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At least 199 records · Page 11Linked to original sources

arXiv2013

Correlated local bending of DNA double helix and its effect on the cyclization of short DNA fragments

We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the persistence length of DNA l_P~150 base pairs) cannot be described by the traditional worm-like chain (WLC) model, e.g., the observed ring closure probability is much higher than predicted. To explain these observations, DNA flexibility is investigated with explicit considerations of a new length scale l_D~10 base pairs, over which DNA local bend angles are correlated. In this correlated worm-like chain (C-WLC) model, a finite length correction term is analytically derived and the persistence length is found to be contour length dependent. While our model reduces to the traditional worm-like chain model when treating long DNA at length scales much larger than l_P, it predicts that DNA becomes much more flexible at shorter sizes, which helps explain recent cyclization measurements of short DNA fragments around 100 base pairs.

cond-mat.soft↗

arXiv2013

Piezoelectric Drop-on-Demand Inkjet Printing of Rat Fibroblast Cells: Survivability Study and Pattern Printing

A novel piezoelectric, drop-on-demand (DOD) inkjet system has been developed and used to print L929 rat fibroblast cells. We investigate the survivability of the cells subjected to the large stresses during the printing process. These stresses are varied by changing the diameter of the orifice (36 to 119 microns) through which the cells are dispensed, as well as changing the electrical pulse used to drive the piezoelectric element. It is shown that for the smallest 36 microns diameter orifice, cell survival rates fall from 95% to approximately 76% when the ejection velocity is increased from 2 to 16 m/s. This decrease in survival rates is less significant when the larger orifice diameters of 81 microns and 119 microns are used. Analysis shows that there is a clear inverse relationship between cell survival rates and the mean shear rates during drop formation. By using the same printing set-up, fibroblast cells are printed onto alginate and collagen into patterns. Printed cells are cultured over a period of days to verify their long-term viability. Fibroblasts printed onto the collagen are found to successfully adhere, spread and proliferate, subsequently forming a denser patterns after 5 days in culture. Cell agglomeration is found to affect the printing performance, especially for the printhead with the smallest orifice, leading to frequent clogging of the nozzle. We also study the number of cells in each droplet, when printed under optimal conditions. The probability density of this number follows a binomial distribution, which consistent with a uniform distribution of cells in the medium and within the printhead.

physics.bio-ph↗

arXiv2013

Observation of Coherence in the Photosystem II Reaction Center

Photosynthesis powers life on our planet. The basic photosynthetic architecture comprises antenna complexes to harvest solar energy and reaction centers to convert the energy into a stable charge separated state. In oxygenic photosynthesis, the initial charge separation event occurs in the photosystem II reaction center; the only known natural enzyme that uses solar energy to split water. Energy transfer and charge separation in photosynthesis are rapid and have high quantum efficiencies. Recently, nonlinear spectroscopic experiments have suggested that electronic coherence may play a role in energy transfer efficiency in antenna complexes. Here we report the observation of coherence in the photosystem II reaction center by two dimensional electronic spectroscopy. The frequencies of the observed coherences match exciton difference frequencies and/or known vibrational modes of the photosystem II reaction center. These observations raise questions about the possible role of electronic and/or vibrational coherence in the fundamental charge separation process in oxygenic photosynthesis.

physics.bio-ph↗

arXiv2013

Geometric analysis on the unidirectionality of the pulmonary veins for atrial reentry

It is widely believed that the pulmonary veins (PVs) of the atrium play the central role in the generation of atrial reentry leading to atrial fibrillation, but its mechanism has not been analytically explained. In order to improve the current clinical procedures for atrial reentry by understanding its mechanism, geometrical analysis is proposed on the conditions of conduction failure at the PVs and is validated by various computational modeling. To achieve this, a new analytic approach is proposed by adapting the geometric relative acceleration analysis from spacetime physics on the hypothesis that a large relative acceleration can translate to a dramatic increase in the curvature of the wavefront and subsequently to conduction failure. This analytic method is applied to a simplified model of the PV to reveal the strong dependency of the propagational direction and the magnitude of anisotropy for conduction failure. The unidirectionality of the PVs follows directly and is validated by computational tests in a T-shaped domain, computational simulations for three-dimensional atrial reentry and previous in-silico reports for atrial reentry.

