Mechanism of Deep-focus Earthquakes Anomalous Statistics

Analyzing the NEIC-data we have shown that the spatial deep-focus earthquake distribution in the Earth interior over the 1993-2006 is characterized by the clearly defined periodical fine discrete structure with period L=50 km, which is solely generated by earthquakes with magnitude M 3.9 to 5.3 and only on the convergent boundary of plates. To describe the formation of this structure we used the model of complex systems by A. Volynskii and S. Bazhenov. The key property of this model consists in the presence of a rigid coating on a soft substratum. It is shown that in subduction processes the role of a rigid coating plays the slab substance (lithosphere) and the upper mantle acts as a soft substratum. Within the framework of this model we have obtained the estimation of average values of stress in the upper mantle and Young's modulus for the oceanic slab (lithosphere) and upper mantle.Comment: 9 pages, 7 figure

Scaling of the buckling transition of ridges in thin sheets

When a thin elastic sheet crumples, the elastic energy condenses into a network of folding lines and point vertices. These folds and vertices have elastic energy densities much greater than the surrounding areas, and most of the work required to crumple the sheet is consumed in breaking the folding lines or ``ridges''. To understand crumpling it is then necessary to understand the strength of ridges. In this work, we consider the buckling of a single ridge under the action of inward forcing applied at its ends. We demonstrate a simple scaling relation for the response of the ridge to the force prior to buckling. We also show that the buckling instability depends only on the ratio of strain along the ridge to curvature across it. Numerically, we find for a wide range of boundary conditions that ridges buckle when our forcing has increased their elastic energy by 20% over their resting state value. We also observe a correlation between neighbor interactions and the location of initial buckling. Analytic arguments and numerical simulations are employed to prove these results. Implications for the strength of ridges as structural elements are discussed.Comment: 42 pages, latex, doctoral dissertation, to be submitted to Phys Rev

Virus shapes and buckling transitions in spherical shells

We show that the icosahedral packings of protein capsomeres proposed by Caspar and Klug for spherical viruses become unstable to faceting for sufficiently large virus size, in analogy with the buckling instability of disclinations in two-dimensional crystals. Our model, based on the nonlinear physics of thin elastic shells, produces excellent one parameter fits in real space to the full three-dimensional shape of large spherical viruses. The faceted shape depends only on the dimensionless Foppl-von Karman number \gamma=YR^2/\kappa, where Y is the two-dimensional Young's modulus of the protein shell, \kappa is its bending rigidity and R is the mean virus radius. The shape can be parameterized more quantitatively in terms of a spherical harmonic expansion. We also investigate elastic shell theory for extremely large \gamma, 10^3 < \gamma < 10^8, and find results applicable to icosahedral shapes of large vesicles studied with freeze fracture and electron microscopy.Comment: 11 pages, 12 figure

Universal Power Law in the Noise from a Crumpled Elastic Sheet

Using high-resolution digital recordings, we study the crackling sound emitted from crumpled sheets of mylar as they are strained. These sheets possess many of the qualitative features of traditional disordered systems including frustration and discrete memory. The sound can be resolved into discrete clicks, emitted during rapid changes in the rough conformation of the sheet. Observed click energies range over six orders of magnitude. The measured energy autocorrelation function for the sound is consistent with a stretched exponential C(t) ~ exp(-(t/T)^{b}) with b = .35. The probability distribution of click energies has a power law regime p(E) ~ E^{-a} where a = 1. We find the same power law for a variety of sheet sizes and materials, suggesting that this p(E) is universal.Comment: 5 pages (revtex), 10 uuencoded postscript figures appended, html version at http://rainbow.uchicago.edu/~krame

Dynamics of Large-Scale Plastic Deformation and the Necking Instability in Amorphous Solids

We use the shear transformation zone (STZ) theory of dynamic plasticity to study the necking instability in a two-dimensional strip of amorphous solid. Our Eulerian description of large-scale deformation allows us to follow the instability far into the nonlinear regime. We find a strong rate dependence; the higher the applied strain rate, the further the strip extends before the onset of instability. The material hardens outside the necking region, but the description of plastic flow within the neck is distinctly different from that of conventional time-independent theories of plasticity.Comment: 4 pages, 3 figures (eps), revtex4, added references, changed and added content, resubmitted to PR

Ocean-bottom seismographs based on broadband MET sensors: architecture and deployment case study in the Arctic

