Microscopic World Research Articles

Observation of a persistent non-equilibrium state in cold atoms

Well before the atomistic nature of matter was experimentally established, Ludwig Boltzmann's audacious effort to explain the macroscopic world of human experience in terms of the workings of an unseen microscopic world met with vigorous opposition. A contentious point was the problem of irreversibility: the microscopic equations of motion are reversible, yet friction and viscosity cause things always to slow down and warm up, never to speed up and cool down. What was worse, Boltzmann himself discovered that his transport equation predicts special cases in which gases never come to thermal equilibrium, a particular example being that the monopole "breathe" mode of gas will never damp if it is confined in 3D to a perfectly isotropic harmonic potential. Such absences of damping were not observed in nature. Nondamping of a monopole mode in lower dimensional systems has only very recently been observed, using cold atoms. Kinoshita et al. and Chevy et al. have experimentally observed suppressed relaxation in highly elongated geometries. The difficulty in generating sufficiently spherical harmonic confinement for ultracold atoms, however, has meant that Boltzmann's fully 3D, isotropic case has never been observed. With the development of a new magnetic trap capable of producing near-spherical harmonic confinement for ultracold atoms, we have been able to make the first observation of this historically significant oddity. We observe a monopole mode for which the collisional contribution to damping vanishes, a long-delayed vindication for Boltzmann's microscopic theory.

Deciphering the Mechanism Involved in the Switch On/Off of Molecular Pistons

AbstractManufacturing machines converting energy to mechanical work at the molecular level is a vital pathway to explore the microscopic world. A kind of operable molecular engines, composed of β‐cyclodextrin (β‐CD), aryl, alkene and amide moiety was investigated using molecular dynamics simulations combined with free‐energy calculations. To understand how the integrated alkene double bond controls the work performed on the engines, two alkene isomers of the prototype were considered as two molecular engines. The free‐energy profiles delineating the binding process of the amide (Z)‐ and (E)‐isomers for each alkene isomer with 1‐adamantanol indicate that for the alkene (E)‐isomer, the apparent work performed on the amide bond is 1.6 kcal/mol, while the alkene (Z)‐isomer is incapable to perform work. Direct switch on/off of engines caused by the isomerization of the alkene bond was, therefore, witnessed, in line with experimental measurements. Decomposition of the free‐energy profile into different components and structural analyses suggest that the isomerization of the alkene bond controls the position of the aryl unit relative to the cavity of the CD, resulting in the difference among the free‐energy profiles and the stark contrast of the work performed on engines.

Those Wonderful Pioneer Years of SSRL: A Personal Reflection

It is a rare moment in the history of science when a new capability is born that transforms our ability to “see” what is happening in the world in which we live. The use of the light emitted from accelerating electrons as they are bent by magnetic fields that was pioneered at SSRL in the 1970s is not just another example of this, but arguably is the most important development in the history of science in enabling us to “see” the world of electrons and atoms. There is, in addition, a special feature of the new capability enabled by synchrotron radiation: it is likely to remain, in the future, the best way to see the microscopic world forever. This is because the light used to “see” does not only have all the intensity one needs, but also because all its properties can be adjusted so as to provide the ideal illumination for the particular thing one wants to “see.” Thus, literally what was born at SSRL, which has since then been and will be continually improved, will forever provide our species the ability to “see” and understand the microscopic world in which we live.

Meiofauna international workshop “MeioScool 2013: a dive into a microscopic world”

This issue contains selected studies presented during the Meiofauna International Workshop “MeioScool 2013: a dive in a microscopic world”, held in Brest, France, 26–29 November 2013. The main objectives of MeioScool were to bring together several meiofaunal experts in several meiofauna-related sub-disciplines from around the world in order to increase awareness among researchers, students and the general public of the fundamental role of meiofauna in marine ecosystems from the coastal zone to abyssal depths; and to train students and researchers in the identification and description of meiofauna through several complementary disciplines (taxonomy, ecology, molecular biology), and stimulate a new generation of meiobenthologists. The MeioScool workshop lasted 4 days. The first 2 days were devoted to conferences, while the other 2 days were focused on field and laboratory work (sampling, extraction, morphological and molecular identification of major meiofaunal taxonomic groups). The workshop attracted 126 scientists and students from 26 countries to study a wide range of aspects and topics related to meiofauna. This Special Issue of Marine Biodiversity presents selected results of the workshop, grouped in sections by topic as follows: 1) meiofauna taxonomy, with six contributions; 2) meiofauna ecology, with seven contributions; and 3) meiofauna sampling and identification methods, with three contributions.

