Static Barrier Research Articles

Lateral Diffusion of Membrane Proteins in the Presence of Static and Dynamic Corrals: Suggestions for Appropriate Observables

We consider the possibility of inferring the nature of cytoskeletal interaction with transmembrane proteins via optical experiments such as single-particle tracking (SPT) and near-field scanning optical microscopy (NSOM). In particular, we demonstrate that it may be possible to differentiate between static and dynamic barriers to diffusion by examining the time-dependent variance and higher moments of protein population inside cytoskeletal “corrals.” Simulations modeling Band 3 diffusion on the surface of erythrocytes provide a concrete demonstration that these statistical tools might prove useful in the study of biological systems.

Origin of the anomalous temperature dependence of luminescence in semiconductor nanocrystallites

The temperature dependence of the luminescence intensity in nanocrystalline semiconductors, amorphous semiconductors, and chalcogenides has been reported to be of the Berthelot type $\mathrm{exp}{(T/T}_{B}),$ where ${T}_{B}$ is some characteristic temperature. A similar behavior has been reported for transport properties in certain semiconductors and in porous silicon. We propose a simple microscopic model for the origin of the Berthelot term. We assume that luminescence arises from a competition between radiative and hopping processes. The hopping process is modeled by assuming that the carrier tunnels through a static barrier. Optimizing this tunneling in a fashion similar to Mott's treatment of variable range hopping leads to the Berthelot-type behavior. The class of barriers for which our result holds is large. We examine alternative proposals and find them wanting. Our model predicts that acceptable values of the barrier width (1 nm) yields Berthelot temperatures ${T}_{B}$ in the range 30--300 K. The experimentally reported ${T}_{B}$ in diverse systems ranging from nanocrystalline semiconductors to amorphous chalcogenides fall in our predicted range. Thus we demonstrate that the Berthelot temperature dependence has a definite and reasonable physical basis.

Enzymology takes a quantum leap forward

Enzymes are biological molecules that accelerate chemical reactions. They are central to the existence of life. Since the discovery of enzymes just over a century ago, we have witnessed an explosion in our understanding of enzyme catalysis, leading to a more detailed appreciation of how they work. A key breakthrough came from understanding how enzymes surmount the potential-energy barrier that separates reactants from products. The genetic engineering revolution has provided tools for dissecting enzyme structure and enabling design of novel function. Despite the huge efforts to redesign enzyme molecules for specific applications, progress in this area has been generally disappointing. This stems from our limited understanding of the subtleties by which enzymes enhance reaction rates. Based on current dogma, the vast majority of studies have concentrated on understanding how enzymes facilitate passage of the reaction over a static potential-energy barrier. However, recent studies have revealed that passage through, rather than over, the barrier can occur. These studies reveal that quantum mechanical phenomena, driven by protein dynamics, can play a pivotal role in enzyme action. The new millennium will witness a flurry of activity directed at understanding the role of quantum mechanics and protein motion in enzyme action. We discuss these new developments and how they will guide enzymology into the new millennium.

"Ab initio" studies of hydrogen-enhanced oxygen diffusion in silicon

A novel microscopic mechanism for hydrogen-enhanced oxygen diffusion in p-doped silicon is proposed. A path for joint diffusion of O and H is obtained from an ab-initio molecular dynamics "kick" simulation. The migration pathway consists of a two-step mechanism, with a maximum energy of 1.46 eV. This path represents a 0.54 eV reduction in the static barrier when compared with the diffusion of isolated O in Si, in excellent agreement with experiments.

Direct Evidence for Grain Boundary Potential Barrier Breakdown via In Situ Electron Holography.

: Static and dynamic grain boundary potential barrier effects are directly observed at high spatial resolution for a varistor of model structure and chemistry. Grain boundary mechanisms for nonlinear electrical behavior are investigated for Nb-doped SrTiO(3) bicrystals by in situ high-resolution electron holography under applied current coupled with electrical measurements. For the static case, holography reveals a positive grain boundary barrier of about 0.45 V, which is indicative of positive grain boundary charge adjoined by negative space charge regions. Under high applied current, in situ holography records the breakdown of this grain boundary barrier in accord with the macroscopic varistor effect, which is reflected in bulk I-V experiments.