physics.med-ph↗

arXiv2013

Spontaneous ordering of a bacterial drop into a spiral vortex

In this fluid dynamics video we explore the nature and causes of the spontaneous ordering that emerges in a dense bacterial suspension under confinement. Recent experiments with B. Subtilis confined within small flattened drops show that the bacteria form a steady single-vortex state with a counterrotating cell boundary layer. Using simulations that capture oriented cell-cell and cell-fluid interactions, we show that hydrodynamics is crucial in reproducing and explaining the phenomenon. We give new insights into the microscopic arrangement of the bacteria, which are confirmed by new experiments.

cond-mat.soft↗

arXiv2013

Lagerkvist versus Crick

Present day data allow significant reconsideration of ideas on mechanisms underlying the degeneracy in the genetic code. Here a hypothesis is presented which links the degeneracy to possible conformational alterations in the codon-anticodon duplex. This enables explanation of Rumer symmetry in the table of the genetic code, coding of methionine and tryptophane without degeneracy and predict significant difference between thymine and uracyl. The suggested hypothesis has something in common with Lagerkvist idea that only two nucleotides in codon are coding.

physics.bio-ph↗

arXiv2013

Fluid fragmentation from hospital toilets

Hospital-acquired infections represent significant health and financial burdens to society. Clostridium difficile (C. difficile) is a particularly challenging bacteria with the potential to cause severe diarrhea and death. One mode of transmission for C. difficile, as well as other pathogens, which has received little attention is the potential air contamination by pathogen-bearing droplets emanating from toilets. In the fluid dynamics video submitted to the APS DFD Gallery of Fluid Motion 2013, we present flow visualizations via high-speed recordings showing the capture of the product of the fluid fragmentation generated by hospital toilet high-pressure flushes. Important quantities of both large and small droplets are observed. We illustrate how high-pressure flushes and cleaning products currently used in hospital toilets result in aggravating, rather than alleviating, the suspension and recirculation of tenacious airborne pathogen-bearing droplets.

physics.flu-dyn↗

arXiv2013

Sensing viruses by mechanical tension of DNA in responsive hydrogels

The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much needed. To be relevant for a broad application in local health care centers, such tools should be relatively cheap and easy to use. Here we discuss the biophysical potential for the macroscopic detection of viruses based on the induction of a mechanical stress in a bundle of pre-stretched DNA molecules upon binding of viruses to the DNA. We show that the affinity of the DNA to the charged virus surface induces a local melting of the double-helix into two single-stranded DNA. This process effects a mechanical stress along the DNA chains leading to an overall contraction of the DNA. Our results suggest that when such DNA bundles are incorporated in a supporting matrix such as a responsive hydrogel, the presence of viruses may indeed lead to a significant, macroscopic mechanical deformation of the matrix. We discuss the biophysical basis for this effect and characterize the physical properties of the associated DNA melting transition. In particular, we reveal several scaling relations between the relevant physical parameters of the system. We promote this DNA-based assay for efficient and specific virus screening.

q-bio.BM↗

arXiv2013

A Cell-Level Mechanism of Contrast Gain Control

The gain of neurons' responses in the auditory cortex is sensitive to contrast changes in the stimulus within a spectrotemporal range similar to their receptive fields, which can be interpreted to represent the tuning of the input to a neuron. This indicates a local mechanism of contrast gain control, which we explore with a minimal mechanistic model here. Gain control through noisy input has been observed in vitro and in a range of computational models. We investigate the behaviour of the simplest of such models to showcase gain control, a stochastic leaky integrate-and-fire (sLIF) neuron, which exhibits gain control through divisive normalisation of the input both with and without accompanying subtractive shift of the input-response curve, depending on whether input noise is proportional to or independent of its mean. To get a more direct understanding of how the input statistics change the response, we construct an analytic approximation to the firing rate of a sLIF neuron constituted of the expression for the deterministic case and a weighted average over the derived approximate steady-state distribution of conductance due to poissonian synaptic inputs. This analytic approximation qualitatively produces the same behaviour as simulations and could be extended by spectrotemporally tuned inputs to give a simple, physiological and local mechanism of contrast gain control in auditory sensing, building on recent experimental work that has hitherto only been described by phenomenological models. By comparing our weighted average firing rate curve with the commonly used sigmoidal input-response function, we demonstrate a nearly linear relationship between both the horizontal shift (or stimulus inflection point) and the inverse gain of the sigmoid and statistics derived from the sLIF model parameters, thus providing a structural constraint on the sigmoid parameter choice.

