Biomedical subjects

Bruce R Johnson

Publications and source records attributed to Bruce R Johnson.

11 recordsLinked to original sources

PubMed2006

Two-dimensional quantum propagation using wavelets in space and time.

A recent method for solving the time-dependent Schrodinger equation has been developed using expansions in compact-support wavelet bases in both space and time [H. Wang et al., J. Chem. Phys. 121, 7647 (2004)]. This method represents an exact quantum mixed time-frequency approach, with special initial temporal wavelets used to solve the initial value problem. The present work is a first extension of the method to multiple spatial dimensions applied to a simple two-dimensional (2D) coupled anharmonic oscillator problem. A wavelet-discretized version of norm preservation for time-independent Hamiltonians discovered in the earlier one-dimensional investigation is verified to hold as well in 2D and, by implication, in higher numbers of spatial dimensions. The wavelet bases are not restricted to rectangular domains, a fact which is exploited here in a 2D adaptive version of the algorithm.

Journal Article↗

PubMed2006

Multimode wavelet basis calculations via the molecular self-consistent-field plus configuration-interaction method.

Wavelets provide potentially useful quantum bases for coupled anharmonic vibrational modes in polyatomic molecules as well as many other problems. A single compact support wavelet family provides a flexible basis with properties of orthogonality, localization, customizable resolution, and systematic improvability for general types of one-dimensional and separable systems. While direct product wavelet bases can be used in coupled multidimensional problems, exponential scaling of basis size with dimensionality ultimately provides limits on the number of coupled modes that can be treated simultaneously in exact quantum calculations. The molecular self-consistent-field plus configuration-interaction method is used here in multimode wavelet calculations to reduce the basis size without sacrificing flexibility or the ability to systematically control errors. Both two-dimensional Cartesian coordinate and three-dimensional curvilinear coordinate systems are examined with wavelets serving as universal bases in each case. The first example uses standard Daubechies [Ten Lectures on Wavelets (SIAM, Philadelphia (1992)] wavelets for each mode and the second adapts symmlet wavelets to intervals for each of the curvilinear coordinates.

Journal Article↗

PubMed2006

Density-matrix calculation of surface-enhanced Raman scattering for p-mercaptoaniline on silver nanoshells.

A theoretical analysis of recent experiments measuring the 782 nm surface-enhanced Raman scattering of p-mercaptoaniline bound to silver nanoshells of different core and shell radii [J. B. Jackson and N. J. Halas, Proc. Natl. Acad. Sci. U.S.A. 101, 17930 (2004)] is performed. Electronic structure Hartree-Fock and density-functional theory calculations for Ag salts of p-mercaptoaniline are used to characterize observed vibrational modes and configuration-interaction singles calculations are carried out to examine excited states. Multimode vibronic density-matrix calculations are then made including one excited electronic state, using a classical description of the strong local fields and a phenomenological treatment of relaxations. The spectral behavior as a function of both nanoshell surface-plasmon resonance position and molecular electronic spacing is examined.

Journal Article↗

PubMed2006

Additions to the class of symmetric-antisymmetric multiwavelets: derivation and use as quantum basis functions.

Multiwavelet bases have been shown recently to apply to a variety of quantum problems. There are, however, only a few multiwavelet families that have been defined to date. Chui-Lian-type symmetric and antisymmetric multiwavelets are derived here that equal and exceed the polynomial interpolating power of previously available examples. Adaptations to domain edges are made with a view to use in curvilinear coordinate molecular calculations. The new highest-order multiwavelet family is shown to provide uniformly better performance for (i) basis representation of terms such as 1r(2) in near approach to the singularity at r=0 and (ii) eigenvalue calculation of a bending Hamiltonian taken from a curvilinear model of the ground-state vibrations of nitrosyl chloride.

Journal Article↗

PubMed2006

All-optical nanoscale pH meter.

We show that an Au nanoshell with a pH-sensitive molecular adsorbate functions as a standalone, all-optical nanoscale pH meter that monitors its local environment through the pH-dependent surface-enhanced Raman scattering (SERS) spectra of the adsorbate molecules. Moreover, we also show how the performance of such a functional nanodevice can be assessed quantitatively. The complex spectral output is reduced to a simple device characteristic by application of a locally linear manifold approximation algorithm. The average accuracy of the nano-"meter" was found to be +/-0.10 pH units across its operating range.

Equipment Design↗

PubMed2005

Dopamine modulation of phasing of activity in a rhythmic motor network: contribution of synaptic and intrinsic modulatory actions.

The phasing of neuronal activity in a rhythmic motor network is determined by a neuron's intrinsic firing properties and synaptic inputs; these could vary in their relative importance under different modulatory conditions. In the lobster pyloric network, the firing of eight follower pyloric (PY) neurons is shaped by their intrinsic rebound after pacemaker inhibition and by synaptic input from the lateral pyloric (LP) neuron, which inhibits all PY neurons and is electrically coupled to a subset of them. Under control conditions, LP inhibition is weak and has little influence on PY firing. We examined modulation that could theoretically enhance the LP's synaptic contribution to PY firing. We measured the effects of dopamine (DA) on LP-->PY synapses, driving the LP neuron with trains of realistic waveforms constructed from prerecorded control and DA LP oscillations, which differed in shape and duration. Under control conditions, chemical inhibition underwent severe depression and disappeared; in the mixed synapses, electrical coupling dominated. Switching between control and DA LP waveforms (with or without DA present) caused only subtle changes in synaptic transmission. DA markedly enhanced synaptic inhibition, reduced synaptic depression and weakened electrical coupling, reversing the sign of the mixed synapses. Despite this, removal of the LP from the intact network still had only weak effects on PY firing. DA also enhances PY intrinsic rebound properties, which still control the onset of PY firing. Thus in a rhythmic network, the functional importance of synaptic modulation can only be understood in the context of parallel modulation of intrinsic properties.