Information-geometric approach to the renormalization group

We propose a general formulation of the renormalisation group as a family of quantum channels which connect the microscopic physical world to the observable world at some scale. By endowing the set of quantum states with an operationally motivated information geometry, we induce the space of Hamiltonians with a corresponding metric geometry. The resulting structure allows one to quantify information loss along RG flows in terms of the distinguishability of thermal states. In particular, we introduce a family of functions, expressible in terms of two-point correlation functions, which are non increasing along the flow. Among those, we study the speed of the flow, and its generalization to infinite lattices.

Dielectric Optical-Controllable Magnifying Lens by Nonlinear Negative Refraction.

A simple optical lens plays an important role for exploring the microscopic world in science and technology by refracting light with tailored spatially varying refractive indices. Recent advancements in nanotechnology enable novel lenses, such as, superlens and hyperlens, with sub-wavelength resolution capabilities by specially designed materials’ refractive indices with meta-materials and transformation optics. However, these artificially nano- or micro-engineered lenses usually suffer high losses from metals and are highly demanding in fabrication. Here, we experimentally demonstrate, for the first time, a nonlinear dielectric magnifying lens using negative refraction by degenerate four-wave mixing in a plano-concave glass slide, obtaining magnified images. Moreover, we transform a nonlinear flat lens into a magnifying lens by introducing transformation optics into the nonlinear regime, achieving an all-optical controllable lensing effect through nonlinear wave mixing, which may have many potential applications in microscopy and imaging science.

Proposing new experiments to test the quantum-to-classical transition

An open problem in modern physics is why microscopic quantum objects can be at two places at once (i.e. a superposed quantum state) while macroscpoic classical object never show such a behaviour. Collapse models provides a quantitative answer for this problem and explain how macroscopic classical world emerges out of microscopic quantum world. A universal noise field is postulated in collapse models, inducing appropriate Brownian- motion corrections to standard quantum dynamics. The strength of collapse-driven Brownian fluctuations depend on: (i) the parameters characterizing the system (e.g., mass, size, density), and (ii) two phenomenological parameters defining the statistical properties of the collapse noise. The collapse-driven Brownian motion works such that microscopic systems behave quantum mechanically, while macroscopic objects are classical. At the intermediate mesocopic scale, collapse models predict deviations from standard quantum predictions. This issue has been subject of experimental tests. All experiments to date have been at the scales where collapse effects are negligible for all practical purposes. However, recent experimental progress in revealing quantum features of larger objects, increases the hope for testing at unprecedented scales where collapse models can be falsified. Current experiments are mainly focused on the preparation of macroscopic systems in a spatial quantum superposition state. The collapse effects would then manifest as loss of visibility in the observed inference pattern. However, one needs a quantum interference with single particles of mass ∼ 1010amu for a decisive test of collapse models. Creating such massive superpositionsis quite challenging, and beyond currectstate-of-the-art. Quite recently, an alternative approach has been proposed where the collapse manifests in the fluctuating properties of light interacting with the quantum system. The great advantage of this new approach is that here there is no need for the preparation of a quantum superposed state. It has been discussed that promising results can be revealed in the spectrum of light interacting with a radiation pressure-driven mechanical oscillator in a cavity optomechanics setting. Here, we review the theoretical modelling of the above optomechenical proposal. We discuss how collapse-driven Brownian motion modifies the spectrum. We quantify the collapse effect and explain how it depends on the parameters of the mechanical oscillator (e.g., mass, density, geometry).

Entropy is a consequence of a discrete time

While the basic microscopic physical laws are time reversible, the arrow of time and time irreversibility appears only at the macroscopic physical laws by the second law of thermodynamics with its entropy term S. It is the attempt of the present work to bridge the microscopic physical world with its macroscopic one with an alternative approach than the statistical mechanics theory of Gibbs and Boltzmann. For simplicity a “classical”, single particle in a one dimensional space is selected. In addition, it is assumed that time is discrete with constant step size. As a consequence time irreversibility at the microscopic level is obtained if the present force is of complex nature (F(r) ≠ const). In order to compare this discrete time irreversible mechanics with its classical Newton analog, time reversibility is reintroduced by scaling the time steps for any given time step n by the variable sn leading to the Nosé-Hoover Lagrangian comprising a term NdfkB T In sn (kB the Boltzmann constant, T the temperature, and Ndf the number of degrees of freedom) which is defined as the microscopic entropy Sn at time point n multiplied by T. Upon ensemble averaging of the microscopic entropy in a many particles system in thermodynamic equilibrium it approximates its macroscopic counterpart known from statistical mechanics. The presented derivation with the resulting analogy between the ensemble averaged microscopic entropy and its statistical mechanics analog suggests that the entropy term itself has its root not in statistical mechanics but rather in the discreteness of time.

