De novo inference of protein function from coarse-grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 mu s coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. (C) 2014 Wiley Periodicals, Inc.

A critical examination of the paradox of strength and ductility in ultrafine-grained metals

The paradox of strength and ductility is now well established and denotes the difficulty of simultaneously achieving both high strength and high ductility. This paradox was critically examined using a cast Al-7% Si alloy processed by high-pressure torsion (HPT) for up to 10 turns at a temperature of either 298 or 445 K. This processing reduces the grain size to a minimum of similar to 0.4 mu m and also decreases the average size of the Si particles. The results show that samples processed to high numbers of HPT turns exhibit both high strength and high ductility when tested at relatively low strain rates and the strain rate sensitivity under these conditions is similar to 0.14 which suggests that flow occurs by some limited grain boundary sliding and crystallographic slip. The results are also displayed on the traditional diagram for strength and ductility and they demonstrate the potential for achieving high strength and high ductility by increasing the number of turns in HPT.

The contribution of grain boundary sliding in tensile deformation of an ultrafine-grained aluminum alloy having high strength and high ductility

An as-cast Al-7 % Si alloy was processed by high-pressure torsion (HPT) for up to 10 turns at temperatures of 298 or 445 K. The HPT-processed samples had ultrafine-grained structures and they were tested in tension at room temperature at various strain rates in the range from 1.0 x 10(-4) to 1.0 x 10(-2) s(-1). The contributions of grain boundary sliding (GBS) to the total strain were measured directly using atomic force microscopy. Samples simultaneously showing both high strength and high ductility contained the highest fractions of high-angle grain boundaries (HAGB) and exhibited the highest contributions from GBS, whereas samples showing high strength but low ductility gave negligible values for the sliding contributions. It is concluded that high strength and high ductility require both an ultrafine grain size and a high fraction of HAGB.

Dynamic compression behavior of reactive spark plasma sintered ultrafine grained (Hf, Zr)B-2-SiC composites

This paper reports the dynamic compression behavior of ultrafine grained (Hf, Zr)B-2-SiC composites, sintered using reactive spark plasma sintering at 1600 degrees C for 10 min. Dynamic strength of similar to 2.3 GPa has been measured using Split Hopkinson Pressure Bar (SHPB) tests in a reproducible manner at strain rates of 800-1300 s(-1). A comparison with competing boride based armor ceramics, in reference to the spectrum of properties evaluated, establishes the potential of (Hf, Zr)B-2-SiC composites for armor applications. (C) 2015 Elsevier Ltd and Techna Group S.r.l. All rights reserved.

Al based ultra-fine eutectic with high room temperature plasticity and elevated temperature strength

Developments of aluminum alloys that can retain strength at and above 250 degrees C present a significant challenge. In this paper we report an ultrafine scale Al-Fe-Ni eutectic alloy with less than 3.5 aa transition metals that exhibits room temperature ultimate tensile strength of similar to 400 MPa with a tensile ductility of 6-8%. The yield stress under compression at 300 degrees C was found to be 150 MPa. We attribute it to the refinement of the microstructure that is achieved by suction casting in copper mold. The characterization using scanning and transmission electron microscopy (SEM and TEM) reveals an unique composite structure that contains the Al-Al3Ni rod eutectic with spacing of similar to 90 nm enveloped by a lamellar eutectic of Al-Al9FeNi (similar to 140 nm). Observation of subsurface deformation under Vickers indentation using bonded interface technique reveals the presence of extensive shear banding during deformation that is responsible for the origin of ductility. The dislocation configuration in Al-Al3Ni eutectic colony indicates accommodation of plasticity in alpha-Al with dislocation accumulation at the alpha-Al/Al3Ni interface boundaries. In contrast the dislocation activities in the intermetallic lamellae are limited and contain set of planner dislocations across the plates. We present a detailed analysis of the fracture surface to rationalize the origin of the high strength and ductility in this class of potentially promising cast alloy. (C) 2015 Elsevier B.V. All rights reserved.

An Evaluation of the Effectiveness of a Charged Bilayered Conducting Fine Mesh as a Dust Filter

Aim: To develop a mesh meant to be mounted on a windowpane that will act as a barrier for dust, while allowing wind to pass freely. Materials and Methods: Two small metal meshes separated at 1 cm, connected to an electrostatic generator and holding opposite charges are used. A videographic analysis has been performed. Results: The charged bilayered mesh was able to prevent a large portion of dust from passing through. Conclusion: The device is a simple, economical, and reliable way of reducing the entry of dust into a room, easing the need for periodic cleaning, and thus creating a healthier environment for the inhabitants of the building. It also has potential space applications.

