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At least 163 records · Page 9Linked to original sources

From Clarkia to Escherichia and Janus: the physics of natural and synthetic active colloids

An active colloid is a suspension of particles that transduce free energy from their environment and use the energy to engage in intrinsically non-equilibrium activities such as growth, replication and self-propelled motility. An obvious example of active colloids is a suspension of bacteria such as Escherichia coli, their physical dimensions being almost invariably in the colloidal range. Synthetic self-propelled particles have also become available recently, such as two-faced, or Janus, particles propelled by differential chemical reactions on their surfaces driving a self-phoretic motion. In these lectures, I give a pedagogical introduction to the physics of single-particle and collective properties of active colloids, focussing on self propulsion. I will compare and contrast phenomena in suspensions of `swimmers' with the behaviour of suspensions of passive particles, where only Brownian motion (discovered by Robert Brown in granules from the pollen of the wild flower {\it Clarkia pulchella}) is relevant. I will pay particular attention to issues that pertain to performing experiments using these active particle suspensions, such as how to characterise the suspension's swimming speed distribution, and include an appendix to guide physicists wanting to start culturing motile bacteria.

cond-mat.soft↗

A maximum likelihood based technique for validating detrended fluctuation analysis (ML-DFA)

Detrended Fluctuation Analysis (DFA) is widely used to assess the presence of long-range temporal correlations in time series. Signals with long-range temporal correlations are typically defined as having a power law decay in their autocorrelation function. The output of DFA is an exponent, which is the slope obtained by linear regression of a log-log fluctuation plot against window size. However, if this fluctuation plot is not linear, then the underlying signal is not self-similar, and the exponent has no meaning. There is currently no method for assessing the linearity of a DFA fluctuation plot. Here we present such a technique, called ML-DFA. We scale the DFA fluctuation plot to construct a likelihood function for a set of alternative models including polynomial, root, exponential, logarithmic and spline functions. We use this likelihood function to determine the maximum likelihood and thus to calculate values of the Akaike and Bayesian information criteria, which identify the best fit model when the number of parameters involved is taken into account and over-fitting is penalised. This ensures that, of the models that fit well, the least complicated is selected as the best fit. We apply ML-DFA to synthetic data from FARIMA processes and sine curves with DFA fluctuation plots whose form has been analytically determined, and to experimentally collected neurophysiological data. ML-DFA assesses whether the hypothesis of a linear fluctuation plot should be rejected, and thus whether the exponent can be considered meaningful. We argue that ML-DFA is essential to obtaining trustworthy results from DFA.

q-bio.QM↗

Optical Photon Reassignment Microscopy (OPRA)

To enhance the resolution of a confocal laser scanning microscope the additional information of a pinhole plane image taken at every excitation scan position can be used [C. J. R. Sheppard, Super-resolution in confocal imaging, Optik 80, 5354 (1988)]. This photon reassignment principle is based on the fact that the most probable position of an emitter is at half way between the nominal focus of the excitation laser and the position corresponding to the (off centre) detection position. Therefore, by reassigning the detected photons to this place, an image with enhanced detection efficiency and resolution is obtained. Here we present optical photon reassignment microscopy (OPRA) which realises this concept in an all-optical way obviating the need for image-processing. With the help of an additional intermediate optical beam expansion between descanning and a further rescanning of the detected light, an image with the advantages of photon reassignment can be acquired. Due to its simplicity and flexibility this method has the potential to enhance the performance of nearly every laser scanning microscope and is therefore expected to play an important role in future systems.

physics.optics↗

Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.

physics.bio-ph↗

Probing the viscoelastic properties of polyacrylamide polymer gels in a wide frequency range

Polymer gels have been shown to behave as viscoelastic materials but only a small amount of data is usually provided in the glassy transition. In this paper, the dynamic moduli G' and G" of polyacrylamide hydrogels are investigated using both an AFM in contact force modulation mode and a classical rheometer. The validity is shown by perfect matching of the two techniques. Measurements are carried out on gels of increasing polymer concentration in a wide frequency range. A model based on fractional derivatives is proposed, covering the whole frequency range. G_0^N, the plateau modulus, as well as nf, the slope of the G" modulus, are obtained at low frequencies. The model also predicts the slope a of both moduli in the transition regime, as well as a new transition time T. The whole frequency spectrum is recovered, and the model parameters contain interesting information about the physics of such gels.

