Reports on Progress in Physics

Published by IOP Publishing
Online ISSN: 1361-6633
Publications
Article
Defects are usually seen as imperfections in materials that could significantly degrade their performance. However, at the nanoscale, defects could be extremely useful since they could be exploited to generate novel, innovative and useful materials and devices. Graphene and graphene nanoribbons are no exception. This review therefore tries to categorize defects, emphasize their importance, introduce the common routes to study and identify them and to propose new ways to construct novel devices based on 'defective' graphene-like materials. In particular, we will discuss defects in graphene-like systems including (a) structural (sp(2)-like) defects, (b) topological (sp(2)-like) defects, (c) doping or functionalization (sp(2)- and sp(3)-like) defects and (d) vacancies/edge type defects (non-sp(2)-like). It will be demonstrated that defects play a key role in graphene physicochemical properties and could even be critical to generate biocompatible materials. There are numerous challenges in this emerging field, and we intend to provide a stimulating account which could trigger new science and technological developments based on defective graphene-like materials that could be introduced into other atomic layered materials, such as BN, MoS(2) and WS(2), not discussed in this review.
 
Article
Imaging the Universe during the first hundreds of millions of years remains one of the exciting challenges facing modern cosmology. Observations of the redshifted 21 cm line of atomic hydrogen offer the potential of opening a new window into this epoch. This will transform our understanding of the formation of the first stars and galaxies and of the thermal history of the Universe. A new generation of radio telescopes is being constructed for this purpose with the first results starting to trickle in. In this review, we detail the physics that governs the 21 cm signal and describe what might be learnt from upcoming observations. We also generalize our discussion to intensity mapping of other atomic and molecular lines.
 
Article
Laser ablation of dielectrics by ultrashort laser pulses is reviewed. The basic interaction between ultrashort light pulses and the dielectric material is described, and different approaches to the modeling of the femtosecond ablation dynamics are reviewed. Material excitation by ultrashort laser pulses is induced by a combination of strong-field excitation (multi-photon and tunnel excitation), collisional excitation (potentially leading to an avalanche process), and absorption in the plasma consisting of the electrons excited to the conduction band. It is discussed how these excitation processes can be described by various rate-equation models in combination with different descriptions of the excited electrons. The optical properties of the highly excited dielectric undergo a rapid change during the laser pulse, which must be included in a detailed modeling of the excitations. The material ejected from the dielectric following the femtosecond-laser excitation can potentially be used for thin-film deposition. The deposition rate is typically much smaller than that for nanosecond lasers, but film production by femtosecond lasers does possess several attractive features. First, the strong-field excitation makes it possible to produce films of materials that are transparent to the laser light. Second, the highly localized excitation reduces the emission of larger material particulates. Third, lasers with ultrashort pulses are shown to be particularly useful tools for the production of nanocluster films. The important question of the film stoichiometry relative to that of the target will be thoroughly discussed in relation to the films reported in the literature.
 
Article
This review discusses the recent studies of magnetization dynamics and the role of angular momentum in thin films of ferrimagnetic rare-earth–transition metal (RE–TM) alloys, e.g. GdFeCo, where both magnetization and angular momenta are temperature dependent. It has been experimentally demonstrated that the magnetization can be manipulated and even reversed by a single 40 fs laser pulse, without any applied magnetic field. This switching is found to follow a novel reversal pathway, that is shown however to depend crucially on the net angular momentum, reflecting the balance of the two opposite sublattices. In particular, optical excitation of ferrimagnetic GdFeCo on a time scale pertinent to the characteristic time of the exchange interaction between the RE and TM spins, i.e. on the time scale of tens of femtoseconds, pushes the spin dynamics into a yet unexplored regime, where the two exchange-coupled magnetic sublattices demonstrate substantially different dynamics. As a result, the reversal of spins appears to proceed via a novel transient state characterized by a ferromagnetic alignment of the Gd and Fe magnetic moments, despite their ground-state antiferromagnetic coupling. Thus, optical manipulation of magnetic order by femtosecond laser pulses has developed into an exciting and still expanding research field that keeps being fueled by a continuous stream of new and sometimes counterintuitive results. Considering the progress in the development of plasmonic antennas and compact ultrafast lasers, optical control of magnetic order may also potentially revolutionize data storage and information processing technologies.
 
Article
The measurement of the Planck constant, h, is entering a new phase. The CODATA 2010 recommended value is 6.626 069 57 × 10(-34) J s, but it has been a long road, and the trip is not over yet. Since its discovery as a fundamental physical constant to explain various effects in quantum theory, h has become especially important in defining standards for electrical measurements and soon, for mass determination. Measuring h in the International System of Units (SI) started as experimental attempts merely to prove its existence. Many decades passed while newer experiments measured physical effects that were the influence of h combined with other physical constants: elementary charge, e, and the Avogadro constant, N(A). As experimental techniques improved, the precision of the value of h expanded. When the Josephson and quantum Hall theories led to new electronic devices, and a hundred year old experiment, the absolute ampere, was altered into a watt balance, h not only became vital in definitions for the volt and ohm units, but suddenly it could be measured directly and even more accurately. Finally, as measurement uncertainties now approach a few parts in 10(8) from the watt balance experiments and Avogadro determinations, its importance has been linked to a proposed redefinition of a kilogram unit of mass.The path to higher accuracy in measuring the value of h was not always an example of continuous progress. Since new measurements periodically led to changes in its accepted value and the corresponding SI units, it is helpful to see why there were bumps in the road and where the different branch lines of research joined in the effort. Recalling the bumps along this road will hopefully avoid their repetition in the upcoming SI redefinition debates. This paper begins with a brief history of the methods to measure a combination of fundamental constants, thus indirectly obtaining the Planck constant. The historical path is followed in the section describing how the improved techniques and discoveries in quantum mechanics steadily reduced the uncertainty of h. The central part of this review describes the technical details of the watt balance technique, which is a combination of the mechanical and electronic measurements that now determine h as a direct result, i.e. not requiring measured values of additional fundamental constants. The first technical section describes the basics and some of the common details of many watt balance designs. Next is a review of the ongoing advances at the (currently) seven national metrology institutions where these experiments are pursued. A final summary of the recent h determinations of the last two decades shows how history keeps repeating itself; there is again a question of whether there is a shift in the newest results, albeit at uncertainties that are many orders of magnitude less than the original experiments. The conclusion is that there is room for further development to resolve these differences and find new ideas for a watt balance system with a more universal application. Since the next generation of watt balance experiments are expected to become kilogram realization standards, the historical record suggests that there is yet a need for proof that Planck constant results are finally reproducible at an acceptable uncertainty.
 
