bluuebunny/crossref_metadata_2025 huggingface dataset:
ANISOTROPY OF ELASTIC PROPERTIES AND CENTRAL PEAK BEHAVIORS OF UNIAXIAL STRONTIUM BARIUM NIOBATE RELAXOR SINGLE CRYSTALS
Authors: KO JAE-HYEON , KIM TAE HYUN , KOJIMA SEIJI , LIM KI-SOO , KOO TAE-YEONG
Published: March 2011

The elastic properties of strontium barium niobate single crystals with different strontium content were investigated. The elastic constant and the related hypersonic attenuation showed substantially different values depending on the propagating direction of acoustic waves. This elastic anisotropy was explained based on the uniaxial nature of the order parameter and the diffuse ferroelectric phase transition in this tetragonal system. This observation was correlated with the appearance of strongly polarized central peaks, which reflects strong polarization fluctuations along the uniaxial polar direction.
DEPENDENCE OF MICROWAVE DIELECTRIC PROPERTIES ON STRUCTURAL CHARACTERISTICS OF ILMENITE, TRI-RUTILE AND WOLFRAMITE CERAMICS
Authors: KIM EUNG SOO , JEON CHANG JUN
Published: March 2011

Effects of crystal structures on dielectric properties of ATiO 3 (trigonal ilmenite), ATa 2 O 6 (tetragonal tri-rutile) and AWO 4 (monoclinic wolframite) (A = Ni, Mg, Co) ceramics with A- and B-site oxygen octahedra were investigated at microwave frequencies. The dielectric constant (K) of the specimens was affected by the dielectric polarizabilities of composition and cation bond valence between octahedral cation and oxygen ion per molar volume (V m ). The quality factor (Qf) of ATiO 3 was appreciably larger than those of ATa 2 O 6 and AWO 4 due to the different sharing types of oxygen octahedra. The temperature coefficient of resonant frequency (TCF) of the specimens was dependent on the octahedral distortion per V m .
INFLUENCE OF n ON STRUCTURE AND MICROWAVE DIELECTRIC PROPERTIES OF SOMEAnBn - 1O3nPEROVSKITES
Authors: FANG LIANG , YANG ZHAO , ZHANG HUI , LI CHUNCHUN , SU HEPING
Published: March 2011

Two series of B-site deficient perovskites Ba5+mTimNb4O15+3m(m = 1, 2, 3) and Sr3+mLaTimNb3O12+3m(m = 0, 1, 2) with the general formula AnBn - 1O3n(n = 4 - 8; A = Ba , Sr , La ; B = Nb , Ti ) have been synthesized, and their structure and microwave dielectric properties have been investigated. The effects of n (number of octahedra layers within a perovskite blocks) on structure and properties are investigated. The values of dielectric constant εrand temperature coefficient of resonant frequency τfgradually increase, but quality factors Q × f values significantly decreases as the values of n increase.
An analysis of a variation of hit-and-run for uniform sampling from general regions
Authors: Kiatsupaibul Seksan , Smith Robert L. , Zabinsky Zelda B.
Published: March 2011

Hit-and-run, a class of MCMC samplers that converges to general multivariate distributions, is known to be unique in its ability to
mix fast
for uniform distributions over convex bodies. In particular, its rate of convergence to a uniform distribution is of a low order polynomial in the dimension. However, when the body of interest is difficult to sample from, typically a hyperrectangle is introduced that encloses the original body, and a one-dimensional acceptance/rejection is performed. The fast mixing analysis of hit-and-run does not account for this one-dimensional sampling that is often needed for implementation of the algorithm. Here we show that the effect of the size of the hyperrectangle on the efficiency of the algorithm is only a linear scaling effect. We also introduce a variation of hit-and-run that accelerates the sampler and demonstrate its capability through a computational study.
An analysis of queuing network simulation using GPU-based hardware acceleration
Authors: Park Hyungwook , Fishwick Paul A.
Published: March 2011

Queuing networks are used widely in computer simulation studies. Examples of queuing networks can be found in areas such as the supply chains, manufacturing work flow, and internet routing. If the networks are fairly small in size and complexity, it is possible to create discrete event simulations of the networks without incurring significant delays in analyzing the system. However, as the networks grow in size, such analysis can be time consuming, and thus require more expensive parallel processing computers or clusters. We have constructed a set of tools that allow the analyst to simulate queuing networks in parallel, using the fairly inexpensive and commonly available graphics processing units (GPUs) found in most recent computing platforms. We present an analysis of a GPU-based algorithm, describing benefits and issues with the GPU approach. The algorithm clusters events, achieving speedup at the expense of an approximation error which grows as the cluster size increases. We were able to achieve 10-x speedup using our approach with a small error in a specific implementation of a synthetic closed queuing network simulation. This error can be mitigated, based on error analysis trends, obtaining reasonably accurate output statistics. The experimental results of the mobile ad hoc network simulation show that errors occur only in the time-dependent output statistics.
The stochastic root-finding problem
Authors: Pasupathy Raghu , Kim Sujin
Published: March 2011

