2004 - Abstracts
1. Akamatsu, S., M. Plapp, G. Faivre and A. Karma (2004). "Overstability of lamellar eutectic growth below the minimum-undercooling spacing." Metallurgical and Materials Transactions a-Physical Metallurgy and Materials Science 35A(6): 1815-1828.
We investigate the stability of lamellar eutectic growth by thin-sample directional solidification experiments and two-dimensional phase-field simulations. We find that lamellar patterns can be morphologically stable for spacings smaller than the minimum undercooling spacing lambda(m). Key to this finding is the direct experimental measurement of the relationship between the front undercooling and spacing, which identifies lambda(m) independently of the Jackson and Hunt (JH) theory and of uncertainties of alloy parameters. This finding conflicts with the common belief that patterns with lambda < lambda(m) should be unstable, which is based on the Jackson-Hunt-Cahn assumption that lamellae grow normal to the envelope of the front. Our simulation results reveal that lamellae also move parallel to this envelope to reduce spacing gradients, thereby weakly violating this assumption but strongly overstabilizing patterns for a range of spacing below lambda(m) that increases with G/V (temperature gradient to growth rate ratio). This range is much larger than predicted by previous stability analyses and can be significant for standard experimental conditions. An analytical expression is obtained phenomenologically, which predicts well the variation of the smallest stable spacing with G/V. We also present results that shed light on the history-dependent selection and long-time evolution of the experimentally observed range of spacings.
2. Cao, W. X., X. Ye, G. Y. Georgiev, S. Berezhna, T. Sjodin, A. A. Demidov, W. Wang, J. T. Sage and P. M. Champion (2004). "Proximal and distal influences on ligand binding kinetics in microperoxidase and heme model compounds." Biochemistry 43(22): 7017-7027.
We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound heme complexes to study proximal and distal influences on ligand rebinding kinetics. We report kinetics of CO rebinding to microperoxidase (MP) and 2-methylimidazole ligated Fe protoporphyrin IX in the 10 ns to 10 ms time window. We also report CO rebinding kinetics of MP in the 150 fs to 140 ps time window. For dilute, micelle-encapsulated (monodisperse) samples of MP, we do not observe the large amplitude geminate decay at similar to100 ps previously reported in time-resolved IR measurements on highly concentrated samples [Lim, M., Jackson, T. A., and Anfinrud, P. A. (1997) J. Biol. Inorg. Chem. 2, 531-536]. However, for high concentration aggregated samples, we do observe the large amplitude picosecond CO geminate rebinding and find that it is correlated with the absence of the iron-histidine vibrational mode in the time-resolved Raman spectrum. On the basis of these results, the energetic significance of a putative distal pocket CO docking site proposed by Lim et al. may need to be reconsidered. Finally, when high concentration samples of native myoglobin (Mb) were studied as a control, an analogous increase in the geminate rebinding kinetics was not observed. This verifies that studies of Mb under dilute conditions are applicable to the more concentrated regime found in the cellular milieu.
3. Cao, W. X., X. Ye, T. Sjodin, J. F. Christian, A. A. Demidov, S. Berezhna, W. Wang, D. Barrick, J. T. Sage and P. M. Champion (2004). "Investigations of photolysis and rebinding kinetics in myoglobin using proximal ligand replacements." Biochemistry 43(34): 11109-11117.
We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound H93G myoglobin (Mb) mutants to study the influence of the proximal ligand on the CO rebinding kinetics. In H93G mutants, where the proximal linkage with the protein is eliminated and the heme can bind exogenous ligands (e.g., imidazole, 4-bromoimidazole, pyridine, or dibromopyridine), we observe significant effects on the CO rebinding kinetics in the 10 ns to 10 ms time window. Resonance Raman spectra of the various H93G Mb complexes are also presented to aid in the interpretation of the kinetic results. For CO-bound H93G(dibromopyridine), we observe a rapid large-amplitude geminate phase with a fundamental CO rebinding rate that is similar to45 times faster than for wild-type MbCO at 293 K. The absence of an iron proximal ligand vibrational mode in the 10 ns photoproduct Raman spectrum of CO-bound H93G(dibromopyridine) supports the hypothesis that proximal ligation has a significant influence on the kinetics of diatomic ligand binding to the heme.
4. Champion, P. M., F. Rosca, D. Ionascu, W. X. Cao and X. Ye (2004). "Rapid timescale processes and the role of electronic surface coupling in the photolysis of diatomic ligands from heme proteins." Faraday Discussions 127: 123-135.