Article
The minimal structural unit that defines living organisms is a single cell. By proliferating and mechanically interacting with each other, cells can build complex organization such as tissues that ultimately organize into even more complex multicellular living organisms, such as mammals, composed of billions of single cells interacting with each other. As opposed to passive materials, living cells actively respond to the mechanical perturbations occurring in their environment. Tissue cell adhesion to its surrounding extracellular matrix or to neighbors is an example of a biological process that adapts to physical cues. The adhesion of tissue cells to their surrounding medium induces the generation of intracellular contraction forces whose amplitude adapts to the mechanical properties of the environment. In turn, solicitation of adhering cells with physical forces, such as blood flow shearing the layer of endothelial cells in the lumen of arteries, reinforces cell adhesion and impacts cell contractility. In biological terms, the sensing of physical signals is transduced into biochemical signaling events that guide cellular responses such as cell differentiation, cell growth and cell death. Regarding the biological and developmental consequences of cell adaptation to mechanical perturbations, understanding mechanotransduction in tissue cell adhesion appears as an important step in numerous fields of biology, such as cancer, regenerative medicine or tissue bioengineering for instance. Physicists were first tempted to view cell adhesion as the wetting transition of a soft bag having a complex, adhesive interaction with the surface. But surprising responses of tissue cell adhesion to mechanical cues challenged this view. This, however, did not exclude that cell adhesion could be understood in physical terms. It meant that new models and descriptions had to be created specifically for these biological issues, and could not straightforwardly be adapted from dead matter. In this review, we present physical concepts of tissue cell adhesion and the unexpected cellular responses to mechanical cues such as external forces and stiffness sensing. We show how biophysical approaches, both experimentally and theoretically, have contributed to our understanding of the regulation of cellular functions through physical force sensing mechanisms. Finally, we discuss the different physical models that could explain how tissue cell adhesion and force sensing can be coupled to internal mechanosensitive processes within the cell body.
 
Article
We review some of the recent progress in our understanding of the physics of ultrarelativistic heavy ion collisions due to applications of AdS/CFT correspondence.
 
Article
An emerging theme in modern astrophysics is the connection between astronomical observations and the underlying physical phenomena that drive our cosmos. Both the mechanisms responsible for the observed astrophysical phenomena and the tools used to probe such phenomena-the radiation and particle spectra we observe-have their roots in atomic, molecular, condensed matter, plasma, nuclear and particle physics. Chemistry is implicitly included in both molecular and condensed matter physics. This connection is the theme of the present report, which provides a broad, though non-exhaustive, overview of progress in our understanding of the cosmos resulting from recent theoretical and experimental advances in what is commonly called laboratory astrophysics. This work, carried out by a diverse community of laboratory astrophysicists, is increasingly important as astrophysics transitions into an era of precise measurement and high fidelity modeling.
 
Article
Solitons, nonlinear self-trapped wavepackets, have been extensively studied in many and diverse branches of physics such as optics, plasmas, condensed matter physics, fluid mechanics, particle physics and even astrophysics. Interestingly, over the past two decades, the field of solitons and related nonlinear phenomena has been substantially advanced and enriched by research and discoveries in nonlinear optics. While optical solitons have been vigorously investigated in both spatial and temporal domains, it is now fair to say that much soliton research has been mainly driven by the work on optical spatial solitons. This is partly due to the fact that although temporal solitons as realized in fiber optic systems are fundamentally one-dimensional entities, the high dimensionality associated with their spatial counterparts has opened up altogether new scientific possibilities in soliton research. Another reason is related to the response time of the nonlinearity. Unlike temporal optical solitons, spatial solitons have been realized by employing a variety of noninstantaneous nonlinearities, ranging from the nonlinearities in photorefractive materials and liquid crystals to the nonlinearities mediated by the thermal effect, thermophoresis and the gradient force in colloidal suspensions. Such a diversity of nonlinear effects has given rise to numerous soliton phenomena that could otherwise not be envisioned, because for decades scientists were of the mindset that solitons must strictly be the exact solutions of the cubic nonlinear Schrödinger equation as established for ideal Kerr nonlinear media. As such, the discoveries of optical spatial solitons in different systems and associated new phenomena have stimulated broad interest in soliton research. In particular, the study of incoherent solitons and discrete spatial solitons in optical periodic media not only led to advances in our understanding of fundamental processes in nonlinear optics and photonics, but also had a very important impact on a variety of other disciplines in nonlinear science. In this paper, we provide a brief overview of optical spatial solitons. This review will cover a variety of issues pertaining to self-trapped waves supported by different types of nonlinearities, as well as various families of spatial solitons such as optical lattice solitons and surface solitons. Recent developments in the area of optical spatial solitons, such as 3D light bullets, subwavelength solitons, self-trapping in soft condensed matter and spatial solitons in systems with parity-time symmetry will also be discussed briefly.
 
Article
The aggregation of proteins is of fundamental relevance in a number of daily phenomena, as important and diverse as blood coagulation, medical diseases, or cooking an egg in the kitchen. Colloidal food systems, in particular, are examples that have great significance for protein aggregation, not only for their importance and implications, which touches on everyday life, but also because they allow the limits of the colloidal science analogy to be tested in a much broader window of conditions, such as pH, ionic strength, concentration and temperature. Thus, studying the aggregation and self-assembly of proteins in foods challenges our understanding of these complex systems from both the molecular and statistical physics perspectives. Last but not least, food offers a unique playground to study the aggregation of proteins in three, two and one dimensions, that is to say, in the bulk, at air/water and oil/water interfaces and in protein fibrillation phenomena. In this review we will tackle this very ambitious task in order to discuss the current understanding of protein aggregation in the framework of foods, which is possibly one of the broadest contexts, yet is of tremendous daily relevance.
 