The Arctic seas are now of particular interest due to their prospects in terms of hydrocarbon extraction, development of marine transport routes, etc. Thus, various geohazards, including those related to seismicity, require detailed studies, especially by instrumental methods. This paper is devoted to the ocean-bottom seismographs (OBS) based on broadband molecular–electronic transfer (MET) sensors and a deployment case study in the Laptev Sea. The purpose of the study is to introduce the architecture of several modifications of OBS and to demonstrate their applicability in solving different tasks in the framework of seismic hazard assessment for the Arctic seas. To do this, we used the first results of several pilot deployments of the OBS developed by Shirshov Institute of Oceanology of the Russian Academy of Sciences (IO RAS) and IP Ilyinskiy A.D. in the Laptev Sea that took place in 2018–2020. We highlighted various seismological applications of OBS based on broadband MET sensors CME-4311 (60 s) and CME-4111 (120 s), including the analysis of ambient seismic noise, registering the signals of large remote earthquakes and weak local microearthquakes, and the instrumental approach of the site response assessment. The main characteristics of the broadband MET sensors and OBS architectures turned out to be suitable for obtaining high-quality OBS records under the Arctic conditions to solve seismological problems. In addition, the obtained case study results showed the prospects in a broader context, such as the possible influence of the seismotectonic factor on the bottom-up thawing of subsea permafrost and massive methane release, probably from decaying hydrates and deep geological sources. The described OBS will be actively used in further Arctic expeditions

Predictability of evolutionary trajectories in fitness landscapes

Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness landscape. We report an exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding where fitness is equated with robustness to misfolding. This model mimics the essential features of the interactions between amino acids, is consistent with the key paradigms of protein folding and reproduces the universal distribution of evolutionary rates among orthologous proteins. We introduce mean path divergence as a quantitative measure of the degree to which the starting and ending points determine the path of evolution in fitness landscapes. Global measures of landscape roughness are good predictors of path divergence in all studied landscapes: the mean path divergence is greater in smooth landscapes than in rough ones. The model-derived and experimental landscapes are significantly smoother than random landscapes and resemble additive landscapes perturbed with moderate amounts of noise; thus, these landscapes are substantially robust to mutation. The model landscapes show a deficit of suboptimal peaks even compared with noisy additive landscapes with similar overall roughness. We suggest that smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics of protein folding.Comment: 14 pages, 7 figure

Phase-field approach to heterogeneous nucleation

We consider the problem of heterogeneous nucleation and growth. The system is described by a phase field model in which the temperature is included through thermal noise. We show that this phase field approach is suitable to describe homogeneous as well as heterogeneous nucleation starting from several general hypotheses. Thus we can investigate the influence of grain boundaries, localized impurities, or any general kind of imperfections in a systematic way. We also put forward the applicability of our model to study other physical situations such as island formation, amorphous crystallization, or recrystallization.Comment: 8 pages including 7 figures. Accepted for publication in Physical Review

Permeation through the Cell Membrane of a Boron-Based β-Lactamase Inhibitor

Bacteria express beta-lactamases to counteract the beneficial action of antibiotics. Benzo[b]-thiophene-2-boronic acid (BZB) derivatives are β-lactamase inhibitors and, as such, promising compounds to be associated with β-lactam antibacterial therapies. The uncharged form of BZB, in particular, is suggested to diffuse through the outer membrane of Gram negative bacteria. In this study, through the combination of electrophysiological experiments across reconstituted PC/n-decane bilayers and metadynamics-based free energy calculations, we investigate the permeation mechanism of boronic compounds. Our experimental data establish that BZB passes through the membrane, while computer simulations provide hints for the existence of an aqueous, water-filled monomolecular channel. These findings provide new perspectives for the design of boronic acid derivatives with high membrane permeability

Structure and Age Jointly Influence Rates of Protein Evolution

What factors determine a protein's rate of evolution are actively debated. Especially unclear is the relative role of intrinsic factors of present-day proteins versus historical factors such as protein age. Here we study the interplay of structural properties and evolutionary age, as determinants of protein evolutionary rate. We use a large set of one-to-one orthologs between human and mouse proteins, with mapped PDB structures. We report that previously observed structural correlations also hold within each age group – including relationships between solvent accessibility, designabililty, and evolutionary rates. However, age also plays a crucial role: age modulates the relationship between solvent accessibility and rate. Additionally, younger proteins, despite being less designable, tend to evolve faster than older proteins. We show that previously reported relationships between age and rate cannot be explained by structural biases among age groups. Finally, we introduce a knowledge-based potential function to study the stability of proteins through large-scale computation. We find that older proteins are more stable for their native structure, and more robust to mutations, than younger ones. Our results underscore that several determinants, both intrinsic and historical, can interact to determine rates of protein evolution