An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Nucleosynthesis in the outflows associated with accretion disks of type II collapsars

We investigate nucleosynthesis inside the outflows from gamma-ray burst (GRB) accretion disks formed by the Type II collapsars. In these collapsars, massive stars undergo core collapse to form a proto-neutron star initially, and a mild supernova (SN) explosion is driven. The SN ejecta lack momentum, and subsequently this newly formed neutron star gets transformed to a stellar mass black hole via massive fallback. The hydrodynamics and the nucleosynthesis in these accretion disks have been studied extensively in the past. Several heavy elements are synthesized in the disk, and much of these heavy elements are ejected from the disk via winds and outflows. We study nucleosynthesis in the outflows launched from these disks by using an adiabatic, spherically expanding outflow model, to understand which of these elements thus synthesized in the disk survive in the outflow. While studying this, we find that many new elements like isotopes of titanium, copper, zinc, etc., are present in the outflows. Ni-56 is abundantly synthesized in most of the cases in the outflow, which implies that the outflows from these disks in a majority of cases will lead to an observable SN explosion. It is mainly present when outflow is considered from the He-rich, Ni-56/Fe-54-rich zones of the disks. However, outflow from the Si-rich zone of the disk remains rich in silicon. Although emission lines of many of these heavy elements have been observed in the X-ray afterglows of several GRBs by Chandra, BeppoSAX, XMM-Newton, etc., Swift seems to have not yet detected these lines.

Energy Sharing for Multiple Sensor Nodes With Finite Buffers

We consider the problem of finding optimal energy sharing policies that maximize the network performance of a system comprising of multiple sensor nodes and a single energy harvesting (EH) source. Sensor nodes periodically sense the random field and generate data, which is stored in the corresponding data queues. The EH source harnesses energy from ambient energy sources and the generated energy is stored in an energy buffer. Sensor nodes receive energy for data transmission from the EH source. The EH source has to efficiently share the stored energy among the nodes to minimize the long-run average delay in data transmission. We formulate the problem of energy sharing between the nodes in the framework of average cost infinite-horizon Markov decision processes (MDPs). We develop efficient energy sharing algorithms, namely Q-learning algorithm with exploration mechanisms based on the epsilon-greedy method as well as upper confidence bound (UCB). We extend these algorithms by incorporating state and action space aggregation to tackle state-action space explosion in the MDP. We also develop a cross entropy based method that incorporates policy parameterization to find near optimal energy sharing policies. Through simulations, we show that our algorithms yield energy sharing policies that outperform the heuristic greedy method.

PLUTO plus : Near-Complete Modeling of Affine Transformations for Parallelism and Locality

Affine transformations have proven to be very powerful for loop restructuring due to their ability to model a very wide range of transformations. A single multi-dimensional affine function can represent a long and complex sequence of simpler transformations. Existing affine transformation frameworks like the Pluto algorithm, that include a cost function for modern multicore architectures where coarse-grained parallelism and locality are crucial, consider only a sub-space of transformations to avoid a combinatorial explosion in finding the transformations. The ensuing practical tradeoffs lead to the exclusion of certain useful transformations, in particular, transformation compositions involving loop reversals and loop skewing by negative factors. In this paper, we propose an approach to address this limitation by modeling a much larger space of affine transformations in conjunction with the Pluto algorithm's cost function. We perform an experimental evaluation of both, the effect on compilation time, and performance of generated codes. The evaluation shows that our new framework, Pluto+, provides no degradation in performance in any of the Polybench benchmarks. For Lattice Boltzmann Method (LBM) codes with periodic boundary conditions, it provides a mean speedup of 1.33x over Pluto. We also show that Pluto+ does not increase compile times significantly. Experimental results on Polybench show that Pluto+ increases overall polyhedral source-to-source optimization time only by 15%. In cases where it improves execution time significantly, it increased polyhedral optimization time only by 2.04x.

Constant volume combustion of aluminum and cornstarch dust in microgravity

The subject of the present work is to report an experimental comparative study of the effect of dispersion-induced turbulence on dust combustion in constant volume vessel, carried out both in normal gravity and in microgravity environment. Dispersion system with small scale of turbulence, creating uniform homogeneous mixture, was used in experiments. To improve reproducibility of the explosion data an ignitor of small energy, with local soft ignition was developed. Both factors contributed to acquisition of more reproducible experimental data. In experiments under microgravity conditions a dust suspension during combustion remains constant. This makes possible to study dust explosion under stationary dust suspension without influence of turbulence.

Chemical kinetics and self-ignition in a model supersonic hydrogen-air combustor

Self-ignition tests of a model scramjet combustor were conducted by using parallel sonic injection of gaseous hydrogen from the base of a blade-like strut into a supersonic vitiated airstream. The range of stagnation pressure and temperature studied varied from 1.0 to 4.5 MPa and from 1300 to 2200 K, respectively. Experimental results show that the self-ignition limit, in terms of either global or local quantities of pressure and temperature, exhibits a nonmonotonic behavior resembling the classical homogeneous explosion limit of the hydrogen-oxygen system. Specifically, for a given temperature, increasing pressure from a low value can render a nonignitable mixture to first become ignitable, then nonignitable again, This correspondence shows that, despite the globally supersonic nonpremixed configuration studied herein, ignition is strongly influenced by the intricate chemical reaction mechanism and thereby exhibits the homogeneous explosion character. Consequently, self-ignition criteria based on a global reaction rate approximating the complex chemistry are inadequate. An auxiliary computational study on counterflow ignition was also conducted to systematically investigate the contamination effects of vitiated air. Results indicate that the net contamination effects for the present experimental data are expected to be substantially smaller than contributions from the individual contamination species because of the counterbalancing influences of the H2O-inhibition and NO-promotion reactions in effecting ignition.