Article
Topological insulators (TIs) have an insulating bulk but a metallic surface. In the simplest case, the surface electronic structure of a three-dimensional (3D) TI is described by a single two-dimensional (2D) Dirac cone. A single 2D Dirac fermion cannot be realized in an isolated 2D system with time-reversal symmetry, but rather owes its existence to the topological properties of the 3D bulk wavefunctions. The transport properties of such a surface state are of considerable current interest; they have some similarities with graphene, which also realizes Dirac fermions, but have several unique features in their response to magnetic fields. In this review we give an overview of some of the main quantum transport properties of TI surfaces. We focus on the efforts to use quantum interference phenomena, such as weak anti-localization and the Aharonov-Bohm effect, to verify in a transport experiment the Dirac nature of the surface state and its defining properties. In addition to explaining the basic ideas and predictions of the theory, we provide a survey of recent experimental work.
 
Article
The past decade has seen an explosive increase in the number of peer reviewed papers reporting new scientific findings in geomorphology (including fans, channels, floodplains and landscape evolution), geologic mapping, tectonics and faulting, coastal processes, lava flows, hydrology (especially snow and runoff routing), glaciers and geo-archaeology. A common genesis of such findings is often newly available decimeter resolution 'bare Earth' geodetic images, derived from airborne laser swath mapping, a.k.a. airborne LiDAR, observations. In this paper we trace nearly a half century of advances in geodetic science made possible by space age technology, such as the invention of short-pulse-length high-pulse-rate lasers, solid state inertial measurement units, chip-based high speed electronics and the GPS satellite navigation system, that today make it possible to map hundreds of square kilometers of terrain in hours, even in areas covered with dense vegetation or shallow water. To illustrate the impact of the LiDAR observations we present examples of geodetic images that are not only stunning to the eye, but help researchers to develop quantitative models explaining how terrain evolved to its present form, and how it will likely change with time. Airborne LiDAR technology continues to develop quickly, promising ever more scientific discoveries in the years ahead.
 
Article
The molecular mechanism of muscle contraction is one of the most important unresolved problems in biology and biophysics. Notwithstanding the great advances of recent years, it is not yet known in detail how the molecular motor in muscle, the class II myosin, converts the free energy of ATP hydrolysis into work by interacting with its track, the actin filament; neither is it understood how the high efficiency in energy conversion depends on the cooperative action of myosin motors working in parallel along the actin filament. Research in muscle contraction involves the combination of mechanical, biochemical and structural methods in studies that span from tissue to single molecule. Therefore, more than for any other research field, progress in the comprehension of muscle contraction at the molecular level is related to, and in turn contributes to, the advancement of methods in biophysics. This review will focus on the progress achieved by time-resolved small angle x-ray scattering (SAXS) from muscle, an approach made possible by the highly ordered arrangement of both the contractile proteins myosin and actin in the ca 2 µm long structural unit, the sarcomere, that repeats along the whole length of the muscle cell. Among time-resolved structural techniques, SAXS has proved to be the most powerful method of investigation, as it allows the molecular motor to be studied in situ, in intact single muscle cells, where it is possible to combine the structural study with fast mechanical methods that synchronize the action of the molecular motors. The latest development of this technique allows Angstrom-scale measurements of the axial movement of the motors that pull the actin filament towards the centre of the sarcomere, by exploiting the x-ray interference between the two arrays of myosin motors in the two halves of the sarcomere.
 
Article
The recently developed attosecond light sources make the investigation of ultrafast processes in matter possible with unprecedented time resolution. It has been proposed that the very mechanism underlying the attosecond emission allows the imaging of valence orbitals with Ångström space resolution. This controversial idea together with the possibility of combining attosecond and Ångström resolutions in the same measurements has become a hot topic in strong-field science. Indeed, this could provide a new way to image the evolution of the molecular electron cloud during, e.g. a chemical reaction in 'real time'. Here we review both experimental and theoretical challenges raised by the implementation of these prospects. In particular, we show how the valence orbital structure is encoded in the spectral phase of the recombination dipole moment calculated for Coulomb scattering states, which allows a tomographic reconstruction of the orbital using first-order corrections to the plane-wave approach. The possibility of disentangling multi-channel contributions to the attosecond emission is discussed as well as the necessary compromise between the temporal and spatial resolutions.
 
Article
The Helfand-Werthamer (HW) scheme (Helfand and Werthamer 1966 Phys. Rev. 147 288; another part of this work published as a separate paper by Werthamer et al 1966 Phys. Rev. 147 295) of evaluating the orbital upper critical field is generalized to anisotropic superconductors in general, and to two-band clean materials, in particular. Our formal procedure differs from those in the literature; it reproduces not only the isotropic HW limit but also the results of calculations for the two-band superconducting MgB(2) (Miranović et al 2003 J. Phys. Soc. Japan 72 221, Dahm and Schopohl 2003 Phys. Rev. Lett. 91 017001) along with the existing data on H(c2)(T) and its anisotropy γ(T) = H(c2,ab)(T)/H(c2,c)(T) (a, c are the principal directions of a uniaxial crystal). Using rotational ellipsoids as model Fermi surfaces we apply the formalism developed to study γ(T) for a few different anisotropies of the Fermi surface and of the order parameters. We find that even for a single band d-wave order parameter γ(T) decreases on warming; however, relatively weakly. For order parameters of the form Δ(k(z)) = Δ(0)(1 + η cos k(z)a) (Xu et al 2011 Nature Phys. 7 198), according to our simulations γ(T) may either increase or decrease on warming even for a single band depending on the sign of η. Hence, the common belief that the multi-band Fermi surface is responsible for the temperature variation of γ is proven incorrect. For two s-wave gaps, γ decreases on warming for all Fermi shapes examined. For two order parameters of the form Δ(k(z)) = Δ(0)(1 + η cos k(z)a), presumably relevant for pnictides, we obtain γ(T) increasing on warming provided both η(1) and η(2) are negative, whereas for η > 0, γ(T) decreases. We study the ratio of the two order parameters at H(c2)(T) and find that the ratio of the small gap to the large one does not vanish at any temperature, even at H(c2)(T), an indication that this does not happen at lower fields.
 
Article
The theoretical description of the anomalous properties of the pseudogap phase in the underdoped region of the cuprate phase diagram lags behind the progress in spectroscopic and other experiments. A phenomenological ansatz, based on analogies to the approach to Mott localization at weak coupling in lower dimensional systems, has been proposed by Yang et al (2006 Phys. Rev. B 73 174501). This ansatz has had success in describing a range of experiments. The motivation underlying this ansatz is described and the comparisons with experiment are reviewed. Implications for a more microscopic theory are discussed together with the relation to theories that start directly from microscopic strongly coupled Hamiltonians.
 