Action Potentials↗

PubMed2005

Color-blind fluorescence detection for four-color DNA sequencing.

We present an approach called pulsed multiline excitation (PME) for measurements of multicomponent, fluorescence species and demonstrate its application in capillary electrophoresis for DNA sequencing. To fully demonstrate the advantages of PME, a fluorescent dye set has been developed whose absorption maxima span virtually the entire visible spectrum. Unlike emission wavelength-dependent approaches for identifying fluorescent species, the removal of the spectral component in PME confers a number of advantages including higher and normalized signals from all dyes present in the assay, the elimination of spectral cross-talk between dyes, and higher signal collection efficiency. Base-calling is unambiguously determined once dye mobility corrections are made. These advantages translate into significantly enhanced signal quality as illustrated in the primary DNA sequencing data and provide a means for achieving accurate base-calling at lower reagent concentrations.

Base Sequence↗

PubMed2004

Multiscale quantum propagation using compact-support wavelets in space and time.

Orthogonal compact-support Daubechies wavelets are employed as bases for both space and time variables in the solution of the time-dependent Schrodinger equation. Initial value conditions are enforced using special early-time wavelets analogous to edge wavelets used in boundary-value problems. It is shown that the quantum equations may be solved directly and accurately in the discrete wavelet representation, an important finding for the eventual goal of highly adaptive multiresolution Schrodinger equation solvers. While the temporal part of the basis is not sharp in either time or frequency, the Chebyshev method used for pure time-domain propagations is adapted to use in the mixed domain and is able to take advantage of Hamiltonian matrix sparseness. The orthogonal separation into different time scales is determined theoretically to persist throughout the evolution and is demonstrated numerically in a partially adaptive treatment of scattering from an asymmetric Eckart barrier.

Journal Article↗

PubMed2004

Characterizing dependence of pesticide load in surface water on precipitation and pesticide use for the Sacramento River watershed.

Transport of pesticides by surface runoff during rainfall events is a major process contributing to pesticide contamination in rivers. This study presents an empirical regression model that relates pesticide loading over time in the Sacramento River with the precipitation and pesticide use in the Sacramento River watershed. The model closely simulated loading dynamics of diazinon, simazine, and diuron during 1991-1994 and 1997-2000 winter storm seasons. The coefficients of determination for regression ranged from 0.168 to 0.907, all were significant at <0.001. The results of this study provide strong evidence that precipitation and pesticide use are the two major environmental variables dictating the dynamics of pesticide transport into surface water in a watershed. The capability of the statistical model to provide time-series estimates on pesticide loading in rivers is unique and may be useful fortotal maximum daily load (TMDL) assessments.

Agriculture↗

PubMed2003

Activity-independent homeostasis in rhythmically active neurons.

The shal gene encodes the transient potassium current (I(A)) in neurons of the lobster stomatogastric ganglion. Overexpression of Shal by RNA injection into neurons produces a large increase in I(A), but surprisingly little change in the neuron's firing properties. Accompanying the increase in I(A) is a dramatic and linearly correlated increase in the hyperpolarization-activated inward current (I(h)). The enhanced I(h) electrophysiologically compensates for the enhanced I(A), since pharmacological blockade of I(h) uncovers the physiological effects of the increased I(A). Expression of a nonfunctional mutant Shal also induces a large increase in I(h), demonstrating a novel activity-independent coupling between the Shal protein and I(h) enhancement. Since I(A) and I(h) influence neuronal activity in opposite directions, our results suggest a selective coregulation of these channels as a mechanism for constraining cell activity within appropriate physiological parameters.

Action Potentials↗

PubMed2003

Dopamine modulation of calcium currents in pyloric neurons of the lobster stomatogastric ganglion.

We examined the dopamine (DA) modulation of calcium currents (ICa) that could contribute to the plasticity of the pyloric network in the lobster stomatogastric ganglion. Pyloric somata were voltage-clamped under conditions designed to block voltage-gated Na+, K+, and H currents. Depolarizing steps from -60 mV generated voltage-dependent, inward currents that appeared to originate in electrotonically distal, imperfectly clamped regions of the cell. These currents were blocked by Cd2+ and enhanced by Ba2+ but unaffected by Ni2+. Dopamine enhanced the peak ICa in the pyloric constrictor (PY), lateral pyloric (LP), and inferior cardiac (IC) neurons and reduced peak ICa in the ventricular dilator (VD), pyloric dilator (PD), and anterior burster (AB) neurons. All of these effects, except for the AB, are consistent with DA's excitation or inhibition of firing in the pyloric neurons. Enhancement of ICa in PY and LP neurons and reduction of ICa in VD and PD neurons are also consistent with DA-induced synaptic strength changes via modulation of presynaptic ICa. However, the reduction of ICa in AB suggests that DA's enhancement of AB transmitter release is not directly mediated through presynaptic ICa. ICa in PY and PD neurons was more sensitive to nifedipine block than in AB neurons. In addition, nifedipine blocked DA's effects on ICa in the PY and PD neurons but not in the AB neuron. Thus the contribution of specific calcium channel subtypes carrying the total ICa may vary between pyloric neuron classes, and DA may act on different calcium channel subtypes in the different pyloric neurons.

Animals↗