physics.med-ph↗

Link-weight distribution of microRNA co-target networks exhibit universality

MicroRNAs (miRNAs) are small non-coding RNAs which regulate gene expression by binding to the 3' UTR of the corresponding messenger RNAs. We construct miRNA co-target networks for 22 different species using a target prediction database, MicroCosm Tagets. The miRNA pairs of individual species having one or more common target genes are connected and the number of co-targets are assigned as the weight of these links. We show that the link-weight distributions of all the species collapse remarkably onto each other when scaled suitably. It turns out that the scale-factor is a measure of complexity of the species. A simple model, where targets are chosen randomly by miRNAs, could provide the correct scaling function and explain the universality.

q-bio.MN↗

Temperature and Carbon Assimilation Regulate the Chlorosome Biogenesis in Green Sulfur Bacteria

Green photosynthetic bacteria adjust the structure and functionality of the chlorosome - the light absorbing antenna complex - in response to environmental stress factors. The chlorosome is a natural self-assembled aggregate of bacteriochlorophyll (BChl) molecules. In this study we report the regulation of the biogenesis of the Chlorobaculum tepidum chlorosome by carbon assimilation in conjunction with temperature changes. Our studies indicate that the carbon source and thermal stress culture of Cba. tepidum grows slower and incorporates less BChl c in the chlorosome. Compared with the chlorosome from other cultural conditions we investigated, the chlorosome from the carbon source and thermal stress culture displays: (a) smaller cross-sectional radius and overall size; (b) simplified BChl c homologues with smaller side chains; (c) blue-shifted Qy absorption maxima and (d) a sigmoid-shaped circular dichroism (CD) spectra. Using a theoretical model we analyze how the observed spectral modifications can be associated with structural changes of BChl aggregates inside the chlorosome. Our report suggests a mechanism of metabolic regulation for chlorosome biogenesis.

physics.bio-ph↗

Protein Energy Landscapes Determined by 5-Dimensional Crystallography

Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be determined from the same set of X-ray data. We demonstrate here how barriers of activation can be determined solely from five-dimensional crystallography [5]. Directly linking molecular structures with barriers of activation between them allows for gaining insight into the structural nature of the barrier. We analyze comprehensive time series of crystal-lographic data at 14 different temperature settings and determine entropy and enthalpy contributions to the barriers of activation. 100 years after the discovery of X-ray scattering, we advance X-ray structure determination to a new frontier, the determination of energy landscapes.

physics.bio-ph↗

Solvent Sensitivity of Protein Unfolding: Study of Chicken Villin Headpiece Subdomain in Water-Ethanol and Water-DMSO Mixtures

In the present work we study and compare unfolding of a small protein, chicken villin headpiece (HP-36) in two different aqueous binary mixtures, namely water-ethanol (EtOH) and water-dimethyl sulphoxide (DMSO). In both the binary mixtures, HP-36 is found to unfold (fully or partially, depending on the mixture) under ambient conditions, that otherwise requires temperature as high as ~600 K to denature in pure aqueous solvent. In all the cases, first step of unfolding is found to be similar, i.e. separation of the cluster formed by three hydrophobic (phenylalanine) residues, namely Phe-7, Phe-11 and Phe-18, which constitute the hydrophobic core, thereby initiating melting of helix-2 of the protein. Subsequent unfolding steps follow different paths in different chemical environments. As both water-DMSO and water-ethanol show composition dependent anomalies, so do the details of unfolding dynamics. With an increase of co-solvent concentration different partially unfolded intermediates are found to be formed in both the cases. This is reflected in a remarkable non-monotonic composition dependence of several order parameters, including fraction of native contacts and protein-solvent interaction energy. The emergence of such partially unfolded states is particularly attributed to the preferential solvation of the hydrophobic residues by the ethyl groups of ethanol and methyl groups of DMSO. While in DMSO the protein gradually attains a completely unfolded state at xDMSO=0.30, unfolding in water-ethanol appears to be more complex and sensitive to solvent composition.