Study on Raman Spectra of Some Animal and Plant Oils

The spectral characteristics of different kinds of oil, either from plant seeds or animal fat, were studied with Raman spectroscopy. The experimental data were processed with the adaptive iteratively reweighted penalized least squares method to realize baseline correction, and provide evident information about their microscopic world. The spectra were analyzed and compared with each other in three parts: the Raman spectra comparison among different samples of plant oils, the analysis of the animal fat and the comparison between plant oils and the animal fat. The differences among the oils were observed in the analysis, including Raman shift and Raman intensity differences. This study not only yields the spectral basis for distinguishing or recognizing the different edible oils, but also confirms that Raman spectroscopy is an effective tool for identifying different oils.

Namibian fairy circles and epithelial cells share emergent geometric order

Fairy circles are enigmatic features of the Namib desert landscape. They are large, almost perfectly circular patches of barren soil in sparse grassland. Although a matter of continuing debate, we make no attempt to explain their origin. The focus of our approach is a statistical analysis of the spatial patterns. These are easily accessible via aerial and satellite imagery. Observations over extended periods of time have revealed that they have a life-cycle of birth, growth and death. It has also been known for some time that the fairy circles are not randomly distributed. Our novel finding is that the connectivity patterns of fairy circles and metazoan epithelial cells are statistically indistinguishable, while remaining clearly distinct from other commonly observed polygonal patternings. This result identifies an analogy between the microscopic world of epithelial cells and the macroscopic realm of the Namib, suggesting that approaches developed specifically for the analysis of microscopic structures may extend into ecologically relevant, macroscopic dimensions.

Lurking Within Reach: Stereoscopic Photomicrography in the 1860s

In the 1860s, the debate over whether photography was an accurate and useful tool for recording microscopic specimens was unresolved. Albert Moitessier’s La photographie appliquée aux recherches micrographiques (1866) was one of the first instructional books to outline techniques combining photography and microscopy. Moitessier was unique among his contemporaries in his emphasis on stereoscopy and binocular vision. This essay addresses questions arising from Moitessier’s unusual inclusion of a stereograph in his plates and his description of stereoscopic techniques in his text. While an ordinary photomicrograph renders the invisible microscopic world visible, the stereoscope brings this intangible realm within reach. The stereoscope is imbued, in this context, with a unique machinic vision as well as a haptic faculty that supersedes human perceptual ability. The apparent objectivity these extra-human capabilities facilitate, in turn, lends autonomy to stereo-photomicrographic tools. As the gulf between human and machine perception widens, the spectre of artificial intelligence grows, contributing to the disorientation in the nineteenth century over an expanded sense of existence.

Unravelling the effect of temperature on viscosity-sensitive fluorescent molecular rotors.

Viscosity and temperature variations in the microscopic world are of paramount importance for diffusion and reactions. Consequently, a plethora of fluorescent probes have evolved over the years to enable fluorescent imaging of both parameters in biological cells. However, the simultaneous effect of both temperature and viscosity on the photophysical behavior of fluorophores is rarely considered, yet unavoidable variations in temperature can lead to significant errors in the readout of viscosity and vice versa. Here we examine the effect of temperature on the photophysical behavior of three classes of viscosity-sensitive fluorophores termed 'molecular rotors'. For each of the fluorophores we decouple the effect of temperature from the effect of viscosity. In the case of the conjugated porphyrin dimer, we demonstrate that, uniquely, simultaneous dual-mode lifetime and intensity measurements of this fluorophore can be used for measuring both viscosity and temperature concurrently.

A Microscopic World at the Touch: Learning Biology with Novel 2.5D and 3D Tactile Models

A Microscopic World at the Touch: Learning Biology with Novel 2.5D and 3D Tactile Models

Nature's Invisibilia: The Victorian Microscope and the Miniature Fairy

During the Victorian period, the concept of miniature worlds, invisible to the eye but ever-present to the imagination, captivated both readers of microscopic literature and audiences of fairy texts. The convergence of scale between the microscope and the fairy fostered a strong imaginative link between the two. Natural scientists used the imagery of fairyland to convey the incomprehensible strangeness and minutiae of the microscopic world, while fairy authors and illustrators drew upon microscopic discoveries to lend a sense of reality to their unbelievable imaginings. This essay traces the connection between the microscope and the fairy through scientific and fantastic literature, before culminating in an examination of fairy science texts that directly combine the two.