We have observed coherent oscillations of the heme protein myoglobin (Mb) following femtosecond laser excitation and photodissociation of the CO, O-2, and NO bound ligands. Use of a novel methodology, involving "wavelength selective modulation'' of the pump and/or probe laser pulse train, allows us to discriminate between coherences created by pump fields of differing wavelength within the laser pulse versus signals that arise from the decay of either vibrational or electronic populations. The population driven signals appear when pump field interactions having the same optical frequency are allowed to contribute to the signal detection channel. One surprising result, which will be stressed in the discussion, is the observation of a distinct product state vibrational coherence ( the iron histidine stretching vibration of deoxy Mb at 220 cm(-1)) that depends upon the presence of pump field interactions having a wavelength mismatch that is equal to the 220 cm(-1) vibrational frequency. This observation is surprising because the iron - histidine mode is not observed in the resonance Raman measurements on the six-coordinate reactant species. Thus, the pump-pulse laser excitation between the ground and excited state, which leads to the ligand dissociation, is evidently able to create a "field driven'' vibrational coherence of a resonance Raman inactive mode that extends into non-vertical regions of the reactive excited state potential energy surface. Non-radiative electronic surface crossing, followed by the rapid development of new electronic forces on the nuclei, appears to be ruled out as a source of the coherent signals ( the random phase of the optically uncoupled modes is one possible explanation for this observation). The extremely rapid timescale (much less than 150 fs) for the development of the ( S = 2) high-spin product state of the iron atom from the initial unphotolyzed state ( S = 0) is worthy of further theoretical discussion because of the spin forbidden nature of such a transition. Excited state admixtures of the iron spin states are presumably involved, and the mixing of these states, along with the unpaired electron on NO, may help to explain the ultrafast time scales and large amplitudes that characterize the NO geminate recombination in comparison to CO.
5. Daly, C., J. Zhang and J. B. Sokoloff (2004). "Effects on friction of adsorbed molecules: How they modify dry friction." Dynamics and Friction in Submicrometer Confining Systems 882: 69-84.
Recently, Muser and Robbins have argued that static friction for two weakly interacting flat atomically smooth clean non-metallic solid surfaces should be extremely small, unless there are mobile molecules adsorbed at an interface. Here we will consider "dry friction" (i.e., kinetic friction in the slow sliding speed limit). We will argue that mobile adsorbed molecules at an interface undergo Tomlinson model-like instabilities, which were shown by Caroli and Nozieres to be necessary for "dry friction" to occur.
6. Dobler, S., T. S. Lo, M. Plapp, A. Karma and W. Kurz (2004). "Peritectic coupled growth." Acta Materialia 52(9): 2795-2808.
Even though peritectic coupled growth (PCG) has been often discussed in the literature, it remains poorly understood in comparison to eutectic coupled growth (ECG). We report the results of a combined experimental and numerical study that clearly establishes the existence of PCG in directional solidification of Fe-Ni alloys. Furthermore, the results shed light on the similarities, as well as the differences, between PCG and ECG. The main findings are that: (i) a necessary condition for PCG is a G/nu ratio close to or above the critical value for plane front growth of both solid phases, (ii) both lamellar and fibrous PCG is observed and the transition between the two morphologies correlates with the degree of asymmetry of solid volume fractions, as for ECG, (iii) lamellar PCG can be stable even though the slope of the undercooling-spacing relation is negative, in agreement with recent experimental and numerical findings for ECG, (iv) the stability of PCG is limited at both small and large spacings by short-wavelength oscillatory instabilities, whereas the stability of ECG is limited Lit small spacing by a known long-wavelength instability associated with lamellar elimination, and (v) PCG and ECG can be initiated by different mechanisms. In addition, cellular non-isothermal PCG is found when the G/nu ratio is below the limit for plane front growth of the primary phase and above that for plane front growth of the peritectic phase. The transition from isothermal PCG to cellular PCG with decreasing G/nu is discontinuous (sub-critical). Cellular PCG is characterised by diffusion-coupling between cells of one phase and nearly plane front of the other under the constraint of mechanical equilibrium at the triple junction. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
7. Echebarria, B., R. Folch, A. Karma and M. Plapp (2004). "Quantitative phase-field model of alloy solidification." Physical Review E 70(6): 061604.
