Buckling, stiffening, and negative dissipation in the dynamics of a biopolymer in an active medium

We present a generic theory for the dynamics of a stiff filament under tension, in an active medium with orientational correlations, such as a microtubule in contractile actin. In sharp contrast to the case of a passive medium, we find the filament can stiffen, and possibly oscillate or buckle, depending on both the contractile or tensile nature of the activity and the filament-medium anchoring interaction. We also demonstrate a strong violation of the fluctuation-dissipation (FD) relation in the effective dynamics of the filament, including a negative FD ratio. Our approach is also of relevance to the dynamics of axons, and our model equations bear a remarkable formal similarity to those in recent work [Martin P, Hudspeth AJ, Juelicher F (2001) Proc Natl Acad Sci USA 98: 14380-14385] on auditory hair cells. Detailed tests of our predictions can be made by using a single filament in actomyosin extracts or bacterial suspensions.

Nonspecifically bound proteins spin while diffusing along DNA

It is known that DNA-binding proteins can slide along the DNA helix while searching for specific binding sites, but their path of motion remains obscure. Do these proteins undergo simple one-dimensional (1D) translational diffusion, or do they rotate to maintain a specific orientation with respect to the DNA helix? We measured 1D diffusion constants as a function of protein size while maintaining the DNA-protein interface. Using bootstrap analysis of single-molecule diffusion data, we compared the results to theoretical predictions for pure translational motion and rotation-coupled sliding along the DNA. The data indicate that DNA-binding proteins undergo rotation-coupled sliding along the DNA helix and can be described by a model of diffusion along the DNA helix on a rugged free-energy landscape. A similar analysis including the 1D diffusion constants of eight proteins of varying size shows that rotation-coupled sliding is a general phenomenon. The average free-energy barrier for sliding along the DNA was 1.1 +/- 0.2 k(B)T. Such small barriers facilitate rapid search for binding sites.

The Out-of-India hypothesis: What do molecules suggest?

The remarkable geological and evolutionary history of peninsular India has generated much interest in the patterns and processes that might have shaped the current distributions of its endemic biota. In this regard the Out of India hypothesis, which proposes that rafting peninsular India carried Gondwanan forms to Asia after the break-up of Gondwana super continent, has gained prominence. Here we have reviewed molecular studies undertaken on a range of taxa of supposedly Gondwanan origin to better understand the Out-of-India scenario. This re-evaluation of published molecular studies indicates that there is mounting evidence supporting Out-of-India scenario for various Asian taxa. Nevertheless, in many studies the evidence is inconclusive due to lack of information on the age of relevant nodes. Studies also indicate that not all Gondwanan forms of peninsular India dispersed out of India. Many of these ancient lineages are confined to peninsular India and therefore are relict Gondwanan lineages. Additionally for some taxa an Into India rather than Out-of-India scenario better explains their current distribution. To identify the Out-of-India component of Asian biota it is imperative that we understand the complex biogeographical history of India. To this end, we propose three oversimplified yet explicit phylogenetic predictions. These predictions can be tested through the use of molecular phylogenetic tools in conjunction with palaeontological and geological data.

An adiabatic model for a two-stage double-inlet pulse tube refrigerator

A numerical modelling technique for predicting the detailed performance of a double-inlet type two-stage pulse tube refrigerator has been developed. The pressure variations in the compressor, pulse tube, and reservoir were derived, assuming the stroke volume variation of the compressor to be sinusoidal. The relationships of mass flowrates, volume flowrates, and temperature as a function of time and position were developed. The predicted refrigeration powers are calculated by considering the effect of void volumes and the phase shift between pressure and mass flowrate. These results are compared with the experimental results of a specific pulse tube refrigerator configuration and an existing theoretical model. The analysis shows that the theoretical predictions are in good agreement with each other.

Predicting single-layer technetium dichalcogenides (TcX2, X = S, Se) with promising applications in photovoltaics and photocatalysis