Article
A ubiquitous observation in cell biology is that diffusion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarising their densely packed and heterogeneous structures. The most familiar phenomenon is a power-law increase of the MSD, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations, non-gaussian distributions of the displacements, heterogeneous diffusion, and immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarise some widely used theoretical models: gaussian models like FBM and Langevin equations for visco-elastic media, the CTRW model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Emphasis is put on the spatio-temporal properties of the transport in terms of 2-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even for identical MSDs. Then, we review the theory underlying common experimental techniques in the presence of anomalous transport: single-particle tracking, FCS, and FRAP. We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where model systems mimic physiological crowding conditions. Finally, computer simulations play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.
 
Article
In this work we consider the role of aperiodic order-order without periodicity-in the design of different optical devices in one, two and three dimensions. To this end, we will first study devices based on aperiodic multilayered structures. In many instances the recourse to Fibonacci, Thue-Morse or fractal arrangements of layers results in improved optical properties compared with their periodic counterparts. On this basis, the possibility of constructing optical devices based on a modular design of the multilayered structure, where periodic and quasiperiodic subunits are properly mixed, is analyzed, illustrating how this additional degree of freedom enhances the optical performance in some specific applications. This line of thought can be naturally extended to aperiodic arrangements of optical elements, such as nanospheres or dielectric rods in the plane, as well as to three-dimensional photonic quasicrystals based on polymer materials. In this way, plentiful possibilities for new tailored materials naturally appear, generally following suitable optimization algorithms. Then, we present a detailed discussion on the physical properties supporting the preferential use of aperiodic devices in a number of optical applications, opening new avenues for technological innovation. Finally we suggest some related emerging topics that deserve some attention in the years to come.
 
Article
Nanotechnology is touted as the next logical sequence in technological evolution. This has led to a substantial surge in research activities pertaining to the development and fundamental understanding of processes and assembly at the nanoscale. Both top-down and bottom-up fabrication approaches may be used to realize a range of well-defined nanostructured materials with desirable physical and chemical attributes. Among these, the bottom-up self-assembly process offers the most realistic solution toward the fabrication of next-generation functional materials and devices. Here, we present a comprehensive review on the physical basis behind self-assembly and the processes reported in recent years to direct the assembly of nanoscale functional blocks into hierarchically ordered structures. This paper emphasizes assembly in the synthetic domain as well in the biological domain, underscoring the importance of biomimetic approaches toward novel materials. In particular, two important classes of directed self-assembly, namely, (i) self-assembly among nanoparticle-polymer systems and (ii) external field-guided assembly are highlighted. The spontaneous self-assembling behavior observed in nature that leads to complex, multifunctional, hierarchical structures within biological systems is also discussed in this review. Recent research undertaken to synthesize hierarchically assembled functional materials have underscored the need as well as the benefits harvested in synergistically combining top-down fabrication methods with bottom-up self-assembly.
 
Article
Archaeometallurgy is an important field of study which allows us to assess the quality and value of ancient metal artifacts and better understand the ancient cultures that made them. Scientific investigation of ancient metal artifacts is often necessary due to their lack of well-documented histories. One important requirement of analytical techniques is that they be non-destructive, since many of these artifacts are unique and irreplaceable. Most synchrotron radiation (SR) techniques meet this requirement. In this review, the characteristics, capabilities, and advantages and disadvantages of current and future SR facilities are discussed. I examine the application of SR techniques such as x-ray imaging (radiography/microscopy and tomography), x-ray diffraction, x-ray fluorescence, x-ray spectroscopy, Fourier transform infrared spectroscopy, and lastly combined SR techniques to the field of archaeometallurgy. Previous case studies using these various SR techniques are discussed and potential future SR techniques are addressed.
 
Article
This article overviews topological excitations in spinor Bose-Einstein condensates of dilute atomic gases. Various types of line defects, point defects and skyrmions are discussed. A brief review of homotopy theory is presented for use in the classification of possible topological excitations in individual quantum phases. Some recent experiments are also reviewed.
 
Article
Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to 'see' individual atoms by means of imaging, but is also a tool that is used to 'touch' and 'take' the atoms, or to 'hear' their movements. Therefore, the STM can be considered as the 'eyes', 'hands' and 'ears' of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed.
 
Article
In this review we discuss recent research on driving self-assembly of magnetic particle suspensions subjected to alternating magnetic fields. The variety of structures and effects that can be induced in such systems is remarkably broad due to the large number of variables involved. The alternating field can be uniaxial, biaxial or triaxial, the particles can be spherical or anisometric, and the suspension can be dispersed throughout a volume or confined to a soft interface. In the simplest case the field drives the static or quasistatic assembly of unusual particle structures, such as sheets, networks and open-cell foams. More complex, emergent collective behaviors evolve in systems that can follow the time-dependent field vector. In these cases energy is continuously injected into the system and striking flow patterns and structures can arise. In fluid volumes these include the formation of advection and vortex lattices. At air-liquid and liquid-liquid interfaces striking dynamic particle assemblies emerge due to the particle-mediated coupling of the applied field to surface excitations. These out-of-equilibrium interface assemblies exhibit a number of remarkable phenomena, including self-propulsion and surface mixing. In addition to discussing various methods of driven self-assembly in magnetic suspensions, some of the remarkable properties of these novel materials are described.
 
Article
Certain classes of astrophysical objects, namely magnetars and central engines of supernovae and gamma-ray bursts (GRBs), are characterized by extreme physical conditions not encountered elsewhere in the Universe. In particular, they possess magnetic fields that exceed the critical quantum field of 44 teragauss. Figuring out how these complex ultra-magnetized systems work requires understanding various plasma processes, both small-scale kinetic and large-scale magnetohydrodynamic (MHD). However, an ultra-strong magnetic field modifies the underlying physics to such an extent that many relevant plasma-physical problems call for building QED-based relativistic quantum plasma physics. In this review, after describing the extreme astrophysical systems of interest and identifying the key relevant plasma-physical problems, we survey the recent progress in the development of such a theory. We discuss how a super-critical field modifies the properties of vacuum and matter and outline the basic theoretical framework for describing both non-relativistic and relativistic quantum plasmas. We then turn to astrophysical applications of relativistic QED plasma physics relevant to magnetar magnetospheres and central engines of supernovae and long GRBs. Specifically, we discuss propagation of light through a magnetar magnetosphere; large-scale MHD processes driving magnetar activity and GRB jet launching and propagation; energy-transport processes governing the thermodynamics of extreme plasma environments; micro-scale kinetic plasma processes important in the interaction of intense magnetospheric electric currents with a magnetar's surface; and magnetic reconnection of ultra-strong magnetic fields. Finally, we point out that future progress will require the development of numerical modeling capabilities.
 