We present a detailed derivation and thin interface analysis of a phase-field model that can accurately simulate microstructural pattern formation for low-speed directional solidification of a dilute binary alloy. This advance with respect to previous phase-field models is achieved by the addition of a phenomenological "antitrapping" solute current in the mass conservation relation [A. Karma, Phys. Rev. Lett. 87, 115701 (2001)]. This antitrapping current counterbalances the physical, albeit artificially large, solute trapping effect generated when a mesoscopic interface thickness is used to simulate the interface evolution on experimental length and time scales. Furthermore, it provides additional freedom in the model to suppress other spurious effects that scale with this thickness when the diffusivity is unequal in solid and liquid [R. F. Almgren, SIAM J. Appl. Math. 59, 2086 (1999)], which include surface diffusion and a curvature correction to the Stefan condition. This freedom can also be exploited to make the kinetic undercooling of the interface arbitrarily small even for mesoscopic values of both the interface thickness and the phase-field relaxation time, as for the solidification of pure melts [A. Karma and W.-J. Rappel, Phys. Rev. E 53, R3017 (1996)]. The performance of the model is demonstrated by calculating accurately within a phase-field approach the Mullins-Sekerka stability spectrum of a planar interface and nonlinear cellular shapes for realistic alloy parameters and growth conditions.
8. Hoyt, J. J., M. Asta, T. Haxhimali, A. Karma, R. E. Napolitano, R. Trivedi, B. B. Laird and J. R. Morris (2004). "Crystal-melt interfaces and solidification morphologies in metals and alloys." Mrs Bulletin 29(12): 935-939.
When liquids solidify, the interface between a crystal and its melt often forms branching structures (dendrites), just as frost spreads across a window. The development of a quantitative understanding of dendritic evolution continues to present a major theoretical and experimental challenge within the metallurgical community. This article looks at key parameters that describe the interface-excess free energy and mobility-and discusses how these important properties relate to our understanding of crystal growth and other interfacial phenomena such as wetting and spreading of droplets and nucleation of the solid phase from the melt. In particular, two new simulation methods have emerged for computing the interfacial free energy and its anisotropy: the cleaving technique and the capillary fluctuation method. These are presented, along with methods for extracting the kinetic coefficient and a comparison of the results to several theories of crystal growth rates.
9. Hoyt, J. J., A. Karma, M. Asta and D. Y. Sun (2004). "From atoms to dendrites." Jom 56(4): 49-54.
Dendritic microstructures control the properties of a wide range of advanced materials ranging from nickel-based superalloys used in turbine blades to lightweight aluminum-based alloys for the automotive industry. This article reviews recent progress in quantitative modeling dendritic growth through the combination of state-of-the-art atomistic and phase field simulations. Also shown is how the combination of these two distinct length-scale modeling approaches can yield a parameter-free prediction of the dendrite growth velocity as a function of undercooling for deeply undercooled nickel melts.
10. Karma, A. and A. E. Lobkovsky (2004). "Unsteady crack motion and branching in a phase-field model of brittle fracture." Physical Review Letters 92(24): 245510
Crack propagation is studied numerically using a continuum phase-field approach to mode III brittle fracture. The results shed light on the physics that controls the speed of accelerating cracks and the characteristic branching instability at a fraction of the wave speed.
11. Karma, A. and M. Plapp (2004). "New insights into the morphological stability of eutectic and peritectic coupled growth." Jom 56(4): 28-32.
Both eutectic and peritectic alloys exhibit three-phase equilibria and are used in diverse practical applications ranging from casting and welding to growing superconducting crystals. In-situ composites formed by the diffusively coupled growth of two solid phases are ubiquitous in eutectic solidification. This growth, however, is generally only stable over a finite range of eutectic spacing. The addition of a dilute ternary impurity can destabilize the interface and produce coarse two-phase cellular structures. Whether coupled growth is theoretically possible in peritectic alloys has been a question for over 40 years. This article reviews the current status of phase-field modeling of polyphase solidification in eutectic and peritectic alloys. Also discussed are new findings from both simulations and experiments that shed new light on the similarities and differences between the morphological stability of eutectic and peritectic coupled growth.
12. Leu, B. M., M. Z. Zgierski, G. R. A. Wyllie, W. R. Scheidt, W. Sturhahn, E. E. Alp, S. M. Durbin and J. T. Sage (2004). "Quantitative vibrational dynamics of iron in nitrosyl porphyrins." Journal of the American Chemical Society 126(13): 4211-4227.