One of the least known compounds among transition metal dichalcogenides (TMDCs) is the layered triclinic technetium dichalcogenides (TcX2, X = S, Se). In this work, we systematically study the structural, mechanical, electronic, and optical properties of TcS2 and TcSe2 monolayers based on density functional theory (DFT). We find that TcS2 and TcSe2 can be easily exfoliated in a monolayer form because their formation and cleavage energy are analogous to those of other experimentally realized TMDCs monolayer. By using a hybrid DFT functional, the TcS2 and TcSe2 monolayers are calculated to be indirect semiconductors with band gaps of 1.91 and 1.69 eV, respectively. However, bilayer TcS2 exhibits direct-bandgap character, and both TcS2 and TcSe2 monolayers can be tuned from semiconductor to metal under effective tensile/compressive strains. Calculations of visible light absorption indicate that 2D TcS2 and TcSe2 generally possess better capability of harvesting sunlight compared to single-layer MoS2 and ReSe2, implying their potential as excellent light-absorbers. Most interestingly, we have discovered that the TcSe2 monolayer is an excellent photocatalyst for splitting water into hydrogen due to the perfect fit of band edge positions with respect to the water reduction and oxidation potentials. Our predictions expand the two-dimensional (2D) family of TMDCs, and the remarkable electronic/optical properties of monolayer TcS2 and TcSe2 will place them among the most promising 2D TMDCs for renewable energy application in the future.

Performance Analysis of Reconstruction Techniques for Frequency-Domain Optical-Coherence Tomography

We address the issue of noise robustness of reconstruction techniques for frequency-domain optical-coherence tomography (FDOCT). We consider three reconstruction techniques: Fourier, iterative phase recovery, and cepstral techniques. We characterize the reconstructions in terms of their statistical bias and variance and obtain approximate analytical expressions under the assumption of small noise. We also perform Monte Carlo analyses and show that the experimental results are in agreement with the theoretical predictions. It turns out that the iterative and cepstral techniques yield reconstructions with a smaller bias than the Fourier method. The three techniques, however, have identical variance profiles, and their consistency increases linearly as a function of the signal-to-noise ratio.

Charge-order-driven multiferroic properties of Y1-xCaxMnO3

Dielectric measurements on the charge-ordered insulators, Y1-xCaxMnO3 (x = 0.4. 0.45 and 0.5), show maxima in the dielectric constant around the charge ordering transition temperature while magnetic measurements show the presence of weak ferromagnetic interactions at low temperatures. Besides the magnetic field dependence of the dielectric constant, these manganites also exhibit second harmonic generation. Thus, the charge-ordered Y1-xCaxMnO3 compositions are multiferroic and magnetoelectric, in accordance with theoretical predictions. Magnetoelectric properties are retained in small particles of Y0.5Ca0.5MnO3. (C) 2008 Elsevier Ltd. All rights reserved.

Crack Tip Fields in a Single Edge Notched Aluminum Single Crystal Specimen

We report a combined experimental and computational study of a low constraint aluminum single crystal fracture geometry and investigate the near-tip stress and strain fields. To this end, a single edge notched tensile (SENT) specimen is considered. A notch, with a radius of 50 µm, is taken to lie in the (010) plane and its front is aligned along the [101] direction. Experiments are conducted by subjecting the specimen to tensile loading using a special fixture inside a scanning electron microscope chamber. Both SEM micrographs and electron back-scattered diffraction (EBSD) maps are obtained from the near-tip region. The experiments are complemented by performing 3D and 2D plane strain finite element simulations within a continuum crystal plasticity framework assuming an isotropic hardening response characterized by the Pierce–Asaro–Needleman model. The simulations show a distinct slip band forming at about 55 deg with respect to the notch line corresponding to slip on (11-bar 1)[011] system, which corroborates well with experimental data. Furthermore, two kink bands occur at about 45 deg and 90 deg with respect to the notch line within which large rotations in the crystal orientation take place. These predictions are in good agreement with the EBSD observations. Finally, the near-tip angular variations of the 3D stress and plastic strain fields in the low constraint SENT fracture geometry are examined in detail.

Experimental studies on a two stage pulse tube cryocooler reaching 2.5K

A two stage Pulse Tube Cryocooler (PTC) is designed and fabricated which reaches a no-load temperature of 2.5K in the second stage and similar to 60 K in the first stage respectively. The system provides a cooling power of similar to 250 mW at 5K in the second stage. Stainless steel meshes (size 200) and lead (Pb) granules are used as the first stage regenerator materials and combination of Pb with Er3Ni / HoCu2 are used as the second stage regenerator materials. The system operates at 1.6 Hz using a 6 kW water cooled helium compressor. Studies conducted by varying the dimensions of Pulse Tubes and regenerators show that the dimensions of the Pulse Tubes are more critical to the performance of the Cryocooler than those of the regenerators. Experimental studies show that the optimum volume ratios of Er3Ni to Pb and HoCu2 to Pb in the second stage regenerator should be 3:2 and 2:3 respectively for the best performance. Further, systems with HoCu2 performed better than those with Er3Ni. The theoretical analysis of the system has been carried out using a simple isothermal model. The experimentally measured cooling powers are in good agreement with the theoretical predictions.