q-bio.BM↗

Reproduction and ferromagnetism

I present a stochastic population model that combines cooperative interactions of the type often used in physics with the process of reproduction and death familiar to biology, and I refer to reasons why such interlocking may be of interest to both fields.

physics.bio-ph↗

Exploring the mechanisms of protein folding

Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the exclusive dominant mechanism of protein folding, and attributes the structural transition from one characteristic state to another to energy barriers. Conversely, the concept of kinetic stability overemphasizes dominant mechanisms that are related to kinetic factors. This article explores the stability condition of protein structures from the viewpoint of meso-science, paying attention to the compromise in the competition between minimum free energy and other dominant mechanisms. Based on our study of complex systems, we propose that protein folding is a meso-scale, dissipative, nonlinear and non-equilibrium process that is dominated by the compromise between free energy and other dominant mechanisms such as environmental factors. Consequently, a protein shows dynamic structures, featuring characteristic states that appear alternately and dynamically, only one of which is the state with minimum free energy. To provide evidence for this concept, we analyzed the time series of energetic and structural changes of three simulations of protein folding/unfolding. Our results indicate that thorough consideration of the multiple dynamic characteristic structures generated by multiple mechanisms may be the key to understanding protein folding.

physics.bio-ph↗

Evidence for periodicities in the extinction record? Response to Melott & Bambach [arXiv:1307.1884]

In a recent paper, we applied time series analysis methods to study the possible influence of the solar motion through the Galaxy on terrestrial extinction (Feng & Bailer-Jones 2013). We drew conclusions about the relative probabilities of how well different models explain the geological extinction record. We found no strong evidence for either a periodicity in the extinction record or for a link between the solar orbit and this extinction record. In response to this, Melott & Bambach (2013) dedicate the majority of their article to criticizing our analysis. Their main objection is to evidence-based model comparison. Here we deal with their criticisms one by one, and show that they are largely misplaced, leaving our conclusions unaffected. The bottom line is that although one can get a periodic model at some period to fit the extinction data, there are other models which explain the data better.

astro-ph.EP↗

Glassy dynamics in three-dimensional embryonic tissues

Many biological tissues are viscoelastic, behaving as elastic solids on short timescales and fluids on long timescales. This collective mechanical behavior enables and helps to guide pattern formation and tissue layering. Here we investigate the mechanical properties of three-dimensional tissue explants from zebrafish embryos by analyzing individual cell tracks and macroscopic mechanical response. We find that the cell dynamics inside the tissue exhibit features of supercooled fluids, including subdiffusive trajectories and signatures of caging behavior. We develop a minimal, three-parameter mechanical model for these dynamics, which we calibrate using only information about cell tracks. This model generates predictions about the macroscopic bulk response of the tissue (with no fit parameters) that are verified experimentally, providing a strong validation of the model. The best-fit model parameters indicate that although the tissue is fluid-like, it is close to a glass transition, suggesting that small changes to single-cell parameters could generate a significant change in the viscoelastic properties of the tissue. These results provide a robust framework for quantifying and modeling mechanically-driven pattern formation in tissues.

cond-mat.soft↗

Realizing Bone-mass Generation Through a Density Type Theoretical Archetype

The dynamic process of the formation of bone-mass in case of humans is studied to gather precise understanding about the same with the motivation of applying these concepts for healing of bone-fracture and non-unions in non-invasive manner. Three cellular ingredients, osteoblasts, osteoclasts and osteocytes are predominant players in generating new bone-mass in which a host of hormones, proteins and minerals have potential supportive role. Considering population density of these three biological cells osteoblasts, osteoclasts and osteocytes as variables, we formulate a theoretical model, in the form of a set of time differential equations in order to emulate the dynamic process of bone-mass creation. High relative abundance of osteocytes at asymptotic scale together with moderate level values of osteoblasts and osteoclasts cell populations signifies formation of bone-matter in our theoretical archetype. The archetype has been studied through both analytical and numerical channels, significant results are emphasized and relevant conclusions are drawn. Certain predictive statements are also made which could be put to future in-vivo clinical test or in-vitro physiological experimentation as well.