Mechanism for hydrogen-enhanced oxygen diffusion in silicon

Oxygen diffuses in silicon with an activation energy of 2.53--2.56 eV. In hydrogenated samples, this activation energy is found to decrease to 1.6--2.0 eV. In this paper, a microscopic mechanism for hydrogen-enhanced oxygen diffusion in p-doped silicon is proposed. A path for joint diffusion of O and H is obtained from an ab initio molecular-dynamics simulation in which the O atom is ``kicked'' away from its equilibrium position with a given initial kinetic energy. After reaching a maximum potential energy of 1.46 eV above the ground state, the system relaxes to a metastable state on which a Si-Si bond is broken and the H atom saturates one of the dangling bonds. With an extra 0.16 eV, the Si-H bond is broken and the system relaxes to an equivalent ground-state configuration. Therefore, the migration pathway is an intriguing two-step mechanism. This path represents a 0.54-eV reduction in the static barrier when compared with the diffusion of isolated O in Si, in excellent agreement with experiments. This mechanism elucidates the role played by the H atom in the process: it not only serves to ``open up'' a Si-Si bond to be attacked by the oxygen, but it also helps in reducing the energy of an important intermediate state in the diffusion pathway.

Revealing broad overlapping resonances by strong laser fields

The resonance states of a periodically driven barrier potential are investigated. We show that narrow shape-type resonances evolve from overlapping resonances of a static barrier as a result of an increase of the field amplitude. These shape-type resonances are associated with the field-induced barrier transparency phenomenon. It is suggested that cross-section experiments in strong laser fields may be used to uncover overlapping resonances.

Surface vacancy diffusion on Cu(111): a computer simulation study

The diffusion of a surface vacancy on Cu(111) has been studied by means of molecular dynamics in conjunction with the many-body potential derived from the second-moment approximation of the tight-binding model. The calculations performed in the high-temperature range reveal that the surface vacancy diffusion occurs mainly via the random nearest-neighbour hops with the activation energy close to the static migration barrier. Small contributions of the third-neighbour surface-layer jumps and jumps between the first and the second layer are also recorded. The latter jumps are likely to be possible due to some dynamical co-operative effect among neighbouring atoms around a vacancy that effectively reduces the inter-layer migration barrier.

Fast structural relaxation of polyvinyl alcohol below the glass-transition temperature

In order to obtain information about structural relaxations of polymers within a time window of several nanoseconds, the absorption, site-selective steady-state fluorescence and time-resolved fluorescence spectra have been measured for polyvinyl alcohol doped with rhodamine 640 in the 150–300 K temperature range. The temperature dependence of the absorption and fluorescence spectra has been analyzed on the basis of one- and two-dimensional configuration-coordinate models. In spite of the measurement below the glass-transition temperature of the matrix, the existence of a fast relaxation process which is completed within a few hundred ps has been clarified. The magnitude of this relaxation increases with increasing temperature, while the relaxation mechanism cannot be ascribed to the thermal crossing of static energy barriers. It has been found that the experimental results are not explained by the two-dimensional configuration coordinate model in which the fast and slow structural relaxations are assumed to occur independently along the two axes. A relaxation process triggered by temperature-dependent release from the constraint preventing the structural change is shown to account for the experimental results well using a one-dimensional configuration coordinate model.

Endothelial cells: role in infection and inflammation.

Infection and resulting sepsis continue to be important causes of morbidity and mortality in surgical patients. Although much has been learned about the pathogens and the leukocyte responses to these pathogens, we are only beginning to understand the role of the host in these pathologies. The endothelium is a dynamic participant in cellular and organ function rather than a static barrier as it was once believed. Emerging evidence implicates the endothelium as a central effector in the inflammatory response. Through the expression of surface proteins and secretion of soluble mediators, the endothelium controls vascular tone and permeability, regulates coagulation and thrombosis, and directs the passage of leukocytes into areas of inflammation. Derangements in these normal functions may contribute significantly to a maladaptive inflammatory response leading to systemic inflammation and multiple organ failure.

Transitions through fluctuating barrier: Role of asymmetry and memory

The kinetics of single transition A→B over a fluctuating barrier is considered. Fluctuations are modeled by dichotomous noise. The average first passage time (AFPT) tp* is defined as the time elapsed from the beginning of the process (system in the state A with probability 1) to the moment when the system attains for the first time the state B with the average probability equal to p. It is found that the non-Markovianity of the barrier fluctuations may introduce oscillations in the process of barrier crossing and in the effective reaction rate, and elongate the AFPTs. Especially, t0.95* may become infinite, even when t0.5* remains finite—the process of barrier crossing is reverted after some time. However, in some cases (strong asymmetry of barrier fluctuations, high AFPTs in the absence of fluctuations, together with long memory characteristic time of the non-Markovian part of the fluctuations) the effective reaction rates can be enhanced and AFPTs shortened in comparison with those for static barrier.