The stochastic root-finding problem (SRFP) is that of finding the zero(s) of a vector function, that is, solving a nonlinear system of equations when the function is expressed implicitly through a stochastic simulation. SRFPs are equivalently expressed as stochastic fixed-point problems, where the underlying function is expressed implicitly via a noisy simulation. After motivating SRFPs using a few examples, we review available methods to solve such problems on constrained Euclidean spaces. We present the current literature as three broad categories, and detail the basic theoretical results that are currently known in each of the categories. With a view towards helping the practitioner, we discuss specific variations in their implementable form, and provide references to computer code when easily available. Finally, we list a few questions that are worthwhile research pursuits from the standpoint of advancing our knowledge of the theoretical underpinnings and the implementation aspects of solutions to SRFPs.
SubsetTrio
Authors: Jin Zhanpeng , Cheng Allen C.
Published: March 2011

Motivated by excessively high benchmarking efforts caused by a rapidly expanding design space, increasing system complexity, and prevailing practices based on ad-hoc and subjective schemes, this article seeks to enhance architecture exploration and evaluation efficiency by strategically integrating a genetic algorithm, 3-D geometrical rendering, and multivariate statistical analysis into one unified methodology framework—
SubsetTrio
—capable of subsetting any given benchmark suite based on its inherent workload characteristics, desired workload space coverage, and the total execution time intended by the user. By encoding both representativity (i.e., workload space coverage represented by the volume of the convex hull of benchmarks) and efficiency (i.e., total run time) as a co-optimization objective of a
survival-of-the-fittest
evolutionary algorithm, we can systematically determine a globally “fittest” (i.e., most representative and efficient) benchmark subset according to the workload space coverage threshold specified by the user. We demonstrate the usage, efficacy, and efficiency of the proposed technique by conducting a thorough case study on the SPEC benchmark suite, and evaluate its validity based on 50 commercial computer systems. Compared to the state-of-the-art statistical subsetting approach based on the Principal Component Analysis (PCA),
SubsetTrio
could select a significantly more time-efficient subset, while covering the same or higher workload space.
Optimizing physical-layer parameters for wireless sensor networks
Authors: Holland Matthew , Wang Tianqi , Tavli Bulent , Seyedi Alireza , Heinzelman Wendi
Published: March 2011

As wireless sensor networks utilize battery-operated nodes, energy efficiency is of paramount importance at all levels of system design. In order to save energy in the transfer of data from the sensor nodes to one or more sinks, the data may be routed through other nodes rather than transmitting it directly to the sink(s). In this article, we investigate the problem of energy-efficient transmission of data over a noisy channel, focusing on the setting of physical-layer parameters. We derive a metric called the energy per successfully received bit, which specifies the expected energy required to transmit a bit successfully over a particular distance given a channel noise model. By minimizing this metric, we can find, for different modulation schemes, the energy-optimal relay distance and the optimal transmit energy as a function of channel noise level and path loss exponent. These results enable network designers to select the hop distance, transmit power, and/or modulation scheme that maximize network lifetime.
A security framework for privacy-preserving data aggregation in wireless sensor networks
Authors: Chan Aldar C-F. , Castelluccia Claude
Published: March 2011

A formal treatment to the security of Concealed Data Aggregation (CDA) and the more general Private Data Aggregation (PDA) is given. While there exist a handful of constructions, rigorous security models and analyses for CDA or PDA are still lacking. Standard security notions for public key encryption, including semantic security and indistinguishability against chosen ciphertext attacks, are refined to cover the multisender nature and aggregation functionality of CDA and PDA in the security model. The proposed security model is sufficiently general to cover most application scenarios and constructions of privacy-preserving data aggregation. An impossibility result on achieving security against adaptive chosen ciphertext attacks in CDA/PDA is shown. A generic CDA construction based on public key homomorphic encryption is given, along with a proof of its security in the proposed model. The security of a number of existing schemes is analyzed in the proposed model.
A model framework for greedy routing in a sensor network with a stochastic power scheme
Authors: Keeler Holger P. , Taylor Peter G.
Published: March 2011

A stochastic model is formulated and analyzed to study the advancements of messages under greedy routing in a sensor network with a power-saving scheme. The aim of this model is give a better understanding of stochastic dependencies arising in the system and to offer a method of computing the advancement of message under greedy routing. We observe that the majority of the stochastic dependence from a routing path is captured by including only the previous forwarding node location. We examine a simple uncoordinated power-saving scheme with a new understanding of its effects on local node density. We propose a method for sensibly limiting the number of transmission reattempts before concluding there is no node in the forwarding region. All expressions involving multidimensional integrals are derived and evaluated readily with quasi-Monte Carlo integration methods. An importance sampling function is derived to speed up the quasi-Monte Carlo methods. The integral expressions are compared to simulations and give very agreeable results.
Sensor network localization using sensor perturbation
Authors: Zhu Yuanchen , Gortler Steven J. , Thurston Dylan
Published: March 2011

Sensor network localization is an instance of the NP-Hard graph realization problem. Thus, methods used in practice are not guaranteed to find the correct localization, even if it is uniquely determined by the input distances.