We use quantitative experimental and theoretical approaches to characterize the vibrational dynamics of the Fe atom in porphyrins designed to model heme protein active sites. Nuclear resonance vibrational spectroscopy (NRVS) yields frequencies, amplitudes, and directions for Fe-57 vibrations in a series of ferrous nitrosyl porphyrins, which provide a benchmark for evaluation of quantum chemical vibrational calculations. Detailed normal mode predictions result from DFT calculations on ferrous nitrosyl tetraphenylporphyrin Fe(TPP)(NO), its cation [Fe(TPP)(NO)]1, and ferrous nitrosyl porphine Fe(P)(NO). Differing functionals lead to significant variability in the predicted Fe-NO bond length and frequency for Fe(TPP)(NO). Otherwise, quantitative comparison of calculated and measured Fe dynamics on an absolute scale reveals good overall agreement, suggesting that DFT calculations provide a reliable guide to the character of observed Fe vibrational modes. These include a series of modes involving Fe motion in the plane of the porphyrin, which are rarely identified using infrared and Raman spectroscopies. The NO binding geometry breaks the four-fold symmetry of the Fe environment, and the resulting frequency splittings of the in-plane modes predicted for Fe(TPP)(NO) agree with observations. In contrast to expectations of a simple three-body model, mode energy remains localized on the FeNO fragment for only two modes, an N-O stretch and a mode with mixed Fe-NO stretch and FeNO bend character. Bending of the FeNO unit also contributes to several of the in-plane modes, but no primary FeNO bending mode is identified for Fe(TPP)(NO). Vibrations associated with hindered rotation of the NO and heme doming are predicted at low frequencies, where Fe motion perpendicular to the heme is identified experimentally at 73 and 128 cm(-1). Identification of the latter two modes is a crucial first step toward quantifying the reactive energetics of Fe porphyrins and heme proteins.
13. Lobkovsky, A. E., A. Karma, M. I. Mendelev, M. Haataja and D. J. Srojovitz (2004). "Grain shape, grain boundary mobility and the Herring relation." Acta Materialia 52(2): 285-292.
Motivated by recent experiments on grain boundary migration in Al, we examine the question: does interface mobility depend on the nature of the driving force? We investigate this question in the Ising model and conclude that the answer is "no." This conclusion highlights the importance of including the second derivative of the interface energy with respect to inclination gamma" in the Herring relation in order to correctly describe the motion of grain boundaries driven by capillarity. The importance of this term can be traced to the entropic part of gamma", which can be highly anisotropic, such that the reduced mobility (i.e., the product of interface stiffness gamma + gamma" and mobility) can be nearly isotropic even though the mobility itself is highly anisotropic. The cancellation of these two anisotropies (associated with stiffness and mobility) originates in the Ising model from the fact that the number of geometrically necessary kinks, and hence the kink configurational entropy, varies rapidly with inclination near low-energy/low mobility, but slowly near high-energy/high-mobility interfaces, where the kink density is high. This implies that the stiffness is high where the mobility is low and vice versa. Consequently, the grain shape can appear isotropic or highly anisotropic depending on whether its motion is driven by curvature or an external field, respectively, but the mobility itself is independent of driving force. We discuss the implications of these results for interpreting experimental observations and computer simulations of microstructural evolution, where gamma" is routinely neglected. (C) 2003 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
14. Pant, K., R. L. Karpel, L. Rouzina and M. C. Williams (2004). "Mechanical measurement of single-molecule binding rates: Kinetics of DNA helix-destabilization by T4 gene 32 protein." Journal of Molecular Biology 336(4): 851-870.
Bacteriophage T4 gene 32 protein (gp32) is a single-stranded DNA (ssDNA) binding protein, and is essential for DNA replication, recombination and repair. While gp32 binds preferentially and cooperatively to ssDNA, it has not been observed to lower the thermal melting temperature of natural double-stranded DNA (dsDNA). However, in single-molecule stretching experiments, gp32 significantly destabilizes lambda DNA. In this study, we develop a theory of the effect of the protein on single dsDNA stretching curves, and apply it to the measured dependence of the DNA overstretching force on pulling rate in the presence of the full-length and two truncated forms of the protein. This allows us to calculate the rate of cooperative growth of single clusters of protein along ssDNA that are formed as the dsDNA molecule is stretched, as well as determine the site size of the protein binding to ssDNA. The rate of cooperative binding (k(a)) of both gp32 and of its proteolytic fragment *I (which lacks 48 residues from the C terminus) varies non-linearly with protein concentration, and appears to exceed the diffusion limit. We develop a model of protein association with the ends of growing clusters of cooperatively bound protein enhanced by 1-D diffusion along dsDNA, under the condition of protein excess. Upon globally fitting k(a) versus protein concentration, we determine the binding site size and the non-cooperative binding constants to dsDNA for gp32 and *I. Our experiment mimics the growth of clusters of gp32 that likely exist at the DNA replication fork in vivo, and explains the origin of the "kinetic block" to dsDNA melting by gene 32 protein observed in thermal melting experiments. (C) 2004 Elsevier Ltd. All rights reserved.