How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.

Developing and testing readability measurements for second language learners

This research constructed a readability measurement for French speakers who view English as a second language. It identified the true cognates, which are the similar words from these two languages, as an indicator of the difficulty of an English text for French people. A multilingual lexical resource is used to detect true cognates in text, and Statistical Language Modelling to predict the predict the readability level. The proposed enhanced statistical language model is making a step in the right direction by improving the accuracy of readability predictions for French speakers by up to 10% compared to state of the art approaches. The outcome of this study could accelerate the learning process for French speakers who are studying English. More importantly, this study also benefits the readability estimation research community, presenting an approach and evaluation at sentence level as well as innovating with the use of cognates as a new text feature.

Acceleration of the Cosmological Expansion as an Effect of Inhomogeneities

The cosmological observations of light from type Ia supernovae, the cosmic microwave background and the galaxy distribution seem to indicate that the expansion of the universe has accelerated during the latter half of its age. Within standard cosmology, this is ascribed to dark energy, a uniform fluid with large negative pressure that gives rise to repulsive gravity but also entails serious theoretical problems. Understanding the physical origin of the perceived accelerated expansion has been described as one of the greatest challenges in theoretical physics today. In this thesis, we discuss the possibility that, instead of dark energy, the acceleration would be caused by an effect of the nonlinear structure formation on light, ignored in the standard cosmology. A physical interpretation of the effect goes as follows: due to the clustering of the initially smooth matter with time as filaments of opaque galaxies, the regions where the detectable light travels get emptier and emptier relative to the average. As the developing voids begin to expand the faster the lower their matter density becomes, the expansion can then accelerate along our line of sight without local acceleration, potentially obviating the need for the mysterious dark energy. In addition to offering a natural physical interpretation to the acceleration, we have further shown that an inhomogeneous model is able to match the main cosmological observations without dark energy, resulting in a concordant picture of the universe with 90% dark matter, 10% baryonic matter and 15 billion years as the age of the universe. The model also provides a smart solution to the coincidence problem: if induced by the voids, the onset of the perceived acceleration naturally coincides with the formation of the voids. Additional future tests include quantitative predictions for angular deviations and a theoretical derivation of the model to reduce the required phenomenology. A spin-off of the research is a physical classification of the cosmic inhomogeneities according to how they could induce accelerated expansion along our line of sight. We have identified three physically distinct mechanisms: global acceleration due to spatial variations in the expansion rate, faster local expansion rate due to a large local void and biased light propagation through voids that expand faster than the average. A general conclusion is that the physical properties crucial to account for the perceived acceleration are the growth of the inhomogeneities and the inhomogeneities in the expansion rate. The existence of these properties in the real universe is supported by both observational data and theoretical calculations. However, better data and more sophisticated theoretical models are required to vindicate or disprove the conjecture that the inhomogeneities are responsible for the acceleration.

Monte Carlo Simulations of Molecular Clusters in Nucleation

A better understanding of the limiting step in a first order phase transition, the nucleation process, is of major importance to a variety of scientific fields ranging from atmospheric sciences to nanotechnology and even to cosmology. This is due to the fact that in most phase transitions the new phase is separated from the mother phase by a free energy barrier. This barrier is crossed in a process called nucleation. Nowadays it is considered that a significant fraction of all atmospheric particles is produced by vapor-to liquid nucleation. In atmospheric sciences, as well as in other scientific fields, the theoretical treatment of nucleation is mostly based on a theory known as the Classical Nucleation Theory. However, the Classical Nucleation Theory is known to have only a limited success in predicting the rate at which vapor-to-liquid nucleation takes place at given conditions. This thesis studies the unary homogeneous vapor-to-liquid nucleation from a statistical mechanics viewpoint. We apply Monte Carlo simulations of molecular clusters to calculate the free energy barrier separating the vapor and liquid phases and compare our results against the laboratory measurements and Classical Nucleation Theory predictions. According to our results, the work of adding a monomer to a cluster in equilibrium vapour is accurately described by the liquid drop model applied by the Classical Nucleation Theory, once the clusters are larger than some threshold size. The threshold cluster sizes contain only a few or some tens of molecules depending on the interaction potential and temperature. However, the error made in modeling the smallest of clusters as liquid drops results in an erroneous absolute value for the cluster work of formation throughout the size range, as predicted by the McGraw-Laaksonen scaling law. By calculating correction factors to Classical Nucleation Theory predictions for the nucleation barriers of argon and water, we show that the corrected predictions produce nucleation rates that are in good comparison with experiments. For the smallest clusters, the deviation between the simulation results and the liquid drop values are accurately modelled by the low order virial coefficients at modest temperatures and vapour densities, or in other words, in the validity range of the non-interacting cluster theory by Frenkel, Band and Bilj. Our results do not indicate a need for a size dependent replacement free energy correction. The results also indicate that Classical Nucleation Theory predicts the size of the critical cluster correctly. We also presents a new method for the calculation of the equilibrium vapour density, surface tension size dependence and planar surface tension directly from cluster simulations. We also show how the size dependence of the cluster surface tension in equimolar surface is a function of virial coefficients, a result confirmed by our cluster simulations.