In this article, we show the following: if the sensors are allowed to wiggle, giving us perturbed distance data, we can apply a novel algorithm to realize arbitrary Generically Globally Rigid graphs (GGR), or certain vertex subsets in non-GGR graphs whose relative positions are fixed (which include vertex sets of GGR subgraphs). And this strategy works in any dimension.

In the language of structural rigidity theory, our approach corresponds to calculating the approximate kernel of a generic stress matrix for the given graph and distance data. To make our algorithm suitable for real-world applications, we also present: (i) various techniques for improving the robustness of the algorithm in the presence of measurement noise; (ii) an algorithm for detecting certain subsets of graph vertices whose relative positions are fixed in any generic realization of the graph and robustly localizing these subsets of vertices, (iii) a strategy for reducing the number of measurements needed by the algorithm.

We provide simulation results of our algorithm.
Optimal layered multicast
Authors: Gopinathan Ajay , Li Zongpeng
Published: March 2011

Recent advances in network coding research dramatically changed the underlying structure of optimal multicast routing algorithms and made them efficiently computable. While most such algorithm design assumes a single file/layer being multicast, layered coding introduces new challenges into the paradigm due to its cumulative decoding nature. Layered coding is designed to handle heterogeneity in receiver capacities, and a node may decode layer
k
only if it successfully receives all layers in 1..
k
. We show that recently proposed optimization models for layered multicast do not correctly address this challenge. We argue that in order to achieve the absolute maximum throughput (or minimum cost), it is necessary to decouple the application-layer throughput from network-layer throughput. In particular, a node should be able to receive a nonconsecutive layer or a partial layer even if it cannot decode and utilize it (e.g., for playback in media streaming applications). The rationale is that nodes at critical network locations need to receive data just for helping other peers. We present a mathematical programming model that addresses these challenges and achieves absolute optimal performance. Simulation results show considerable throughput gain (cost reduction) compared with previous models, in a broad range of network scenarios. We then provide a formal proof that the layered multicast problem is NP-complete. We design a randomized rounding algorithm to approximate the optimal layered multicast, and show the efficacy of our technique using simulations. We then proceed to further generalize our model by studying the optimal progression of layer sizes. We show that such optimization is nonconvex, and apply a simulated annealing algorithm to solve it, with flexible trade-off between solution quality and running time. We verify the effectiveness of the new model and the simulated annealing algorithm through extensive simulations, and point out insights on the connection between optimal layer size progression and node capacity distribution.
Knowledge discovery from 3D human motion streams through semantic dimensional reduction
Authors: Jin Yohan , Prabhakaran Balakrishnan
Published: March 2011

3D human motion capture is a form of multimedia data that is widely used in entertainment as well as medical fields (such as orthopedics, physical medicine, and rehabilitation where gait analysis is needed). These applications typically create large repositories of motion capture data and need efficient and accurate content-based retrieval techniques. 3D motion capture data is in the form of multidimensional time-series data. To reduce the dimensions of human motion data while maintaining semantically important features, we quantize human motion data by extracting spatio-temporal features through SVD and translate them onto a symbolic sequential representation through our proposed sGMMEM (semantic Gaussian Mixture Modeling with EM). In order to handle variations in motion capture data due to human body characteristics and speed of motion, we transform the semantically quantized values into a histogram representation. This representation is used as a signature for classification and similarity-based retrieval. We achieved good classification accuracies for “coarse” human motion categories (such as walking 92.85%, run 91.42%, and jump 94.11%) and even for subtle categories (such as dance 89.47%, laugh 83.33%, basketball signal 85.71%, golf putting 80.00%). Experiments also demonstrated that the proposed approach outperforms earlier techniques such as the wMSV (weighted Motion Singular Vector) approach and LB_Keogh method.
Modeling progressive mesh streaming
Authors: Cheng Wei , Ooi Wei Tsang , Mondet Sebastien , Grigoras Romulus , Morin Géraldine
Published: March 2011