Review: Overcoming the paradox of strength and ductility in ultrafine-grained materials at low temperatures

Ultrafine-grained (UFG) materials with grain sizes in the submicrometer or nanometer range may be prepared through the application of severe plastic deformation (SPD) to bulk coarse-grained solids. These materials generally exhibit high strength but only very limited ductility in low-temperature testing, thereby giving rise to the so-called paradox of strength and ductility. This paradox is examined and a new quantitative diagram is presented which permits the easy insertion of experimental data. It is shown that relatively simple procedures are available for achieving both high strength and high ductility in UFG materials including processing the material to a very high strain and/or applying a very short-term anneal immediately after the SPD processing. Significant evidence is now available demonstrating the occurrence of grain boundary sliding in these materials at low temperatures, where this is attributed to the presence of non-equilibrium grain boundaries and the occurrence of enhanced diffusion along these boundaries.

A comparison of the fine-scale structure of the diurnal cycle of tropical rain and lightning

In this study, the fine-scale structure of the diurnal variability of ground-based lightning is systematically compared with satellite-based rain. At the outset, it is shown that tropical variability of lightning exhibits a prominent diurnal mode, much like rain. A comparison of the geographical distribution of the timing of the diurnal maximum shows that there is very good agreement between the two observables over continental and coastal regions throughout the tropics. Following this global tropical comparison, we focus on two regions, Borneo and equatorial South America, both of which show the interplay between oceanward and landward propagations of the phase of the diurnal maximum. Over Borneo, both rain and lightning clearly show a climatological cycle of ``breathing in'' (afternoon to early morning) and ``breathing out'' (morning to early afternoon). Over the equatorial east coast of South America, landward propagation is noticed in rain and lightning from early afternoon to early morning. Along the Pacific coast of South America, both rain and lightning show oceanward propagation. Though qualitatively consistent, over both regions the propagation is seen to extend further in rainfall. Additionally, given that lightning highlights vigorous convection, the timing of its diurnal maximum often precedes that of rainfall in the convective life cycle. (C) 2015 Elsevier B.V. All rights reserved.

Twinning induced enhancement of fracture toughness in ultrafine grained Hydroxyapatite-Calcium Titanate composites

Despite being highly bioactive and biocompatible, the limitations of monolithic hydroxyapatite (HA) include extremely low fracture toughness, poor electrical conductivity. While addressing these issues, the present study demonstrates how CaTiO3 (CT) addition to HA can be utilized to obtain a combination of long crack fracture toughness (1.7 MPa m(1/2) SEVNB technique) and flexural strength of 98-155 MPa (3-point bending) and a moderate tensile strength (diametral compression) of 17-36 MPa. The enhancement in fracture resistance in spark plasma sintered HA-CT composites has been explained in reference to the observed twin morphology. TEM reveals the presence of twins in CT grains due to 1800 rotation about 101]. The measured properties along with our earlier reports on biocompatibility and electrical properties make HA-CT suitable for bone tissue engineering applications. When compared with other competing HA-based biocomposites, HA-CT composites are found to have a better combination of properties useful for medium load bearing implant applications. (C) 2015 Elsevier Ltd. All rights reserved.

Dust-Cloud Structures behind a Shock Wave Moving Over a Deposited Layer of Fine Particles

The present paper investigates dispersed-phase flow structures of a dust cloud induced by a normal shock wave moving at a constant speed over a flat surface deposited with fine particles. In the shock-fitted coordinates, the general equations of dusty-gas

Earthquake Stability Analysis about Fine Grinded Tailings Dams

Based on the broken characteristics about earthquake to tailings dams, the earthquake stability analysis methods for tailings dams are introduced. Taking fine tailings dam in Longdu Tailings Pool as an example, the stability of the dam with various situations while earthquake with seven magnitude takes place there. The results can be used by Longdu Mine for tailings pool safety management.