Article
A small number of naturally occurring, proton-rich nuclides (the p-nuclei) cannot be made in the s- and r-processes. Their origin is not well understood. Massive stars can produce p-nuclei through photodisintegration of pre-existing intermediate and heavy nuclei. This so-called γ-process requires high stellar plasma temperatures and occurs mainly in explosive O/Ne burning during a core-collapse supernova. Although the γ-process in massive stars has been successful in producing a large range of p-nuclei, significant deficiencies remain. An increasing number of processes and sites has been studied in recent years in search of viable alternatives replacing or supplementing the massive star models. A large number of unstable nuclei, however, with only theoretically predicted reaction rates are included in the reaction network and thus the nuclear input may also bear considerable uncertainties. The current status of astrophysical models, nuclear input and observational constraints is reviewed. After an overview of currently discussed models, the focus is on the possibility to better constrain those models through different means. Meteoritic data not only provide the actual isotopic abundances of the p-nuclei but can also put constraints on the possible contribution of proton-rich nucleosynthesis. The main part of the review focuses on the nuclear uncertainties involved in the determination of the astrophysical reaction rates required for the extended reaction networks used in nucleosynthesis studies. Experimental approaches are discussed together with their necessary connection to theory, which is especially pronounced for reactions with intermediate and heavy nuclei in explosive nuclear burning, even close to stability.
 
Article
Measurements of high-energy photons from cosmic sources of nuclear radiation through ESA's INTEGRAL mission have advanced our knowledge: New data with high spectral resolution showed that characteristic gamma-ray lines from radioactive decays occur throughout the Galaxy, in its interstellar medium and from sources. Although the number of detected sources and often the significance of the astrophysical results remain modest, conclusions derived from this unique astronomical window of radiation originating from nuclear processes are important, complementing the widely-employed atomic-line based spectroscopy. We review the results and insights obtained in the past decade from gamma-ray line measurements of cosmic sources, in the context of their astrophysical questions.
 
Article
Few-body physics has played a prominent role in atomic, molecular and nuclear physics since the early days of quantum mechanics. It is now possible-thanks to tremendous progress in cooling, trapping and manipulating ultracold samples-to experimentally study few-body phenomena in trapped atomic and molecular systems with unprecedented control. This review summarizes recent studies of few-body phenomena in trapped atomic and molecular gases, with an emphasis on small trapped systems. We start by introducing the free-space scattering properties and then investigate what happens when two particles, bosons or fermions, are placed in an external confinement. Next, various three-body systems are treated analytically in limiting cases. Our current understanding of larger two-component Fermi systems and Bose systems is reviewed, and connections with the corresponding bulk systems are established. Lastly, future prospects and challenges are discussed. Throughout this review, commonalities with other systems such as nuclei or quantum dots are highlighted.
 
Article
Microbiology is the science of microbes, particularly bacteria. Many bacteria are motile: they are capable of self-propulsion. Among these, a significant class execute so-called run-and-tumble motion: they follow a fairly straight path for a certain distance, then abruptly change direction before repeating the process. This dynamics has something in common with Brownian motion (it is diffusive at large scales), and also something in contrast. Specifically, motility parameters such as the run speed and tumble rate depend on the local environment and hence can vary in space. When they do so, even if a steady state is reached, this is not generally invariant under time reversal: the principle of detailed balance, which restores the microscopic time-reversal symmetry of systems in thermal equilibrium, is mesoscopically absent in motile bacteria. This lack of detailed balance (allowed by the flux of chemical energy that drives motility) creates pitfalls for the unwary modeller. Here I review some statistical-mechanical models for bacterial motility, presenting them as a paradigm for exploring diffusion without detailed balance. I also discuss the extent to which statistical physics is useful in understanding real or potential microbiological experiments.
 
The protein MatP organizes the Ter macrodomain by specific binding. The circular chromosome of E. coli divided into 4 macrodomains and 2 non structured zones (see figure 1). (A) From (Mercier et al., 2008), ChIP-chip assays for MatP binding show a specific affinity of this protein with Ter macrodomains, indicating that the macrodomain is condensed by MatP, and suggesting that other macrodomains might be condensed by dedicated proteins with a small set of specific binding sites. (B) From (Mercier et al., 2008), the localization bias of MatP binding sites is conserved among enterobacteria, (S. typhimurium LT2 with genome size 4683 Kb, E. carotovora SCRI1043-5064 Kb), Vibrio (V. cholerae Cl 2-961 kbp ), and Pasteurella (Y. pestis KIM 4-600 kbp) species. (C) MatP controls DNA compaction in the Ter macrodomain. The histogram represents the proportion of cells with given interfocal distances between foci of two Ter MD markers in WT and matP deletion mutant cells. (D) Fluorescence microscopy images from the two experiments (scale bars 2µm). These results indicate that the effect of MatP on foci colocalization is associated with compaction. (A-D) reprinted from Mercier et al. (2008), c 2008, with permission from Elsevier.
Examples of high-throughput data an bioinformatic analyses concerning nucleoid organization (A) Left panel: ChIP-seq binding profile of H-NS, plotted using data from Kahramanoglou et al. (2011); right panel: sketch representing the extended protein occupancy domains detected by Vora et al. (2009). These are polymer-like nucleoprotein complexes, presumably related to nucleoid organization. (B) Chromosomal sectors emerge from the local correlation (plotted here) between expression levels for wild type in log-phase growth and a codon bias index, related to translation pressure (from Mathelier & Carbone (2010), reprinted by permission from Macmillan Publishers Ltd: Molecular Systems Biology, c 2010). These sectors correlate well with macrodomain organization. (C) Top panel: effective transcriptional regulatory network (red links) and areas of influence of Fis and H-NS (colored circles) obtained from transcriptomics experiments combining NAP mutants and perturbations in supercoiling background (from Marr et al. (2008), Reprinted by permission from BioMed Central, c 2008). Bottom panel: clusters of transcriptional response to nucleoid perturbations (left, data from Marr et al. (2008) and similar esperiments) and NAP binding (right) correlate with the organization of macrodomains (outer arcs) and chromosomal segments (inner arcs) of the genome (from Scolari et al. (2011), reproduced by permission of The Royal Society of Chemistry).
Article
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.
 