3D triangular meshes are becoming an increasingly prevalent data type in networked applications such as digital museums, online games, and virtual worlds. In these applications, a 3D mesh is typically coded progressively, yielding a multiresolution representation suitable for streaming. While such progressive coding allows incremental rendering for users while data is being transmitted, it introduces dependencies between data, causing delay in rendering when packets are lost. This article quantitatively analyzes the effects of such dependency by modeling the distribution of decoding time as a function of mesh properties and network parameters. We apply our model to study two extreme cases of dependency in progressive meshes and show that the effect of dependencies on decoded mesh quality diminishes with time. Our model provides the expected decoded mesh quality at the receiver at a given time. Based on this expected value, we propose a packetization strategy that improves the decoded mesh quality during the initial stage of streaming. We validate the accuracy of our model under a variety of network conditions, including bursty losses, fluctuating RTT, and varying sending rate. The values predicted from our model match the measured value reasonably well in all cases except when losses are too bursty.
Statistical multiplexing of variable-bit-rate videos streamed to mobile devices
Authors: Hsu Cheng-Hsin , Hefeeda Mohamed
Published: March 2011

We address the problem of broadcasting multiple video streams over a broadcast network to many mobile devices, so that: (i) streaming quality of mobile devices is maximized, (ii) energy consumption of mobile devices is minimized, and (iii) goodput in the network is maximized. We consider two types of broadcast networks: closed-loop networks, in which all video streams are jointly encoded to ensure their total bit rate does not exceed the broadcast network bandwidth, and open-loop networks, in which videos are encoded using standalone coders, and thus must be carefully broadcast to avoid playout glitches. We first show that the problem of optimally broadcasting multiple videos is NP-complete. We then propose an approximation algorithm to construct burst schedules for multiple VBR (Variable-Bit-Rate) streams. The proposed algorithm frees network operators from the manual and error-prone bandwidth reservation process which is currently used in practice. We prove that the proposed algorithm achieves optimal goodput and near-optimal energy saving. We show that it produces glitch-free schedules in closed-loop networks, and it minimizes number of glitches in open-loop networks. We implement the proposed algorithm in a trace-driven simulator, and conduct extensive simulations for both open- and closed-loop networks. The simulation results show that the proposed algorithm outperforms the existing algorithms in many aspects, including number of late frames, number of concurrently broadcast video streams, and energy saving of mobile devices. To show the practicality and efficiency of the proposed algorithm, we also implement it in a real mobile TV testbed as a proof of concept. The results from the testbed confirm that the proposed algorithm: (i) does not result in playout glitches, (ii) achieves high energy saving, and (iii) runs in real time.
Analytical Chemistry in Molecular Electronics
Authors: Bergren Adam Johan , McCreery Richard L.
Published: March 2011

This review discusses the analytical characterization of molecular electronic devices and structures relevant thereto. In particular, we outline the methods for probing molecular junctions, which contain an ensemble of molecules between two contacts. We discuss the analytical methods that aid in the fabrication and characterization of molecular junctions, beginning with the confirmation of the placement of a molecular layer on a conductive or semiconductive substrate. We emphasize methods that provide information about the molecular layer in the junction and outline techniques to ensure molecular layer integrity after the complete fabrication of a device. In addition, we discuss the analytical information derived during the actual device operation.
New Technologies for Glycomic Analysis: Toward a Systematic Understanding of the Glycome
Authors: Rakus John F. , Mahal Lara K.
Published: March 2011

Carbohydrates are the most difficult class of biological molecules to study by high-throughput methods owing to the chemical similarities between the constituent monosaccharide building blocks, template-less biosynthesis, and the lack of clearly identifiable consensus sequences for the glycan modification of cohorts of glycoproteins. These molecules are crucial for a wide variety of cellular processes ranging from cell-cell communication to immunity, and they are altered in disease states such as cancer and inflammation. Thus, there has been a dedicated effort to develop glycan analysis into a high-throughput analytical field termed glycomics. Herein we highlight major advances in applying separation, mass spectrometry, and microarray methods to the fields of glycomics and glycoproteomics. These new analytical techniques are rapidly advancing our understanding of the importance of glycosylation in biology and disease.
High-Throughput Biosensors for Multiplexed Food-Borne Pathogen Detection
Authors: Gehring Andrew G. , Tu Shu-I
Published: March 2011

Incidental contamination of foods by pathogenic bacteria and/or their toxins is a serious threat to public health and the global economy. The presence of food-borne pathogens and toxins must be rapidly determined at various stages of food production, processing, and distribution. Producers, processors, regulators, retailers, and public health professionals need simple and cost-effective methods to detect different species or serotypes of bacteria and associated toxins in large numbers of food samples. This review addresses the desire to replace traditional microbiological plate culture with more timely and less cumbersome rapid, biosensor-based methods. Emphasis focuses on high-throughput, multiplexed techniques that allow for simultaneous testing of numerous samples, in rapid succession, for multiple food-borne analytes (primarily pathogenic bacteria and/or toxins).
The Use of Magnetic Nanoparticles in Analytical Chemistry
Authors: Beveridge Jacob S. , Stephens Jason R. , Williams Mary Elizabeth
Published: March 2011