q-bio.NC↗

arXiv2013

On the internalisation, intraplasmodial carriage and excretion of metallic nanoparticles in the slime mould Physarum polycephalum

The plasmodium of Physarum polycephalum is a large single cell visible with the naked eye. When inoculated on a substrate with attractants and repellents the plasmodium develops optimal networks of protoplasmic tubes which span sites of attractants (i.e. nutrients) yet avoid domains with a high nutrient concentration. It should therefore be possible to program the plasmodium towards deterministic adaptive transformation of internalised nano- and micro-scale materials. In laboratory experiments with magnetite nanoparticles and glass micro-spheres coated with silver metal we demonstrate that the plasmodium of P. polycephalum can propagate the nano-scale objects using a number of distinct mechanisms including endocytosis, transcytosis and dragging. The results of our experiments could be used in the development of novel techniques targeted towards the growth of metallised biological wires and hybrid nano- and micro-circuits.

cs.ET↗

arXiv2013

Tuneable drug-loading capability of chitosan hydrogels with varied network architectures

Advanced bioactive systems with defined macroscopic properties and spatio-temporal sequestration of extracellular biomacromolecules are highly desirable for next generation therapeutics. Here, chitosan hydrogels were prepared with neutral or negatively-charged crosslinkers in order to promote selective electrostatic complexation with charged drugs. Chitosan (CT) was functionalised with varied dicarboxylic acids, such as tartaric acid (TA), poly(ethylene glycol) bis(carboxymethyl) ether (PEG), 1.4-Phenylenediacetic acid (4Ph) and 5-Sulfoisophthalic acid monosodium salt (PhS), whereby PhS was hypothesised to act as a simple mimetic of heparin. ATR FT-IR showed the presence of C=O amide I, N-H amide II and C=O ester bands, providing evidence of covalent network formation. The crosslinker content was reversely quantified by 1H-NMR on partially-degraded network oligomers, so that 18 mol% PhS was exemplarily determined. Swellability, compressability, material morphology, and drug-loading capability were successfully adjusted based on the selected network architecture. Here, hydrogel incubation with model drugs of varied electrostatic charge, i.e. allura red (AR, --), methyl orange (MO, -) or methylene blue (MB, +), resulted in direct hydrogel-dye electrostatic complexation. Importantly, the cationic compound, MB, showed different incorporation behaviours, depending on the electrostatic character of the selected crosslinker. In light of this tuneable drug-loading capability, these CT hydrogels would be highly attractive as drug reservoirs towards e.g. the fabrication of tissue models in vitro.

physics.chem-ph↗

arXiv2013

Auto-chemotactic micro-swimmer suspensions: modeling, analysis and simulations

Microorganisms can preferentially orient and move along gradients of a chemo-attractant (i.e., chemotax) while colonies of many microorganisms can collectively undergo complex dynamics in response to chemo-attractants that they themselves produce. For colonies or groups of micro-swimmers we investigate how an "auto-chemotactic" response that should lead to swimmer aggregation is affected by the non-trivial fluid flows that are generated by collective swimming. For this, we consider chemotaxis models based upon a hydrodynamic theory of motile suspensions that are fully coupled to chemo-attractant production, transport, and diffusion. Linear analysis of isotropically ordered suspensions reveals both an aggregative instability due to chemotaxis that occurs independently of swimmer type, and a hydrodynamic instability when the swimmers are "pushers". Nonlinear simulations show nonetheless that hydrodynamic interactions can significantly modify the chemotactically-driven aggregation dynamics in suspensions of "pushers" or "pullers". Different states of the dynamics resulting from these coupled interactions in the colony are discussed.

physics.bio-ph↗

arXiv2013

Stochastic Turing patterns: analysis of compartment-based approaches

Turing patterns can be observed in reaction-diffusion systems where chemical species have different diffusion constants. In recent years, several studies investigated the effects of noise on Turing patterns and showed that the parameter regimes, for which stochastic Turing patterns are observed, can be larger than the parameter regimes predicted by deterministic models, which are written in terms of partial differential equations for species concentrations. A common stochastic reaction-diffusion approach is written in terms of compartment-based (lattice-based) models, where the domain of interest is divided into artificial compartments and the number of molecules in each compartment is simulated. In this paper, the dependence of stochastic Turing patterns on the compartment size is investigated. It has previously been shown (for relatively simpler systems) that a modeller should not choose compartment sizes which are too small or too large, and that the optimal compartment size depends on the diffusion constant. Taking these results into account, we propose and study a compartment-based model of Turing patterns where each chemical species is described using a different set of compartments. It is shown that the parameter regions where spatial patterns form are different from the regions obtained by classical deterministic PDE-based models, but they are also different from the results obtained for the stochastic reaction-diffusion models which use a single set of compartments for all chemical species. In particular, it is argued that some previously reported results on the effect of noise on Turing patterns in biological systems need to be reinterpreted.