A microstructural investigation of deformation in fine SiC particulate- and whisker-reinforced aluminium-matrix composites

Aluminium-based composites, reinforced with low volume fractions of whiskers and small particles, have been formed by a powder route. The materials have been tested in tension, and the microstructures examined using transmission electron microscopy. The whisker composites showed an improvement in flow stress over the particulate composites, and this was linked to an initially enhanced work-hardening rate in the whisker composites. The overall dislocation densities were estimated to be somewhat higher in the whisker composites than the particulate composites, but in the early stages of deformation the distribution was rather different, with deformation in the whisker material being far more localized and inhomogeneous. This factor, together with differences in the internal stress distribution in the materials, is used to explain the difference in mechanical properties.

Fine scale structures from deformation of aluminium containing small alumina particles

Microstructures and mechanical properties have been studied in aluminium containing a fine dispersion of alumina particles, deformed by cold-rolling to strains between 1.4 and 3.5. The microstructure was characterised by TEM. The deformation structures evolved very rapidly, forming a nanostructured material, with fine subgrains about 0.2 μm in diameter and a fraction of high-angle boundaries which was already high at a strain of 1.4, but continued to increase with rolling strain. The yield stress and ductility of the rolled materials were measured in tension, and properties were similar for all materials. Yield stress measurements were correlated with estimates made using microstructural models. The role of small particles in forming and stabilising the deformation structure is discussed. This nanostructured cold-deformed alloy has mechanical properties which are usefully enhanced at comparatively low cost. This gives it, and similar particle-strengthened alloys, good potential for commercial exploitation. © 2002 Acta Materialia Inc. Published by Elsevier Science Ltd. All rights reserved.

Evaluación de producción de biomasa de Chloris gayana Kunth (Fine Cut) en la Cuenca del Salado

Resumen: El objetivo de este estudio fue evaluar el rendimiento de Chloris gayana Kunth (Grama Rhodes) cv. Fine Cut en relación con los rendimientos del campo natural. Este ensayo experimental se desarrolló en Verónica, Punta Indio, Provincia de Bs As. Las parcelas en donde se realizó el experimento fueron preparadas mediante labranza convencional. La siembra del cultivo se llevó a cabo el 4 Diciembre del 2009. Ésta se realizó en hileras distanciadas en 30cm y con una profundidad de 1cm. En cuanto al modelo experimental utilizado para la medición de biomasa de Chloris gayana Kunth cv. Fine Cut (con fertilización y sin fertilización), y de macollos, se utilizó un Diseño de Bloques al azar, (DBA), tomando como unidad elemental cada parcela con dos tratamientos. En el caso de la medición de biomasa de campo natural vs. Chloris gayana Kunth cv. Fine Cut no fertilizada se utilizó un Diseño Completamente Aleatorizado, (DCA), con tres repeticiones. Los datos obtenidos fueron analizados mediante un análisis de varianzas. El rendimiento de Chloris gayana superó al obtenido en el campo natural, (3548,44 Kg Ms ha‐1 vs. 8447,25 kg MS ha‐1 para campo natural y Chloris gayana, respectivamente). La aplicación de 75 kg de Nitrógeno incrementó la producción de Ch. gayana hasta los 14144,34 kg MS ha‐1. Estos rendimientos fueron obtenidos en un lapso de tiempo que va desde fines de diciembre del 2011 hasta mediados de abril del 2012 período en el cual se realizaron 4 cortes. En el cuarto año de producción (2012‐2013) la pastura no rebrotó, siendo las causas aparentes un anegamiento temporario junto con una posible helada que afectó su rebrote. Los datos recolectados sugieren que esta especie podría ser considerada como una alternativa interesante para el incremento de la producción primaria en este ambiente.

Coarse-to-fine vision-based localization by indexing scale-invariant features

This paper presents a novel coarse-to-fine global localization approach inspired by object recognition and text retrieval techniques. Harris-Laplace interest points characterized by scale-invariant transformation feature descriptors are used as natural landmarks. They are indexed into two databases: a location vector space model (LVSM) and a location database. The localization process consists of two stages: coarse localization and fine localization. Coarse localization from the LVSM is fast, but not accurate enough, whereas localization from the location database using a voting algorithm is relatively slow, but more accurate. The integration of coarse and fine stages makes fast and reliable localization possible. If necessary, the localization result can be verified by epipolar geometry between the representative view in the database and the view to be localized. In addition, the localization system recovers the position of the camera by essential matrix decomposition. The localization system has been tested in indoor and outdoor environments. The results show that our approach is efficient and reliable. © 2006 IEEE.