D. R. Fredkin

Hysteresis in lithographic arrays of permalloy particles: Experiment and theory (invited)

We have investigated the effects of particle size and aspect ratio on the hysteresis in controlled arrays of small magnetic particles. The arrays of permalloy particles were fabricated via electron‐beam lithography. Each array consists of ∼ 106 identical, uniformly spaced particles. Hysteresis loops measured with an alternating‐gradient magnetometer for particles ∼5–0.1 μm are presented. We find an increase in the coercive force as the particle width decreases below 0.3 μm due to a change in the switching mechanism from domain‐wall nucleation and wall motion to vortex nucleation and vortex motion. A novel angular dependence of the loops is described in detail. Results from ab initio micromagnetic calculations on isolated rectangular Permalloy particles are compared, where applicable, with the measurements. We find excellent qualitative and, in selected cases, quantitative agreement between the experiments and calculations.

Maximum Likelihood Estimation and Identification Directly from Single-Channel Recordings

We present a method for analysis of noisy sampled data from a single-channel patch clamp which bypasses restoration of an idealized quantal signal. We show that, even in the absence of a specific model, the conductance levels and mean dwell times within those levels can be estimated. Estimation of the rate constants of a hypothesized kinetic scheme is more difficult. We present examples in which the rate constants can be effectively estimated and examples in which they cannot.

The electronic structure of Fe2+ in reaction centers from Rhodopseudomonas sphaeroides. III. EPR measurements of the reduced acceptor complex

Electron paramagnetic resonance (EPR) spectra of the reduced quinone-iron acceptor complex in reaction centers were measured in a variety of environments and compared with spectra calculated from a theoretical model. Spectra were obtained at microwave frequencies of 1, 9, and 35 GHz and at temperatures from 1.4 to 30 K. The spectra are characterized by a broad absorption peak centered at g = 1.8 with wings extending from g approximately equal to 5 to g less than 0.8. The peak is split with the low-field component increasing in amplitude with temperature. The theoretical model is based on a spin Hamiltonian, in which the reduced quinone, Q-, interacts magnetically with Fe2+. In this model the ground manifold of the interacting Q-Fe2+ system has two lowest doublets that are separated by approximately 3 K. Both perturbation analyses and exact numerical calculations were used to show how the observed spectrum arises from these two doublets. The following spin Hamiltonian parameters optimized the agreement between simulated and observed spectra: the electronic g tensor gFe, x = 2.16, gFe, y = 2.27, gFez = 2.04, the crystal field parameters D = 7.60 K and E/D = 0.25, and the antiferromagnetic magnetic interaction tensor, Jx = -0.13 K, Jy = -0.58 K, Jz = -0.58 K. The model accounts well for the g value (1.8) of the broad peak, the observed splitting of the peak, the high and low g value wings, and the observed temperature dependence of the shape of the spectra. The structural implications of the value of the magnetic interaction, J, and the influence of the environment on the spin Hamiltonian parameters are discussed. The similarity of spectra and relaxation times observed from the primary and secondary acceptor complexes Q-AFe2+ and Fe2+Q-B leads to the conclusion that the Fe2+ is approximately equidistant from QA and QB.

On aggregated Markov processes

A finite-state Markov process is aggregated into several groups. What can be learned about the underlying process from the aggregated one? We provide some partial answers to this question.

Electrostatic calculations of amino acid titration and electron transfer, Q-AQB-->QAQ-B, in the reaction center

The titration of amino acids and the energetics of electron transfer from the primary electron acceptor (QA) to the secondary electron acceptor (QB) in the photosynthetic reaction center of Rhodobacter sphaeroides are calculated using a continuum electrostatic model. Strong electrostatic interactions between titrating sites give rise to complex titration curves. Glu L212 is calculated to have an anomalously broad titration curve, which explains the seemingly contradictory experimental results concerning its pKa. The electrostatic field following electron transfer shifts the average protonation of amino acids near the quinones. The pH dependence of the free energy between Q-AQB and QAQ-B calculated from these shifts is in good agreement with experiment. However, the calculated absolute free energy difference is in severe disagreement (by approximately 230 meV) with the observed experimental value, i.e., electron transfer from Q-A to QB is calculated to be unfavorable. The large stabilization energy of the Q-A state arises from the predominantly positively charged residues in the vicinity of QA in contrast to the predominantly negatively charged residues near QB. The discrepancy between calculated and experimental values for delta G(Q-AQB-->QAQ-B) points to limitations of the continuum electrostatic model. Inclusion of other contributions to the energetics (e.g., protein motion following quinone reduction) that may improve the agreement between theory and experiment are discussed.

Ab initio micromagnetic calculations for particles (invited)

We present the results of first‐principles calculations of the magnetic behavior of particles of varying shapes (sphere, prolate spheroid, and rectangular particles of various aspect ratios) and sizes ranging from ≊0.1 to 10 μm. We use a numerical implementation of micromagnetics in which the only input quantities, aside from the particle geometry, are the material parameters and the magnetic history. We have obtained quantitative agreement with theory for spherical particles and qualitative agreement with experiment in the case of rectangular objects, and we have observed a variety of interesting reversible and irreversible phenomena accompanying magnetic reversal in all objects. We describe key aspects of the numerical implementation and survey selected results.

Magnetization reversal in permalloy particles: Micromagnetic computations

Magnetization distributions in a rectangular permalloy particle with an 8:1 aspect ratio are presented. When a magnetic field is applied along the easy axis of the particle, there is considerable change in the vortex pattern as the applied field varies, but the moment is nearly constant. Magnetization reversal is sudden. When a field is applied oblique to the easy axis the magnetization is rather uniform in most of the particle. When an in‐plane field is applied exactly along the hard axis, a complex domain structure is formed, so that the remanence is zero, in agreement with experiment. Formation of this state requires that the applied field exceed a critical value. Upon application of an easy axis field to this complex state, the domain structure is shifted so that the magnetization increases linearly with the applied field.

Transient x‐ray scattering calculated from molecular dynamics

With the continued development of pulsed x‐ray sources, it may in time be possible to use transient x‐ray diffraction to follow the molecular dynamics of chemical reactions in the liquid and solid states. To explore this possibility from the theoretical side, we have calculated, using classical molecular dynamics, the picosecond time‐resolved x‐ray scattering of a simplified model for a liquid state chemical reaction of substantial interest: the photodissociation of I2 molecules in rare gas and hexane solvents. The time scale of the separation of the I atoms and the effect of the solvent on their motion are observed in the computed transient x‐ray diffraction patterns, and such effects might also be observed in a suitably designed experiment. This illustrates that transient x‐ray diffraction might be an experimental tool for discovering the molecular dynamics of chemical reactions, with the advantage over transient optical spectroscopies such as infrared, electronic, and Raman that the connections between...

Measurement of thermal switching of the magnetization of single domain particles (invited)

We present an experimental study of the thermally activated switching of the magnetization of individual isolated γ‐Fe2O3 particles. These particles are prolate ellipsoids ∼3000 A long and 650 A wide. The measured angular dependence of the switching field, Hs(θ), is consistent at large angles with a uniform rotation, but as θ approaches zero, other modes of reversal appear possible, and most likely the mode of reversal is curling. By measuring the probability of reversal of the moment as a function of time and applied magnetic field at T∼300 K, we found that the switching was thermally assisted, but couldn’t be described by hopping over a single energy barrier. Our results indicate that the dynamics of switching are described by a complex path in the energy landscape.

Ab initio infrared and Raman spectra

We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrodinger equation in the Born–Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational‐rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at...