physics.comp-ph↗

arXiv2013

A pattern-forming instability co-driven by distinct mechanisms increases pattern diversity

We use the context of dryland vegetation to study a general problem of complex pattern forming systems - multiple pattern-forming instabilities that are driven by distinct mechanisms but share the same spectral properties. We find that the co-occurrence of such instabilities results in the growth of a single mode rather than two interacting modes. The interplay between the two mechanisms, which promote or counteract each other, compensates for the simpler dynamics of a single mode by inducing higher pattern diversity. Possible implications to biodiversity of ecosystems are discussed.

nlin.PS↗

arXiv2013

Manipulate the coiling and uncoiling movements of Lepidoptera proboscis by its conformation optimizing

Many kinds of adult Lepidoptera insects possess a long proboscis which is used to suck liquids and has the coiling and uncoiling movements. Although experiments revealed qualitatively that the coiling movement is governed by the hydraulic mechanism and the uncoiling movement is due to the musculature and the elasticity, it needs a quantitative investigation to reveal how insects achieve these behaviors accurately. Here a quasi-one-dimensional (Q1D) curvature elastica model is proposed to reveal the mechanism of these behaviors. We find that the functions of internal stipes muscle and basal galeal muscle which locate at the bottom of proboscis are to adjust the initial states in the coiling and uncoiling processes, respectively. The function of internal galeal muscle which exists along proboscis is to adjust the line tension. The knee bend shape is due to the local maximal spontaneous curvature and is an advantage for nectar-feeding butterfly. When there is no knee bend, the proboscis of fruit-piercing butterfly is easy to achieve the piercing movement which induced by the increase of internal hydraulic pressure. All of the results are in good agreement with experiential observation. Our study provides a revelatory method to investigate the mechanical behaviors of other 1D biologic structures, such as proboscis of marine snail and elephant. Our method and results are also significant in designing the bionic devices.

q-bio.TO↗

arXiv2013

Generalized master equation for modular exciton density transfer

A generalized master equation (GME) governing quantum evolution of modular exciton density (MED) is derived for large scale light harvesting systems composed of weakly interacting modules of multiple chromophores. The GME-MED offers a practical framework to incorporate real time coherent quantum dynamics calculations at small length scales into dynamics over large length scales, without assumptions of time scale separation or specific forms of intra-module quantum dynamics. A test of the GME-MED for four sites of the Fenna-Matthews-Olson complex demonstrates how coherent dynamics of excitonic populations over many coupled chromophores can be accurately described by transitions between subgroups (modules) of delocalized excitons.

quant-ph↗

arXiv2013

Collective foraging in heterogeneous landscapes

Animals foraging alone are hypothesized to optimize the encounter rates with resources through Lévy walks. However, the issue of how the interactions between multiple foragers influence their search efficiency is still not completely understood. To address this, we consider a model to study the optimal strategy for a group of foragers searching for targets distributed heterogeneously. In our model foragers move on a square lattice containing immobile but regenerative targets. At any instant a forager is able to detect only those targets that happen to be in the same site. However, we allow the foragers to have information about the state of other foragers. A forager who has not detected any target walks towards the nearest location, where another forager has detected a target, with probability $\exp{\left(-αd\right)}$, where $d$ is the distance and $α$ is a parameter. The model reveals that neither overcrowding ($α\to 0$) nor independent searching ($α\to\infty$) is beneficial for the group. For patchy distribution of targets the efficiency is maximum for intermediate values of $α$. Also, in the limit $α\to 0$, the length of the walks can become scale-free.

physics.bio-ph↗

arXiv2013

A physicist's view of DNA

Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. Why then would a physicist be interested in these molecules? As we will see, DNA is an interesting molecular tool for physicists to test and explore physical laws and theories, like the ergodic theorem, the theory of elasticity and information theory. DNA also has unique material properties, which attract material scientists, nanotechnologists and engineers. Among interesting developments in this field are DNA-based hybrid materials and DNA origami.

physics.bio-ph↗