Combustion tube studies of dust flame acceleration

A new pneumatic dispersion system for obtaining a good quality uniform dust suspension in a horizontal dust combustion tube was developed. The effect of three different dispersion techniques on self-sustained dust flame acceleration in such a combustion tube was examined. The importance of the dispersion quality in the test tube for maintaining a self-sustained dust flame acceleration was demonstrated. A combustion tube for studies of flame acceleration in fine aluminum dust-air mixture and its transition to detonation under industrial ignition conditions was constructed in the course of the present study. It consists mainly of an initiation section and a test section. The initiation section must be equipped in a well-developed dispersion system for creating a good dispersion condition in the test tube. The length of this section is 3 meters. The test tube requires only to distribute uniformly the dust over the bottom of the tube prior to the experiment. The aluminum dust spherical in shape with 6 mu m in diameter was used for tests. Experimental results demonstrated that the increase in flame velocity is roughly linear through the entire length of the test tube. The highest flame propagation velocity in fine aluminum dust-air mixture approaches some 1200m/s at a distance of 4.8m from the ignition plate.

Magnetic properties of sintered sm2fe17ny magnets

Sintered magnets of Sm2Fe17Ny nitrides, with a density of 6.0-7.4 g/cm3, have been prepared by using an explosion technique. Both crystalline structure and the magnetic properties of Sm2Fe17Ny nitrides were retained in the process. The sintered magnet had a remanence B(r)=0.83 T, an intrinsic coercivity mu(0i)H(c)=0.57 T and an energy product (BH)max=88 kJ/m3. The temperature dependence of coercivity and remanence were also measured. The temperature coefficients alpha of remanence and beta of coercivity are -0.076%/degrees-C and -0.51%/degrees-C, respectively.

高能、含铝和温压炸药爆炸抛撒实验研究

采用高速运动分析系统观察了高能炸药、含铝炸药和温压炸药爆炸产物抛撒的过程;分析比较了三种炸药的爆炸产物抛撒运动及后燃特点,得到了温压炸药具有爆炸和后燃二个过程,爆炸场范围大,温度高,后燃持续时间长;高能炸药与温压炸药相比爆炸场范围小,温度低,几乎没有后燃过程;含铝炸药介于温压炸药和高能炸药之间。

室内泄漏燃气浓度分布的一个量级估算方法

在对室内液化石油气泄漏流动过程进行量级估算分析的基础上,提出了一种预测室内泄漏液化石油气浓度分布的简化方法.并结合一次居民室内液化气爆炸事故,讨论了此方法在实际应用中的简易可行性.

温压炸药爆炸抛撒的运动规律

采用高速运动分析系统观察了高能炸药、含铝炸药和温压炸药爆炸产物抛撒的过程;比较了这3种炸药的爆炸产物抛撒运动及后燃特点,通过比较直观地观察到温压炸药爆炸和后燃2个过程,以及后燃火球的成长历程,根据实验结果确定了温压炸药爆炸产物抛撒半径随时同变化的数学表达式.

柱形容器开口泄爆过程中的火焰传播特性

泄爆过程中流动与燃烧的相互作用机制是研究开口泄爆问题的关键.对柱形容器泄爆过程中压力与火焰发展传播过程的观测与分析表明,不同泄爆条件下压力与火焰的发展传播具有明显特点.泄爆诱导流动通过加速火焰传播、加剧火焰变形、增大火焰面积对容器内燃烧产生增强作用,泄爆流动大小主要由泄爆面积决定.小口中低压泄爆过程压力与火焰的发展过程与封闭燃烧中类似;小口高压以及大口泄爆过程中,火焰变形剧烈,传播速度明显上升,并导致压力的回升.

爆炸容器内冲击波系演化及壳体响应的数值研究

对中心装药爆炸后冲击波的产生、传播和壳体动态响应全过程进行了数值研究。认为RDX瞬时爆炸，爆炸近场采用自相似解；冲击波传播和波系演化采用PPM(the Piecewise Parabolic Method)格式求解Euler方程；壳体响应采用有限元方法求解拉氏坐标系下由虚功原理得到的动力学方程。壳体内壁面边界条件分别采用强耦合和弱耦合方法处理。结果表明：（1）当装药量相同时，薄壁壳体振型比厚壁宙体复杂得多，振幅也大；（2）当装药量不同，壳体厚度相同时，爆炸场冲击波的演化过程不同；（3）对少量装药，产生的冲击波强度低，壳体变形小，是否考虑内边界运动，对计算结果的影响不大；（4）在本文条件下，爆炸容器封头顶点所受的载荷最大，是取易发生破坏的地方，侧壁与爆点所在横截面的交线，也易破坏。

The Droplet Group Micro-Explosions, Viscosity and Atomization Characteristics of W/O Emulsions

The spray of emulsified fuel, composed of diesel fuel, water and methanol can make micro-explosion under high temperature conditions, and the viscosity and the atomization characteristics of emulsion have significant effects on the micro- explosion of emulsions. To clarify the combustion mechanism of water-in-oil emulsion sprays, combustion bomb experiments were carried out, and the droplet group micro- explosions in W/O fuel emulsion sprays in a high-pressure, high-temperature bomb were observed clearly by a multi-pulsed, off-axis, image-plane ruby laser holocamera and continuously by a high-speed CCD camera.The viscosity and atomization characteristics of emulsions were also studied experimentally. The experimental results show that the higher concentration of the aqueous phase (water-methanol) (<50%) increases the viscosity of the emulsions, especially for higher agent concentration, and higher aqueous phase concentration and higher viscosity results in lager Sauter Mean Diameter (SMD). The experiment results also show that the different kinds of emulsifying agents, with different Hydrophile-Lipophile Balance (HLB) values, have significant influence on the viscosity of the emulsions.