Article
Over the past quarter of a century the Arctic has warmed more than any other region on Earth, causing a profound impact on the Greenland ice sheet (GrIS) and its contribution to the rise in global sea level. The loss of ice can be partitioned into processes related to surface mass balance and to ice discharge, which are forced by internal or external (atmospheric/oceanic/basal) fluctuations. Regardless of the measurement method, observations over the last two decades show an increase in ice loss rate, associated with speeding up of glaciers and enhanced melting. However, both ice discharge and melt-induced mass losses exhibit rapid short-term fluctuations that, when extrapolated into the future, could yield erroneous long-term trends. In this paper we review the GrIS mass loss over more than a century by combining satellite altimetry, airborne altimetry, interferometry, aerial photographs and gravimetry data sets together with modelling studies. We revisit the mass loss of different sectors and show that they manifest quite different sensitivities to atmospheric and oceanic forcing. In addition, we discuss recent progress in constructing coupled ice-ocean-atmosphere models required to project realistic future sea-level changes.
 
Article
The composite nature of baryons manifests itself in the existence of a rich spectrum of excited states, in particular in the important mass region 1-2 GeV for the light-flavoured baryons. The properties of these resonances can be identified by systematic investigations using electromagnetic and strong probes, primarily with beams of electrons, photons, and pions. After decades of research, the fundamental degrees of freedom underlying the baryon excitation spectrum are still poorly understood. The search for hitherto undiscovered but predicted resonances continues at many laboratories around the world. Recent results from photo- and electroproduction experiments provide intriguing indications for new states and shed light on the structure of some of the known nucleon excitations. The continuing study of available data sets with consideration of new observables and improved analysis tools have also called into question some of the earlier findings in baryon spectroscopy. Other breakthrough measurements have been performed in the heavy-baryon sector, which has seen a fruitful period in recent years, in particular at the B factories and the Tevatron. First results from the large hadron collider indicate rapid progress in the field of bottom baryons. In this review, we discuss the recent experimental progress and give an overview of theoretical approaches.
 
A conceptual merit of the AdS/CFT correspondence, for a possible bridge between elementary particle physics, hadron physics and nuclear physics.  
The appearance of two kinds of matrices X and w. X connects baryon D-branes (depicted as two black blobs), while w connects a baryon D-brane and a flavor D-brane (depicted as three parallel sheets). w obtains nonzero VEV to satisfy the Gauss's law on each baryon D-brane, which is equivalent to N c open strings.  
A schematic picture of the baryon D-brane on the flavor D-brane. The harmonic oscillator excitation on the baryon D-brane is the size fluctuation ρ and the fluctuation of the D-brane location along the holographic direction X 4 . The horizontal direction is our space x 1 , x 2 , x 3 .  
A plot of a nuclear density inside the nucleus, calculated in AdS/CFT [10].  
NN potentials in quenched QCD at m π 730 MeV [4]. The spin singlet sector ( 1 S 0 ) belongs to the 27 representation while the triplet to the 10 * in the flavor SU(3).
Article
We provide, for non-experts, a brief overview of holographic QCD and a review of a recent proposal of matrix-description of multi-baryon systems in holographic QCD. Based on the matrix model, we derive the baryon interaction at short distances in multi-flavor holographic QCD. We show that there is a very universal repulsive core of inter-baryon forces for generic number of flavors. This is consistent with a recent lattice QCD analysis for N_f = 2, 3 where repulsive core looks universal. We also provide a comparison of our results with the lattice QCD and the operator product expansion (OPE) analysis.
 
Article
Quantum error correction (QEC) and fault-tolerant quantum computation represent one of the most vital theoretical aspects of quantum information processing. It was well known from the early developments of this exciting field that the fragility of coherent quantum systems would be a catastrophic obstacle to the development of large-scale quantum computers. The introduction of quantum error correction in 1995 showed that active techniques could be employed to mitigate this fatal problem. However, quantum error correction and fault-tolerant computation is now a much larger field and many new codes, techniques, and methodologies have been developed to implement error correction for large-scale quantum algorithms. In response, we have attempted to summarize the basic aspects of quantum error correction and fault-tolerance, not as a detailed guide, but rather as a basic introduction. The development in this area has been so pronounced that many in the field of quantum information, specifically researchers who are new to quantum information or people focused on the many other important issues in quantum computation, have found it difficult to keep up with the general formalisms and methodologies employed in this area. Rather than introducing these concepts from a rigorous mathematical and computer science framework, we instead examine error correction and fault-tolerance largely through detailed examples, which are more relevant to experimentalists today and in the near future.
 
Article
Neutrinoless double-beta decay, which is a very old and yet elusive process, is reviewed. Its observation will signal that the lepton number is not conserved and that the neutrinos are Majorana particles. More importantly it is our best hope for determining the absolute neutrino-mass scale at the level of a few tens of meV. To achieve the last goal certain hurdles must be overcome involving particle, nuclear and experimental physics.Nuclear physics is important for extracting useful information from the data. One must accurately evaluate the relevant nuclear matrix elements—a formidable task. To this end, we review the sophisticated nuclear structure approaches which have recently been developed, and which give confidence that the required nuclear matrix elements can be reliably calculated employing different methods: (a) the various versions of the quasiparticle random phase approximations, (b) the interacting boson model, (c) the energy density functional method and (d) the large basis interacting shell model. It is encouraging that, for the light neutrino-mass term at least, these vastly different approaches now give comparable results.From an experimental point of view it is challenging, since the life times are long and one has to fight against formidable backgrounds. One needs large isotopically enriched sources and detectors with high-energy resolution, low thresholds and very low background.If a signal is found, it will be a tremendous accomplishment. The real task then, of course, will be the extraction of the neutrino mass from the observations. This is not trivial, since current particle models predict the presence of many mechanisms other than the neutrino mass, which may contribute to or even dominate this process. In particular, we will consider the following processes: The neutrino induced, but neutrino-mass independent contribution.Heavy left and/or right-handed neutrino-mass contributions.Intermediate scalars (doubly charged, etc).Supersymmetric (SUSY) contributions. We will show that it is possible to disentangle the various mechanisms and unambiguously extract the important neutrino-mass scale, if all the signatures of the reaction are searched for in a sufficient number of nuclear isotopes.
 