Study on extending the depth of field in reconstructed image for a micro digital hologram

Digital micro holography offers an in-situ, non-contact and three-dimensional way to explore the microscopic world. However, as it is difficult to focalize the whole object in one single reconstructed image, the application of digital micro holography to cases with a large longitudinal object volume is limited by the microscopes depth of field. By extending the depth of field in reconstructed micro holograms in the wavelet domain, this paper fully takes advantage of numerical reconstruction algorithms to solve this problem. First, a recorded hologram is rebuilt using the wavelet transform approach by setting up an appropriate longitudinal interval to obtain a series of reconstructed hologram planes. Then each plane is decomposed with wavelet into its sub-images of both high and low frequencies. Furthermore, the local variance of the maximum intensity gradients of the high- and low-frequency coefficients is calculated and utilized as the focus criterion. Finally, the image planes are fused into a single one with the depth of field extended to a large extent. The feasibility and robustness of this reconstruction procedure for both continuum and particle fields are investigated. One of the demonstrations is made in an experiment of a tilted continuum:carbon fiber. It is different from most of the previous applications where the interrogated is the particles and where the area involved is parallel to the CCD. The carbon fiber gets successfully reconstructed in three dimensions, and the measurement errors of its diameter are presented together with the reconstruction distances. Another is an experiment of a dispersed particle field:micro transparent particles are generated by an ultrasonic atomizer, for which the reconstruction procedure achieves an extended depth of field. In addition, a numerical model based on generalized Lorenz-Mie theory is used to simulate the holograms of both opaque and transparent particles of 1-15 m in diameter. Variations of the longitudinal location errors with the Fraunhofer number are analyzed, and comparisons are made between the results of opaque and transparent particles. Both the experimental and simulation outcomes show that this reconstruction procedure is a reliable one to acquire an extended-depth-of-field hologram for both the continuum and the dispersed particle fields, and then to accurately measure the objects.

AN ANTHOLOGY OF THE DISTINGUISHED ACHIEVEMENTS IN A SCIENCE AND TECHNIQUE. PART 23: INVENTION OF MICROSCOPE AND STUDY OF MICROSCOPIC WORLD.

A short essay is resulted from world history of invention of microscopes. The basic types of microscopes are described; directions and some results of their application are indicated at the study of microscopic world.

Origin of probabilities and their application to the multiverse

We argue using simple models that all successful practical uses of probabilities originate in quantum fluctuations in the microscopic physical world around us, often propagated to macroscopic scales. Thus we claim there is no physically verified fully classical theory of probability. We comment on the general implications of this view, and specifically question the application of classical probability theory to cosmology in cases where key questions are known to have no quantum answer. We argue that the ideas developed here may offer a way out of the notorious measure problems of eternal inflation.

The uncreated energies – the spiritual foundation of knowledge

By the Orthodox teaching’s point of view on the uncreated energies, the science has the possibility to be spiritually substantiated. As far back as the patristic epoch, the theology speaks of the inward rationality of creation backed up by the uncreated energies, by which the world can be gathered in man and lifted to the highest level of its existence, to its being transfigured into a new heaven and a new earth. The microscopic world is found at the basis of the visible material world, but by knowing it, the science has exactly discovered this rationality. In accordance with Einstein discovery concerning the hierarchy of the physics laws, the universe’s rationality goes beyond its manifestation described with the help of the laws of symmetry, of finality, of cause and effect, all of which are conspicuous at the macroscopic level; it was this reality which has induced the men of science to assert that this is the work of God’s Mind.

The quantified cell.

The microscopic world of a cell can be as alien to our human-centered intuition as the confinement of quarks within protons or the event horizon of a black hole. We are prone to thinking by analogy—Golgi cisternae stack like pancakes, red blood cells look like donuts—but very little in our human experience is truly comparable to the immensely crowded, membrane-subdivided interior of a eukaryotic cell or the intricately layered structures of a mammalian tissue. So in our daily efforts to understand how cells work, we are faced with a challenge: how do we develop intuition that works at the microscopic scale?

Ebola and art.

The cover image of the current issue of our journal shows an embroidered image of the Ebola virus. The complex shape of viruses has inspired artist to render these microscopic sized particles (1,2). In a submission to our Art-and-Medicine series in 2013, which includes the cover image of this issue, artist Mia Weiner described her interest in the correlation between working in fibers and the microscopic world (1). She described that by embroidering images of Ebola, the virus becomes an object of beauty, with its destructive nature and danger to the human body hidden.