15. Ramirez, J. C., C. Beckermann, A. Karma and H. J. Diepers (2004). "Phase-field modeling of binary alloy solidification with coupled heat and solute diffusion." Physical Review E 69(5): 051607.
A phase-field model is developed for simulating quantitatively microstructural pattern formation in solidification of dilute binary alloys with coupled heat and solute diffusion. The model reduces to the sharp-interface equations in a computationally tractable thin-interface limit where (i) the width of the diffuse interface is about one order of magnitude smaller than the radius of curvature of the interface but much larger than the real microscopic width of a solid-liquid interface, and (ii) kinetic effects are negligible. A recently derived antitrapping current [A. Karma, Phys. Rev. Lett. 87, 115701 (2001)] is used in the solute conservation equation to recover precisely local equilibrium at the interface and to eliminate interface stretching and surface diffusion effects that arise when the solutal diffusivities are unequal in the solid and liquid. Model results are first compared to analytical solutions for one-dimensional steady-state solidification. Two-dimensional thermosolutal dendritic growth simulations with vanishing solutal diffusivity in the solid show that both the microstructural evolution and the solute profile in the solid are accurately modeled by the present approach. Results are then presented that illustrate the utility of the model for simulating dendritic solidification for the large ratios of the liquid thermal to solutal diffusivities (Lewis numbers) typical of alloys.
16. Stepanyants, A., G. Tamas and D. B. Chklovskii (2004). "Are spatial positions of dendritic and axonal branches correlated or independent?" Neurocomputing 58-60: 477-485.
Because direct investigation of synaptic connectivity is difficult, neurobiologists often resort to indirect methods. One method is to infer connectivity from the densities of axonal and dendritic arbors, and the arbor overlap volume. This method is valid only under the assumption that spatial positions of dendritic and axonal branches are uncorrelated on a micrometer lengthscale. We test this assumption by using 3D reconstructions of neuronal pairs from the rat neocortex. We find that the positions of GABAergic interneuron axons are correlated with their targets, while the positions of pyramidal neuron axons are independent of their targets. (C) 2004 Elsevier B.V. All rights reserved.
17. Stepanyants, A., G. Tamas and D. B. Chklovskii (2004). "Class-specific features of neuronal wiring." Neuron 43(2): 251-259.
Brain function relies on specificity of synaptic connectivity patterns among different classes of neurons. Yet, the substrates of specificity in complex neuropil remain largely unknown. We search for imprints of specificity in the layout of axonal and dendritic arbors from the rat neocortex. An analysis of 3D reconstructions of pairs consisting of pyramidal cells (PCs) and GABAergic interneurons (GIs) revealed that the layout of GI axons is specific. This specificity is manifested in a relatively high tortuosity, small branch length of these axons, and correlations of their trajectories with the positions of postsynaptic neuron dendrites. Axons of PCs show no such specificity, usually taking a relatively straight course through neuropil. However, wiring patterns among PCs hold a large potential for circuit remodeling and specificity through growth and retraction of dendritic spines. Our results define distinct class-specific rules in establishing synaptic connectivity, which could be crucial in formulating a canonical cortical circuit.
18. Williams, M. C., K. Pant, I. Rouzina and R. L. Karpel (2004). "Single molecule force spectroscopy studies of DNA denaturation by T4 gene 32 protein." Spectroscopy-an International Journal 18(2): 203-211.
Single molecule force spectroscopy is an emerging technique that can be used to measure the biophysical properties of single macromolecules such as nucleic acids and proteins. In particular, single DNA molecule stretching experiments are used to measure the elastic properties of these molecules and to induce structural transitions. We have demonstrated that double-stranded DNA molecules undergo a force-induced melting transition at high forces. Force-extension measurements of single DNA molecules using optical tweezers allow us to measure the stability of DNA under a variety of solution conditions and in the presence of DNA binding proteins. Here we review the evidence of DNA melting in these experiments and discuss the example of DNA force-induced melting in the presence of the single-stranded DNA binding protein T4 gene 32. We show that this force spectroscopy technique is a useful probe of DNA-protein interactions, which allows us to obtain binding rates and binding free energies for these interactions.