q-bio.TO↗

Universal scaling function for the two-dimensional Ising model in an external field: A pragmatic approach

We report an effective functional form for the spin-spin correlation function of the 2D Ising model as a function of temperature and field. Although the Ising model has been well studied, no analytical result for the spin-spin correlation function exists for arbitrary magnetic fields and temperatures. We show the validity of our form by comparison with simulations using the Wolff algorithm, and obtain remarkable precision by including analytic corrections to scaling. Given recent interest in comparing biomembrane heterogeneity to Ising criticality, our spin-spin correlation function may be used as a predictive quantitative measure for FRET or NMR membrane experiments.

cond-mat.stat-mech↗

Asymmetrical free diffusion with orientation-dependence of molecules in finite timescales

Using molecular dynamics simulations, we show that free diffusion of a nanoscale particle (molecule) with asymmetric structure critically depends on the orientation in a finite timescale of picoseconds to nanoseconds. In a timescale of ~100 ps, there are ~10% more possibilities for the particle moving along the initial orientation than moving opposite to the orientation; and the diffusion distances of the particle reach ~1 nm. We find that the key to this observation is the orientation-dependence of the damping force to the moving of the nanoscale particle and a finite time is required to regulate the particle orientation. This finding extends the work of Einstein to nano-world beyond random Brownian motion, thus will have a critical role in the understanding of the nanoscale world.

cond-mat.soft↗

The increased efficiency of fish swimming in a school

There is increasing evidence that fish gain energetic benefits when they swim in a school. The most recent indications of such benefits are a lower tail (or fin) beat at the back of a school and reduced oxygen consumption in schooling fish versus solitary ones. How such advantages may arise is poorly understood. Current hydrodynamic theories concern either fish swimming side by side or in a diamond configuration and they largely ignore effects of viscosity and interactions among wakes and individuals. In reality, however, hydrodynamic effects are complex and fish swim in many configurations. Since these hydrodynamic effects are difficult to study empirically, we investigate them in a computer model by incorporating viscosity and interactions among wakes and with individuals. We compare swimming efficiency of mullets of 12.6 cm travelling solitarily and in schools of four different configurations at several inter-individual distances. The resulting Reynolds number (based on fish length) is approximately 1150. We show that these fish always swim more efficiently in a school than alone (except in a dense phalanx). We indicate how this efficiency may emerge from several kinds of interactions among wakes and individuals. Since individuals in our simulations are not even intending to exploit the wake, gains in efficiency are obtained more easily than previously thought.

q-bio.QM↗

Analysis of the volatiles in the headspace above the plasmodium and sporangia of the slime mould (Physarum polycephalum) by SPME-GCMS

Solid phase micro-extraction (SPME) coupled with Gas Chromatography Mass Spectrometry (GC-MS) was used to extract and analyse the volatiles in the headspace above the plasmodial and sporulating stages of the slime mould Physarum Polycephalum. In total 115 compounds were identified from across a broad range of chemical classes. Although more (87) volatile organic compounds (VOCs) were identified when using a higher incubation temperature of 75oC, a large number of compounds (79) were still identified at the lower extraction temperature of 30oC and where the plasmodial stage was living. Far fewer compounds were extracted after sporulation at the two extraction temperatures. There were some marked differences between the VOCs identified in the plasmodial stage and after sporulation. In particular the nitrogen containing compounds acetonitrile, pyrrole, 2, 5-dimethyl-pyrazine and trimethyl pyrazine seemed to be associated with the sporulating stage. There were many compounds associated predominantly with the plasmodial stage including a number of furans and alkanes. Interestingly, a number of known fungal metabolites were identified including 1-octen-3-ol, 3-octanone, 1-octen-3-one, 3-octanol. In addition known metabolites of cyanobacteria and actinobacteria in particular geosmin was identified in the headspace. Volatile metabolites that had previously been identified as having a positive chemotactic response to the plasmodial stage of P. polycephalum were also identified including β-farnesene, β-myrcene, limonene and 3-octanone. This study constitutes the first comprehensive analysis of the headspace volatiles emitted from Physarum Polycephalum. Further work to understand the origin and function of the volatiles identified is required.

physics.bio-ph↗