Magnetic nanoparticles uniquely combine superparamagnetic behavior with dimensions that are smaller than or the same size as molecular analytes. The integration of magnetic nanoparticles with analytical methods has opened new avenues for sensing, purification, and quantitative analysis. Applied magnetic fields can be used to control the motion and properties of magnetic nanoparticles; in analytical chemistry, use of magnetic fields provides methods for manipulating and analyzing species at the molecular level. In this review, we describe applications of magnetic nanoparticles to analyte handling, chemical sensors, and imaging techniques.
The Chemical Composition of Comets—Emerging Taxonomies and Natal Heritage
Authors: Mumma Michael J. , Charnley Steven B.
Published: March 2011

Cometary nuclei contain the least modified material from the formative epoch of our planetary system, and their compositions reflect a range of processes experienced by material prior to its incorporation in the cometary nucleus. Dynamical models suggest that icy bodies in the main cometary reservoirs (Kuiper Belt, Oort Cloud) formed in a range of environments in the protoplanetary disk, and (for the Oort Cloud) even in disks surrounding neighboring stars of the Sun's birth cluster. Photometric and spectroscopic surveys of more than 100 comets have enabled taxonomic groupings based on free radical species and on crystallinity of rocky grains. Since 1985, new surveys have provided emerging taxonomies based on the abundance ratios of primary volatiles. More than 20 primary chemical species are now detected in bright comets. Measurements of nuclear spin ratios (in water, ammonia, and methane) and of isotopic ratios (D/H in water and HCN;14N/15N in CN and HCN) have provided critical insights on factors affecting formation of the primary species. The identification of an abundant product species (HNC) has provided clear evidence of chemical production in the inner coma. Parallel advances have occurred in astrochemistry of hot corinos, circumstellar disks, and dense cloud cores. In this review, we address the current state of cometary taxonomy and compare it with current astrochemical insights.
Comets as Building Blocks
Authors: A'Hearn Michael F.
Published: March 2011

Recent results, many but not all from flybys of comets by spacecraft, particularly the results from Deep Impact, have dramatically improved our understanding of the physical properties of cometary nuclei. Characteristic features are modest size (R<20 km), high porosity, low strength, and heterogeneity. There is also evidence that can be interpreted as showing the original cometesimals in a cometary nucleus and suggesting radial migration of macroscopic cometesimals during the aggregation of nuclei, which in turn aggregated into the cores of the giant planets.
Dynamics of Protoplanetary Disks
Authors: Armitage Philip J.
Published: March 2011

Protoplanetary disks are quasi-steady structures whose evolution and dispersal determine the environment for planet formation. I review the theory of protoplanetary disk evolution and its connection to observations. Substantial progress has been made in elucidating the physics of potential angular momentum transport processes—including self-gravity, magnetorotational instability, baroclinic instabilities, and magnetic braking—and in developing testable models for disk dispersal via photoevaporation. The relative importance of these processes depends upon the initial mass, size, and magnetization of the disk, and subsequently on its opacity, ionization state, and external irradiation. Disk dynamics is therefore coupled to star formation, pre-main-sequence stellar evolution, and dust coagulation during the early stages of planet formation and may vary dramatically from star to star. The importance of validating theoretical models is emphasized, with the key observations being those that probe disk structure on the scales between 1 AU and 10 AU, where theory is most uncertain.
Laboratory Astrochemistry: Gas-Phase Processes
Authors: Smith Ian W.M.
Published: March 2011

A major aim of astrochemistry is to explain the nature and abundance of the molecules observed in the interstellar medium (ISM). Three kinds of activity are involved: (a) the spectroscopic identification of the species that are present in the ISM; (b) the construction of large chemical models that attempt to explain the syntheses of the observed molecules; and (c) efforts to measure or predict crucial information, such as rate coefficients for the chemical reactions that are included in the models. Models can also be employed to identify the processes that exert a major influence on the predicted abundances of observed species. Clearly, it is important that the fundamental aspects of these processes—for example, the chemical rate coefficients—are quantified as accurately as possible. This is the role of laboratory experiments, aided by theory, and this review provides a critical examination of the experimental methods that provide these data and summarizes both the results that have been obtained for gas-phase processes and their reliability.
An Interesting Voyage
Authors: Rubin Vera C.
Published: March 2011

My life has been an interesting voyage. I became an astronomer because I could not imagine living on Earth and not trying to understand how the Universe works. My scientific career has revolved around observing the motions of stars within galaxies and the motions of galaxies within the Universe. In 1965, if you were very lucky and interested in using telescopes, you could walk into a research laboratory that was building instruments that reduced exposure times by a factor of 10 and end up making remarkable discoveries. Women generally required more luck and perseverance than men did. It helped to have supportive parents and a supportive husband.
The First Galaxies
Authors: Bromm Volker , Yoshida Naoki
Published: March 2011

