Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea

Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli. We found the quantity of MPh per cell increases as cultures transition from exponential growth to stationary phase, and absolute quantities of MPh were 3-fold higher in M. acetivorans than in M. barkeri. The concentration of MPh suggests the cell membrane of M. acetivorans, but not of M. barkeri, is electrically quantized as if it were a single conductive metal sheet and near optimal for rate of electron transport. Similarly, stationary (but not exponentially growing) E. coli cells also have electrically quantized membranes on the basis of quinone content. Consistent with our hypothesis, we demonstrated that the exogenous addition of phenazine increases the growth rate of M. barkeri three times that of M. acetivorans. Our work suggests electron flux through MPh is naturally higher in M. acetivorans than in M. barkeri and that hydrogen cycling is less efficient at conserving energy than scalar proton translocation using MPh

Phase-field Crystals with Elastic Interactions

We report on a novel extension of the recent phase-field crystal (PFC) method introduced in [Elder et al., Phys. Rev. Lett., Vol. 88, 245701:1-4 (2002)], which incorporates elastic interactions as well as crystal plasticity and diffusive dynamics. In our model, elastic interactions are mediated through wave modes that propagate on time scales many orders of magnitude slower than atomic vibrations but still much faster than diffusive times scales. This allows us to preserve the quintessential advantage of the PFC model: the ability to simulate atomic-scale interactions and dynamics on time scales many orders of magnitude longer than characteristic vibrational time scales. We demonstrate the two different modes of propagation in our model and show that simulations of grain growth and elasto-plastic deformation are consistent with the microstructural properties of nanocrystals.Comment: 4 pages, 6 figure

Phase field crystal dynamics for binary systems: Derivation from dynamical density functional theory, amplitude equation formalism, and applications to alloy heterostructures

The dynamics of phase field crystal (PFC) modeling is derived from dynamical density functional theory (DDFT), for both single-component and binary systems. The derivation is based on a truncation up to the three-point direct correlation functions in DDFT, and the lowest order approximation using scale analysis. The complete amplitude equation formalism for binary PFC is developed to describe the coupled dynamics of slowly varying complex amplitudes of structural profile, zeroth-mode average atomic density, and system concentration field. Effects of noise (corresponding to stochastic amplitude equations) and species-dependent atomic mobilities are also incorporated in this formalism. Results of a sample application to the study of surface segregation and interface intermixing in alloy heterostructures and strained layer growth are presented, showing the effects of different atomic sizes and mobilities of alloy components. A phenomenon of composition overshooting at the interface is found, which can be connected to the surface segregation and enrichment of one of the atomic components observed in recent experiments of alloying heterostructures.Comment: 26 pages, 5 figures; submitted to Phys. Rev.

Stein variational gradient descent: Many-particle and long-time asymptotics

Stein variational gradient descent (SVGD) refers to a class of methods for Bayesian inference based on interacting particle systems. In this paper, we consider the originally proposed deterministic dynamics as well as a stochastic variant, each of which represent one of the two main paradigms in Bayesian computational statistics: emphvariational inference and emphMarkov chain Monte Carlo. As it turns out, these are tightly linked through a correspondence between gradient flow structures and large-deviation principles rooted in statistical physics. To expose this relationship, we develop the cotangent space construction for the Stein geometry, prove its basic properties, and determine the large-deviation functional governing the many-particle limit for the empirical measure. Moreover, we identify the emphStein-Fisher information (or emphkernelised Stein discrepancy) as its leading order contribution in the long-time and many-particle regime in the sense of $Gamma$-convergence, shedding some light on the finite-particle properties of SVGD. Finally, we establish a comparison principle between the Stein-Fisher information and RKHS-norms that might be of independent interest

Relative entropy as a measure of inhomogeneity in general relativity

We introduce the notion of relative volume entropy for two spacetimes with preferred compact spacelike foliations. This is accomplished by applying the notion of Kullback-Leibler divergence to the volume elements induced on spacelike slices. The resulting quantity gives a lower bound on the number of bits which are necessary to describe one metric given the other. For illustration, we study some examples, in particular gravitational waves, and conclude that the relative volume entropy is a suitable device for quantitative comparison of the inhomogeneity of two spacetimes.Comment: 15 pages, 7 figure

Mutual cross-talk between fibronectin integrins and the EGF receptor: Molecular basis and biological significance

Extension of the plasma membrane is one of the first steps in cell migration. Understanding how cells “choose” between various types of membrane protrusion enhances our knowledge of both normal and cancer cell physiology. The EGF receptor is a paradigm for understanding how transmembrane receptor tyrosine kinases regulate intracellular signaling following ligand stimulation. Evidence from the past decade indicates that EGF receptors also form macromolecular complexes with integrin receptors leading to EGF receptor transactivation during cell adhesion. However, relatively little is known about how these complexes form and impact cell migration. Our recent work characterized a molecular complex between EGF receptor and β3 integrin which recognizes RGD motifs in extracellular matrix proteins. Complex formation requires a dileucine motif (679-LL) in the intracellular juxtamembrane region of the EGF receptor that also controls whether or not the receptor undergoes Src kinase-dependent phosphorylation at Tyr-845. In contrast to wild-type receptors, mutant EGF receptors defective for Tyr-845 phosphorylation form complexes with β1 integrin that also binds RGD motifs. In addition, we have discovered that EGF receptor antagonizes small GTPase RhoA by mediating membrane recruitment of its regulatory GAP p190RhoGAP. In this addendum we discuss a potential new role for Src-dependent EGF receptor transactivation in integrin/EGF receptor complex formation. We also discuss how our study fits with previous observations linking p190RhoGAP to RhoA-dependent cytoskeletal rearrangements involved in cell migration, and provide new data that the EGF receptor is compartmentalized to relatively immature zyxin-poor focal adhesions which are the likely site of p190RhoGAP signaling

Amplitude expansion of the binary phase field crystal model

Amplitude representations of a binary phase field crystal model are developed for a two dimensional triangular lattice and three dimensional BCC and FCC crystal structures. The relationship between these amplitude equations and the standard phase field models for binary alloy solidification with elasticity are derived, providing an explicit connection between phase field crystal and phase field models. Sample simulations of solute migration at grain boundaries, eutectic solidification and quantum dot formation on nano-membranes are also presented.Comment: 11 pages, 8 figure