr) internalization specifically, and cellular protein concentrations and activation states in general, has been recently improved by the use of appropriately functionalized quantum dots (QDs), as a result of the long-lasting fluorescence, brightness and multicolour of these nanoparticles. However, important quantitative information about locational proteomics is based on the analysis of the properties of many cells and cell cultures on a per-cell basis, rather than tracking individual events within one cell. Moreover, relative positional information is often gained from traditional staining protocols of distinct cellular compartments that are prone to noise, fading and low contrast. We apply a novel multiscale image segmentation based on region growing to classify automatically objects in fixed cell preparations and to define regional zones in all cells prior to QD concentration measures. This allows rapid quantitative description of EGFr internalization as it changes with incubation time. The capabilities realizable by simultaneous application of confocal imaging and functionalized QDs in conjunction with advanced image analysis are a prerequisite for automated and multiplexed cytomics assays.

Biotin↗
PubMed2006

Quantum trajectory dynamics in arbitrary coordinates.

The quantum trajectory approach is generalized to arbitrary coordinate systems, including curvilinear coordinates. This allows one to perform an approximate quantum trajectory propagation, which scales favorably with system size, in the same framework as standard quantum wave packet dynamics. The trajectory formulation is implemented in Jacobi coordinates for a nonrotating triatomic molecule. Wave packet reaction probabilities are computed for the O(3P) + H2 --> OH + H reaction using the approximate quantum potential. The latter is defined by the nonclassical component of the momentum operator expanded in terms of linear and exponential functions. Unlike earlier implementations with linear functions, the introduction of the exponential function provides an accurate description of asymptotic dynamics for this system and gives good agreement of approximate reaction probabilities with accurate quantum calculations.

Journal Article↗