We review our current understanding of how the first galaxies formed at the end of the cosmic dark ages a few 100 million years after the Big Bang. Modern large telescopes discovered galaxies at redshifts greater than seven, whereas theoretical studies have just reached the degree of sophistication necessary to make meaningful predictions. A crucial ingredient is the feedback exerted by the first generation of stars, through UV radiation, supernova blast waves, and chemical enrichment. The key goal is to derive the signature of the first galaxies to be observed with upcoming or planned next-generation facilities, such as the James Webb Space Telescope or Atacama Large Millimeter Array. From the observational side, ongoing deep-field searches for very high-redshift galaxies begin to provide us with empirical constraints on the nature of the first galaxies.
The Astrophysics of Ultrahigh-Energy Cosmic Rays
Authors: Kotera Kumiko , Olinto Angela V.
Published: March 2011

The origin of the highest energy cosmic rays is still unknown. The discovery of their sources is expected to reveal the workings of the most energetic astrophysical accelerators in the Universe. Current observations show a spectrum consistent with an origin in extragalactic astrophysical sources. Candidate sources range from the birth of compact objects to explosions related to gamma-ray bursts or to events in active galaxies. We discuss the main effects of propagation from cosmologically distant sources, including interactions with cosmic background radiation and magnetic fields. We examine possible acceleration mechanisms leading to a survey of candidate sources and their signatures. New questions arise from an observed hint of sky anisotropies and an unexpected evolution of composition indicators. Future observations may reach the necessary sensitivity to achieve charged particle astronomy and to observe ultrahigh-energy photons and neutrinos, which may further illuminate the workings of the Universe at these extreme energies. In addition to fostering a new understanding of high-energy astrophysical phenomena, the study of ultrahigh-energy cosmic rays can constrain the structure of the Galactic and extragalactic magnetic fields as well as probe particle interactions at energies orders of magnitude higher than achieved in terrestrial accelerators.
Deformable Medical Image Registration: Setting the State of the Art with Discrete Methods
Authors: Glocker Ben , Sotiras Aristeidis , Komodakis Nikos , Paragios Nikos
Published: March 2011

This review introduces a novel deformable image registration paradigm that exploits Markov random field formulation and powerful discrete optimization algorithms. We express deformable registration as a minimal cost graph problem, where nodes correspond to the deformation grid, a node's connectivity corresponds to regularization constraints, and labels correspond to 3D deformations. To cope with both iconic and geometric (landmark-based) registration, we introduce two graphical models, one for each subproblem. The two graphs share interconnected variables, leading to a modular, powerful, and flexible formulation that can account for arbitrary image-matching criteria, various local deformation models, and regularization constraints. To cope with the corresponding optimization problem, we adopt two optimization strategies: a computationally efficient one and a tight relaxation alternative. Promising results demonstrate the potential of this approach. Discrete methods are an important new trend in medical image registration, as they provide several improvements over the more traditional continuous methods. This is illustrated with several key examples where the presented framework outperforms existing general-purpose registration methods in terms of both performance and computational complexity. Our methods become of particular interest in applications where computation time is a critical issue, as in intraoperative imaging, or where the huge variation in data demands complex and application-specific matching criteria, as in large-scale multimodal population studies.
How Do Control-Based Approaches Enter into Biology?
Authors: LeDuc Philip R , Messner William C. , Wikswo John P.
Published: March 2011

Control is intrinsic to biological organisms, whose cells are in a constant state of sensing and response to numerous external and self-generated stimuli. Diverse means are used to study the complexity through control-based approaches in these cellular systems, including through chemical and genetic manipulations, input-output methodologies, feedback approaches, and feed-forward approaches. We first discuss what happens in control-based approaches when we are not actively examining or manipulating cells. We then present potential methods to determine what the cell is doing during these times and to reverse-engineer the cellular system. Finally, we discuss how we can control the cell's extracellular and intracellular environments, both to probe the response of the cells using defined experimental engineering-based technologies and to anticipate what might be achieved by applying control-based approaches to affect cellular processes. Much work remains to apply simplified control models and develop new technologies to aid researchers in studying and utilizing cellular and molecular processes.
Bioengineering Heart Muscle: A Paradigm for Regenerative Medicine
Authors: Vunjak-Novakovic Gordana , Lui Kathy O. , Tandon Nina , Chien Kenneth R.
Published: March 2011