Article
Metamaterials are rationally designed man-made structures composed of functional building blocks that are densely packed into an effective (crystalline) material. While metamaterials are mostly associated with negative refractive indices and invisibility cloaking in electromagnetism or optics, the deceptively simple metamaterial concept also applies to rather different areas such as thermodynamics, classical mechanics (including elastostatics, acoustics, fluid dynamics and elastodynamics), and, in principle, also to quantum mechanics. We review the basic concepts, analogies and differences to electromagnetism, and give an overview on the current state of the art regarding theory and experiment-all from the viewpoint of an experimentalist. This review includes homogeneous metamaterials as well as intentionally inhomogeneous metamaterial architectures designed by coordinate-transformation-based approaches analogous to transformation optics. Examples are laminates, transient thermal cloaks, thermal concentrators and inverters, 'space-coiling' metamaterials, anisotropic acoustic metamaterials, acoustic free-space and carpet cloaks, cloaks for gravitational surface waves, auxetic mechanical metamaterials, pentamode metamaterials ('meta-liquids'), mechanical metamaterials with negative dynamic mass density, negative dynamic bulk modulus, or negative phase velocity, seismic metamaterials, cloaks for flexural waves in thin plates and three-dimensional elastostatic cloaks.
 
Article
We review the electronic properties of bilayer graphene, beginning with a description of the tight-binding model of bilayer graphene and the derivation of the effective Hamiltonian describing massive chiral quasiparticles in two parabolic bands at low energies. We take into account five tight-binding parameters of the Slonczewski-Weiss-McClure model of bulk graphite plus intra- and interlayer asymmetry between atomic sites which induce band gaps in the low-energy spectrum. The Hartree model of screening and band-gap opening due to interlayer asymmetry in the presence of external gates is presented. The tight-binding model is used to describe optical and transport properties including the integer quantum Hall effect, and we also discuss orbital magnetism, phonons and the influence of strain on electronic properties. We conclude with an overview of electronic interaction effects.
 
The 'optical trapping interferometer' used by Svoboda et al [6] to measure, for the first time, a Kinesin molecule walking along a microtubule. It exploits the shearing interferometer used in DIC microscopy to create two overlapping, orthogonally polarized laser foci in the sample. This enables highly accurate one-dimensional force measurements.
Various interfaces for OTs: (a) a LabVIEW control program [80, 85], (b) a multitouch tablet [131], (c) a 3D force-feedback joystick [127, 128], 3D motion tracking of the user's fingertips (d) [130] and hands (e) [132], and a custom multitouch table [133]. Panel (e) courtesy of David McGloin.
Particles spin about their axes due to spin angular momentum, and feel a torque about the beam axis due to orbital angular momentum. OAM causes large particles (trapped on the beam axis) to spin, while smaller particles (trapped in the ring-shaped focus of the Laguerre-Gaussian beam in this figure) orbit around the beam axis [30].
Article
The phenomenon of light's momentum was first observed in the laboratory at the beginning of the twentieth century, and its potential for manipulating microscopic particles was demonstrated by Ashkin some 70 years later. Since that initial demonstration, and the seminal 1986 paper where a single-beam gradient-force trap was realized, optical trapping has been exploited as both a rich example of physical phenomena and a powerful tool for sensitive measurement. This review outlines the underlying theory of optical traps, and explores many of the physical observations that have been made in such systems. These phenomena include 'optical binding', where trapped objects interact with one another through the trapping light field. We also discuss a number of the applications of 'optical tweezers' across the physical and life sciences, as well as covering some of the issues involved in constructing and using such a tool.
 
Article
Microorganisms can form biofilms, which are multicellular communities surrounded by a hydrated extracellular matrix of polymers. Central properties of the biofilm are governed by this extracellular matrix, which provides mechanical stability to the 3D biofilm structure, regulates the ability of the biofilm to adhere to surfaces, and determines the ability of the biofilm to adsorb gases, solutes, and foreign cells. Despite their critical relevance for understanding and eliminating of biofilms, the materials properties of the extracellular matrix are understudied. Here, we offer the reader a guide to current technologies that can be utilized to specifically assess the permeability and mechanical properties of the biofilm matrix and its interacting components. In particular, we highlight technological advances in instrumentation and interactions between multiple disciplines that have broadened the spectrum of methods available to conduct these studies. We review pioneering work that furthers our understanding of the material properties of biofilms.
 
Article
DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement-including the effect of varying ionic strength-and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.
 
Article
Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics.
 
Article
Living organisms are made of cells that are capable of responding to external signals by modifying their internal state and subsequently their external environment. Revealing and understanding the spatio-temporal dynamics of these complex interaction networks is the subject of a field known as systems biology. To investigate these interactions (a necessary step before understanding or modelling them) one needs to develop means to control or interfere spatially and temporally with these processes and to monitor their response on a fast timescale (< minute) and with single-cell resolution. In 2012, an EMBO workshop on 'single-cell physiology' (organized by some of us) was held in Paris to discuss those issues in the light of recent developments that allow for precise spatio-temporal perturbations and observations. This review will be largely based on the investigations reported there. We will first present a non-exhaustive list of examples of cellular interactions and developmental pathways that could benefit from these new approaches. We will review some of the novel tools that have been developed for the observation of cellular activity and then discuss the recent breakthroughs in optical super-resolution microscopy that allow for optical observations beyond the diffraction limit. We will review the various means to photo-control the activity of biomolecules, which allow for local perturbations of physiological processes. We will end up this review with a report on the current status of optogenetics: the use of photo-sensitive DNA-encoded proteins as sensitive reporters and efficient actuators to perturb and monitor physiological processes.
 
Article
Precision measurement is a hallmark of physics but the small length scale (∼nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single-molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ∼0.3 nm precision at ∼1 ms time resolution, as well as how these new tools are providing fundamental insights into how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate the movements of multiple components. Finally, we will discuss recent progress in combining angstrom-precision optical tweezers with single-molecule fluorescent detection, opening new windows for multi-dimensional single-molecule nanometry for biological physics.
 