On gravitational fields of stars in f(R) gravity theories

Einstein's general relativity is a classical theory of gravitation: it is a postulate on the coupling between the four-dimensional, continuos spacetime and the matter fields in the universe, and it yields their dynamical evolution. It is believed that general relativity must be replaced by a quantum theory of gravity at least at extremely high energies of the early universe and at regions of strong curvature of spacetime, cf. black holes. Various attempts to quantize gravity, including conceptually new models such as string theory, have suggested that modification to general relativity might show up even at lower energy scales. On the other hand, also the late time acceleration of the expansion of the universe, known as the dark energy problem, might originate from new gravitational physics. Thus, although there has been no direct experimental evidence contradicting general relativity so far - on the contrary, it has passed a variety of observational tests - it is a question worth asking, why should the effective theory of gravity be of the exact form of general relativity? If general relativity is modified, how do the predictions of the theory change? Furthermore, how far can we go with the changes before we are face with contradictions with the experiments? Along with the changes, could there be new phenomena, which we could measure to find hints of the form of the quantum theory of gravity? This thesis is on a class of modified gravity theories called f(R) models, and in particular on the effects of changing the theory of gravity on stellar solutions. It is discussed how experimental constraints from the measurements in the Solar System restrict the form of f(R) theories. Moreover, it is shown that models, which do not differ from general relativity at the weak field scale of the Solar System, can produce very different predictions for dense stars like neutron stars. Due to the nature of f(R) models, the role of independent connection of the spacetime is emphasized throughout the thesis.

Investigations of planetary boundary layer processes and particle formation in the atmosphere of planet Mars

The planet Mars is the Earth's neighbour in the Solar System. Planetary research stems from a fundamental need to explore our surroundings, typical for mankind. Manned missions to Mars are already being planned, and understanding the environment to which the astronauts would be exposed is of utmost importance for a successful mission. Information of the Martian environment given by models is already now used in designing the landers and orbiters sent to the red planet. In particular, studies of the Martian atmosphere are crucial for instrument design, entry, descent and landing system design, landing site selection, and aerobraking calculations. Research of planetary atmospheres can also contribute to atmospheric studies of the Earth via model testing and development of parameterizations: even after decades of modeling the Earth's atmosphere, we are still far from perfect weather predictions. On a global level, Mars has also been experiencing climate change. The aerosol effect is one of the largest unknowns in the present terrestrial climate change studies, and the role of aerosol particles in any climate is fundamental: studies of climate variations on another planet can help us better understand our own global change. In this thesis I have used an atmospheric column model for Mars to study the behaviour of the lowest layer of the atmosphere, the planetary boundary layer (PBL), and I have developed nucleation (particle formation) models for Martian conditions. The models were also coupled to study, for example, fog formation in the PBL. The PBL is perhaps the most significant part of the atmosphere for landers and humans, since we live in it and experience its state, for example, as gusty winds, nightfrost, and fogs. However, PBL modelling in weather prediction models is still a difficult task. Mars hosts a variety of cloud types, mainly composed of water ice particles, but also CO2 ice clouds form in the very cold polar night and at high altitudes elsewhere. Nucleation is the first step in particle formation, and always includes a phase transition. Cloud crystals on Mars form from vapour to ice on ubiquitous, suspended dust particles. Clouds on Mars have a small radiative effect in the present climate, but it may have been more important in the past. This thesis represents an attempt to model the Martian atmosphere at the smallest scales with high resolution. The models used and developed during the course of the research are useful tools for developing and testing parameterizations for larger-scale models all the way up to global climate models, since the small-scale models can describe processes that in the large-scale models are reduced to subgrid (not explicitly resolved) scale.