The idea of extending the lifetime of our organs is as old as humankind, fueled by major advances in organ transplantation, novel drugs, and medical devices. However, true regeneration of human tissue has become increasingly plausible only in recent years. The human heart has always been a focus of such efforts, given its notorious inability to repair itself following injury or disease. We discuss here the emerging bioengineering approaches to regeneration of heart muscle as a paradigm for regenerative medicine. Our focus is on biologically inspired strategies for heart regeneration, knowledge gained thus far about how to make a “perfect” heart graft, and the challenges that remain to be addressed for tissue-engineered heart regeneration to become a clinical reality. We emphasize the need for interdisciplinary research and training, as recent progress in the field is largely being made at the interfaces between cardiology, stem cell science, and bioengineering.
Nuclear Mechanics in Disease
Authors: Zwerger Monika , Ho Chin Yee , Lammerding Jan
Published: March 2011

Over the past two decades, the biomechanical properties of cells have emerged as key players in a broad range of cellular functions, including migration, proliferation, and differentiation. Although much of the attention has focused on the cytoskeletal networks and the cell's microenvironment, relatively little is known about the contribution of the cell nucleus. Here, we present an overview of the structural elements that determine the physical properties of the nucleus and discuss how changes in the expression of nuclear components or mutations in nuclear proteins can not only affect nuclear mechanics but also modulate cytoskeletal organization and diverse cellular functions. These findings illustrate that the nucleus is tightly integrated into the surrounding cellular structure. Consequently, changes in nuclear structure and composition are highly relevant to normal development and physiology and can contribute to many human diseases, such as muscular dystrophy, dilated cardiomyopathy, (premature) aging, and cancer.
Amphipols From A to Z
Authors: Popot J.-L. , Althoff T. , Bagnard D. , Banères J.-L. , Bazzacco P. , Billon-Denis E. , Catoire L.J. , Champeil P. , Charvolin D. , Cocco M.J. , Crémel G. , Dahmane T. , de la Maza L.M. , Ebel C. , Gabel F. , Giusti F. , Gohon Y. , Goormaghtigh E. , Guittet E. , Kleinschmidt J.H. , Kühlbrandt W. , Le Bon C. , Martinez K.L. , Picard M. , Pucci B. , Sachs J.N. , Tribet C. , van Heijenoort C. , Wien F. , Zito F. , Zoonens M.
Published: March 2011

Amphipols (APols) are short amphipathic polymers that can substitute for detergents to keep integral membrane proteins (MPs) water soluble. In this review, we discuss their structure and solution behavior; the way they associate with MPs; and the structure, dynamics, and solution properties of the resulting complexes. All MPs tested to date form water-soluble complexes with APols, and their biochemical stability is in general greatly improved compared with MPs in detergent solutions. The functionality and ligand-binding properties of APol-trapped MPs are reviewed, and the mechanisms by which APols stabilize MPs are discussed. Applications of APols include MP folding and cell-free synthesis, structural studies by NMR, electron microscopy and X-ray diffraction, APol-mediated immobilization of MPs onto solid supports, proteomics, delivery of MPs to preexisting membranes, and vaccine formulation.
Decision Making in Living Cells: Lessons from a Simple System
Authors: Golding Ido
Published: March 2011

The life cycle of bacteriophage lambda serves as a simplified paradigm for cell-fate decisions. The ongoing quantitative, high-resolution experimental investigation of this life cycle has produced some important insights in recent years. These insights have to do with the way cells choose among alternative fates, how they maintain long-term memory of their gene-expression state, and how they switch from one stable state to another. The recent studies have highlighted the role of spatiotemporal effects in cellular processes and the importance of distinguishing chemical stochasticity from possible hidden variables in cellular decision making.
Equilibrium Sampling in Biomolecular Simulations
Authors: Zuckerman Daniel M.
Published: March 2011

Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to parallelization to novel uses of hardware. Special focus is placed on classifying algorithms—most of which are underpinned by a few key ideas—in order to understand their fundamental strengths and limitations. Although algorithms have proliferated, progress resulting from novel hardware use appears to be more clear-cut than from algorithms alone, due partly to the lack of widely used sampling measures.
Kinesin Assembly and Movement in Cells
Authors: Verhey Kristen J. , Kaul Neha , Soppina Virupakshi
Published: March 2011

Long-distance transport in eukaryotic cells is driven by molecular motors that move along microtubule tracks. Molecular motors of the kinesin superfamily contain a kinesin motor domain attached to family-specific sequences for cargo binding, regulation, and oligomerization. The biochemical and biophysical properties of the kinesin motor domain have been widely studied, yet little is known about how kinesin motors work in the complex cellular environment. We discuss recent studies on the three major families involved in intracellular transport (kinesin-1, kinesin-2, and kinesin-3) that have begun to bridge the gap in knowledge between the in vitro and in vivo behaviors of kinesin motors. These studies have increased our understanding of how kinesin subunits assemble to produce a functional motor, how kinesin motors are affected by biochemical cues and obstacles present on cellular microtubules, and how multiple motors on a cargo surface can work collectively for increased force production and travel distance.
Nucleosome Structure(s) and Stability: Variations on a Theme
Authors: Andrews Andrew J. , Luger Karolin
Published: March 2011