Barrier suppression in high intensity photodissociation of diatomics: Electronic and permanent dipole moment effects

The infrared multiphoton photodissociation of a molecular ion, HCl+ in intense (I>1013 W/cm2), short (τ⩽1 ps) laser pulses is studied numerically by solving the nonperturbative time-dependent Schrödinger equation for this system. In particular, since molecular ions have large permanent moments upon dissociation, the present calculation examines the relative importance of electronic and permanent dipole moments effects at high intensities. Both long (λ=20.6 μm) and short (λ=1.064 μm) wavelength are compared to previous experiments and barrier suppression models. It is found in general that at long wavelength electronic effects predominate, thus justifying the use of a static field barrier suppression mechanism to predict the onset of dissociation. High intensity low frequency photodissociation also implies considerable redistribution of ponderomotive energies for light particles such as protons by charge transfer effects.

Thermally activated magnetization reversal through multichannels

Magnetization reversal of an isolated single-domain particle through multichannels was analytically studied. Results for a dichotomic channel of barriers demonstrate that the dynamical reversal process shows a multiexponential relaxation. At low attempting rate, the magnetization encounters a nearly static barrier, and at high attempting rate, it relaxes through an average of barrier heights. For the intermediate attempting rate, the magnetization usually relaxes multiexponentially, but only one relaxation time remains dominated at the low temperature.

Passage of peptides across the blood-brain barrier: pathophysiological perspectives.

Blood-borne peptides are capable of affecting the central nervous system (CNS) despite being separated from the CNS by the blood-brain barrier (BBB), a monolayer comprised of brain endothelial and ependymal cells. Blood-borne peptides can directly affect the CNS after they cross the BBB by nonsaturable and saturable transport mechanisms. The ability of peptides to cross the BBB to a meaningful degree suggests that the BBB may act as a modulatory pathway in the exchange of informational molecules between the brain and the peripheral circulation. The permeability of the BBB to peptides is a regulatory process affected by developmental, physiological, and pathological events. This regulation sets the stage for the relation between peptides and the BBB to be involved in pathophysiological events. For example, some of the classic actions of melanocortins on the CNS are explained by their abilities to cross the BBB, whereas aspects of feeding and alcohol-related behaviors are associated with the passage of other specific peptides across the BBB. The BBB should no longer be considered a static barrier but should be recognized as a regulatory interface controlling the exchange of informational molecules, such as peptides, between the blood and CNS.

Self-diffusion on low-index metallic surfaces: Ag and Au (100) and (111).

Using molecular-dynamics simulations and the embedded-atom method, we study the homodiffusion of single adatoms on flat Ag and Au (100) and (111) surfaces. Our results for the (111) surfaces indicate that when the thermal energies of the atoms become larger than the energy barriers, diffusion can no longer be represented by a simple random walk since correlations between successive jumps become important. We present a simple model that takes into account these correlated jumps and reproduces the molecular dynamics data very well. We also demonstrate that knowledge of the energy barriers is not sufficient to determine the preferred mechanism for diffusion on the (100) surface, since the prefactors for the various mechanisms can vary significantly from the value that is usually assumed. The ability of a simple transition-state theory to describe diffusion is also tested. We find, in the cases considered here, that the static barrier is equivalent to the dynamical activation energy and that the prefactor is also well described as long as the relaxation of the substrate remains small. \textcopyright{} 1996 The American Physical Society.

Energy relaxation dynamics in the optical excited state of myoglobin

In order to obtain information on the fast dynamics of the conformational fluctuation of a protein, absorption, steady-state, and time-resolved fluorescence spectra have been measured in the spectral region of the lowest optical absorption band of Zn-substituted myoglobin between 170 and 290 K. The obtained spectra have been analyzed using the single-site spectra calculated from the experimentally determined effective density of states of vibrational modes of Zn-substituted myoglobin. A configuration-coordinate model has been adopted to take into account the inhomogeneous broadening of the spectra. The fluorescence spectrum has also been compared with that calculated from the absorption spectrum on the basis of the Einstein relation. The results of the analyses show that the conformational relaxation occurs in the excited state, but is not completed within the lifetime of the excited state even at room temperature. The dynamic Stokes shift, which is expected in such a case, has not been observed in the whole temperature range examined. This indicates that the excited-state dynamics in myoglobin is different from that due to the thermal crossing over static potential barriers. The experimental results are explained well by a model based on hierarchically constrained dynamics. \textcopyright{} 1996 The American Physical Society.