Article
Critical biological processes, such as synaptic plasticity and transmission, activation of genes by transcription factors, or double-strained DNA break repair, are controlled by diffusion in structures that have both large and small spatial scales. These may be small binding sites inside or on the surface of the cell, or narrow passages between subcellular compartments. The great disparity in spatial scales is the key to controlling cell function by structure. We report here recent progress on resolving analytical and numerical difficulties in extracting properties from experimental data, from biophysical models, and from Brownian dynamics simulations of diffusion in multi-scale structures. This progress is achieved by developing an analytical approximation methodology for solving the model equations. The reported results are applied to analysis and simulations of subcellular processes and to the quantification of their biological functions.
 
Article
Noise permeates biology on all levels, from the most basic molecular, sub-cellular processes to the dynamics of tissues, organs, organisms and populations. The functional roles of noise in biological processes can vary greatly. Along with standard, entropy-increasing effects of producing random mutations, diversifying phenotypes in isogenic populations, limiting information capacity of signaling relays, it occasionally plays more surprising constructive roles by accelerating the pace of evolution, providing selective advantage in dynamic environments, enhancing intracellular transport of biomolecules and increasing information capacity of signaling pathways. This short review covers the recent progress in understanding mechanisms and effects of fluctuations in biological systems of different scales and the basic approaches to their mathematical modeling.
 
Article
Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump-probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a 'diffract-and-destroy' mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.
 
Article
While the energy landscape theory of protein folding is now a widely accepted view for understanding how relatively weak molecular interactions lead to rapid and cooperative protein folding, such a framework must be extended to describe the large-scale functional motions observed in molecular machines. In this review, we discuss (1) the development of the energy landscape theory of biomolecular folding, (2) recent advances toward establishing a consistent understanding of folding and function and (3) emerging themes in the functional motions of enzymes, biomolecular motors and other biomolecular machines. Recent theoretical, computational and experimental lines of investigation have provided a very dynamic picture of biomolecular motion. In contrast to earlier ideas, where molecular machines were thought to function similarly to macroscopic machines, with rigid components that move along a few degrees of freedom in a deterministic fashion, biomolecular complexes are only marginally stable. Since the stabilizing contribution of each atomic interaction is on the order of the thermal fluctuations in solution, the rigid body description of molecular function must be revisited. An emerging theme is that functional motions encompass order-disorder transitions and structural flexibility provides significant contributions to the free energy. In this review, we describe the biological importance of order-disorder transitions and discuss the statistical-mechanical foundation of theoretical approaches that can characterize such transitions.
 
Article
Over the past couple of decades there has been a tremendous amount of progress on the development of ultrasensitive nanomechanical instruments, which has enabled scientists to peer for the first time into the mechanical world of biomolecular systems. Currently, work-horse instruments such as the atomic force microscope and optical/magnetic tweezers have provided the resolution necessary to extract quantitative force data from various molecular systems down to the femtonewton range, but it remains difficult to access the intracellular environment with these analytical tools as they have fairly large sizes and complicated feedback systems. This review is focused on highlighting some of the major milestones and discoveries in the field of biomolecular mechanics that have been made possible by the development of advanced atomic force microscope and tweezer techniques as well as on introducing emerging state-of-the-art nanomechanical force transducers that are addressing the size limitations presented by these standard tools. We will first briefly cover the basic setup and operation of these instruments, and then focus heavily on summarizing advances in in vitro force studies at both the molecular and cellular level. The last part of this review will include strategies for shrinking down the size of force transducers and provide insight into why this may be important for gaining a more complete understanding of cellular activity and function.
 
Article
Polymers with their tunable functionalities offer the ability to rationally design micro- and nano-engineered materials. Their synthesis as thin films have significant advantages due to the reduced amounts of materials used, faster processing times and the ability to modify the surface while preserving the structural properties of the bulk. Furthermore, their low cost, ease of fabrication and the ability to be easily integrated into processing lines, make them attractive alternatives to their inorganic thin film counterparts. Chemical vapor deposition (CVD) as a polymer thin-film deposition technique offers a versatile platform for fabrication of a wide range of polymer thin films preserving all the functionalities. Solventless, vapor-phase deposition enable the integration of polymer thin films or nanostructures into micro- and nanodevices for improved performance. In this review, CVD of functional polymer thin films and the polymerization mechanisms are introduced. The properties of the polymer thin films that determine their behavior are discussed and their technological advances and applications are reviewed.
 
Article
The existence of massive black holes (MBHs) was postulated in the 1960s, when the first quasars were discovered. In the late 1990s their reality was proven beyond doubt in the Milky way and a handful nearby galaxies. Since then, enormous theoretical and observational efforts have been made to understand the astrophysics of MBHs. We have discovered that some of the most massive black holes known, weighing billions of solar masses, powered luminous quasars within the first billion years of the Universe. The first MBHs must therefore have formed around the time the first stars and galaxies formed. Dynamical evidence also indicates that black holes with masses of millions to billions of solar masses ordinarily dwell in the centers of today's galaxies. MBHs populate galaxy centers today, and shone as quasars in the past; the quiescent black holes that we detect now in nearby bulges are the dormant remnants of this fiery past. In this review we report on basic, but critical, questions regarding the cosmological significance of MBHs. What physical mechanisms led to the formation of the first MBHs? How massive were the initial MBH seeds? When and where did they form? How is the growth of black holes linked to that of their host galaxy? The answers to most of these questions are works in progress, in the spirit of these reports on progress in physics.
 
Article
The transport of sand and dust by wind is a potent erosional force, creates sand dunes and ripples, and loads the atmosphere with suspended dust aerosols. This paper presents an extensive review of the physics of wind-blown sand and dust on Earth and Mars. Specifically, we review the physics of aeolian saltation, the formation and development of sand dunes and ripples, the physics of dust aerosol emission, the weather phenomena that trigger dust storms, and the lifting of dust by dust devils and other small-scale vortices. We also discuss the physics of wind-blown sand and dune formation on Venus and Titan.
 
Top-cited authors
Leon Balents
  • University of California, Santa Barbara
Felix Höfling
  • Freie Universität Berlin
Thomas Franosch
  • Friedrich-Alexander-University of Erlangen-Nürnberg
Din Ping Tsai
  • Academia Sinica
Ru-Shi Liu
  • National Taiwan University