Chromatin is a highly regulated, modular nucleoprotein complex that is central to many processes in eukaryotes. The organization of DNA into nucleosomes and higher-order structures has profound implications for DNA accessibility. Alternative structural states of the nucleosome, and the thermodynamic parameters governing its assembly and disassembly, need to be considered in order to understand how access to nucleosomal DNA is regulated. In this review, we provide a brief historical account of how the overriding perception regarding aspects of nucleosome structure has changed over the past thirty years. We discuss recent technical advances regarding nucleosome structure and its physical characterization and review the evidence for alternative nucleosome conformations and their implications for nucleosome and chromatin dynamics.
Protein Self-Organization: Lessons from the Min System
Authors: Loose Martin , Kruse Karsten , Schwille Petra
Published: March 2011

One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell.
Respice, Adspice, and Prospice
Authors: Scheraga Harold A.
Published: March 2011

The title, “Look to the past, Look to the present, and Look to the future,” the motto of City College of New York, expresses how my family life and education led me to an academic career in physical chemistry and ultimately to a study of proteins. The economic depression of the 1930s left a lasting impression on my outlook and career aspirations. With fortunate experiences at several stages in my life, I was able to participate in the great adventure of the last half of the twentieth century: the revolution in biology that advanced the field of protein chemistry to so great an extent. The future is bright and limitless, with greater understanding of biology yet to come.
Stochastic Conformational Pumping: A Mechanism for Free-Energy Transduction by Molecules
Authors: Astumian R. Dean
Published: March 2011

Proteins and other macromolecules can act as molecular machines that convert energy from one form to another through cycles of conformational transitions. In a macroscopically fluctuating environment or at the single-molecule level, the probability for a molecule to be in any state j fluctuates, and the probability current from any other state i to state j is given as the sum of a steady-state current and a pumped current, Iij=Issij+FijdPj/dt, where Fij is the fraction of the fluctuating current into and out of state j coming directly from state i, and dPj/dt is the rate of change of the probability for the molecule to be in state j. If the fluctuations arise from an equilibrium source, microscopic reversibility guarantees that the time average of the pumped current is zero. If, however, the fluctuations arise due to the action of a nonequilibrium source, the time average of the pumped current is not in general zero and can be opposite in sign to the steady-state current. The pumped current provides a mechanism by which fluctuations, whether generated externally or arising from an internal nonequilibrium chemical reaction, can do electrical, mechanical, or chemical work on a system by coupling into the equilibrium conformational transitions of a protein. In this review I examine work elaborating the mechanism of stochastic pumping and also discuss a thermodynamically consistent approach for modeling the effects of dynamic disorder on enzymes and other proteins.
Actin Structure and Function
Authors: Dominguez Roberto , Holmes Kenneth C.
Published: March 2011

Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. These properties, along with its ability to transition between monomeric (G-actin) and filamentous (F-actin) states under the control of nucleotide hydrolysis, ions, and a large number of actin-binding proteins, make actin a critical player in many cellular functions, ranging from cell motility and the maintenance of cell shape and polarity to the regulation of transcription. Moreover, the interaction of filamentous actin with myosin forms the basis of muscle contraction. Owing to its central role in the cell, the actin cytoskeleton is also disrupted or taken over by numerous pathogens. Here we review structures of G-actin and F-actin and discuss some of the interactions that control the polymerization and disassembly of actin.
Battery Technologies for Large-Scale Stationary Energy Storage
Authors: Soloveichik Grigorii L.
Published: March 2011

In recent years, with the deployment of renewable energy sources, advances in electrified transportation, and development in smart grids, the markets for large-scale stationary energy storage have grown rapidly. Electrochemical energy storage methods are strong candidate solutions due to their high energy density, flexibility, and scalability. This review provides an overview of mature and emerging technologies for secondary and redox flow batteries. New developments in the chemistry of secondary and flow batteries as well as regenerative fuel cells are also considered. Advantages and disadvantages of current and prospective electrochemical energy storage options are discussed. The most promising technologies in the short term are high-temperature sodium batteries with β″-alumina electrolyte, lithium-ion batteries, and flow batteries. Regenerative fuel cells and lithium metal batteries with high energy density require further research to become practical.
Low–Dielectric Constant Insulators for Future Integrated Circuits and Packages
Authors: Kohl Paul A.
Published: March 2011

Future integrated circuits and packages will require extraordinary dielectric materials for interconnects to allow transistor advances to be translated into system-level advances. Exceedingly low-permittivity and low-loss materials are required at every level of the electronic system, from chip-level insulators to packages and printed wiring boards. In this review, the requirements and goals for future insulators are discussed followed by a summary of current state-of-the-art materials and technical approaches. Much work needs to be done for insulating materials and structures to meet future needs.