Role of percolation in diffusion on random lattices.

Diffusion of single particles on lattices with random distributions of static barriers (random-barrier model) is investigated by Monte Carlo simulations and the time-dependent effective-medium approximation. The crossover from anomalous to linear diffusive behavior is discussed in terms of a percolation model. For a discrete distribution of barrier heights with a small concentration of ``defect'' barriers at the percolation threshold, an alternative kind of transition from bulk-controlled to defect-controlled diffusion is observed as the temperature decreases.

Molecular dynamics simulations of the Mg2+-stabilized Na+- beta ''-alumina

Ion transport mechanisms in Mg2+-stabilized Na+- beta ''-alumina were investigated by molecular dynamics simulations. Two compositions, different Mg2+ distributions, and different system sizes were used in the temperature range from 200 K to 1700 K. The trajectory plots of Na+ ions and the Na+-Na+ radial distribution function demonstrated the formation of a vacancy superlattice at low temperature. The stability of the superlattice was found to depend crucially on the Mg2+ distribution. The ionic motions in the Na+- beta ''-alumina were found to be highly correlated. The sodium tracer self-diffusion coefficient and zero-frequency ionic conductivity were found to depend strongly on the Mg2+ distribution. This explains why the conductivity depends on the thermal history of Na+- beta ''-alumina samples. The simulations show that the electrical conductivity can be increased by one order of magnitude at room temperature if the Mg2+ ions occupy optimal sites. The activation energy for Na+ transport was shown not to be a static single-ion energy barrier, but it is numerically close to the pseudo-potential energy difference along conduction paths at high temperature. Correlated ionic motion was suggested to be the main reason for the very low activation energy in Na+- beta ''-alumina.

Static Barrier MIMD: Architecture and Performance Analysis

In this paper, we describe and analyze the performance of a new architectural construct - an efficient synchronization mechanism called "Static Barrier MIMD" or SBM. Unlike traditional barrier synchronization, the proposed barriers are designed to allow static (compile-time) code scheduling to eliminate some synchronizations. The static barrier MIMD hardware is more general than most hardware barrier mechanisms, allowing any subset of the processors to participate in each barrier. The barriers execute in a small number of clock ticks, and processors proceed simultaneously past the barrier. The performance of idealized barrier schedules is examined to gain insights into code scheduling for barrier MIMD machines.

A molecular-dynamics simulation study of the adsorption and diffusion dynamics of short n-alkanes on Pt(111)

Using molecular-dynamics studies and static potential-energy minimization, we have resolved the mechanisms by which n-alkanes (ethane through n-decane) diffuse on a model Pt(111) surface in the low-coverage limit of a single adsorbed molecule. Our simulations reproduce all of the experimental trends seen for the adsorption and diffusion of C3–C6 on Pt(111) and Ru(001). The short alkanes (C2–C8) behave as rigid rods and their motion involves coupled translation and rotation in the surface plane. For this series, there is a linear increase of the diffusion barrier with the molecular chain length. We have analyzed the compliance of the motion of the assumptions of a nearest-neighbor hopping model. Although hopping motion can be observed for all of the molecules at sufficiently low temperatures, the hopping involves a significant fraction of long jumps. As the temperature increases, the adsorption becomes virtually delocalized. Despite the extensive deviations of the motion from the assumptions of a nearest-neighbor hopping model, the static diffusion-energy barriers, arising from the minimum-energy path for hops between nearest-neighbor binding sites, agree well with those obtained from the tracer-diffusion coefficients for butane, hexane, and octane. For these molecules, multiple-site hops and long flights appear to influence the values of the preexponential factors, which are too large. Neither the diffusion barrier nor the preexponential factor for ethane agrees well with theoretical estimates. We attribute these discrepancies to the smallness of the static diffusion barrier and/or the existence of unique dynamical behavior for this molecule. Due to the increased difficulty of in-plane rotation and increased mismatch between the geometries of the molecule and the surface, the diffusion barrier for n-decane drops below that for n-hexane. The characteristic mechanism of motion for n-decane involves significant C–C–C bond-angle bending.