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At least 235 records · Page 13Linked to original sources
arXiv2013

Estimations of local thermal impact on living organisms irradiated by non-thermal microwaves

Pennes' differential equation for bioheat transfer and the heat transfer equation are solved for the temperature distribution in a living tissue with spherical inclusions, irradiated by microwave power. It is shown that relative temperature excess in a small inclusion in the tissue in some cases is inversely proportional to its radius and does not depend on the applied power. In pulsing RF fields the effect is amplified proportionally to the ratio of the pulse period to the pulse duration. The local temperature rise significantly outpaces the averaged one and therefore the Watt to Weight SAR limits may be insufficient to estimate the safety of RF radiation and the conventional division of the biological effects of electromagnetic fields on the thermal and non-thermal needs to be revised.

physics.bio-ph↗
arXiv2013

Undulations in a weakly interacting mechanically generated molecular braid under tension

We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid, steric interactions between the molecules, and external mechanical forces. In this model, both sets of ends, of the two molecules, are considered to be separated by a fixed distance apart much larger than the radius of the braid. One set of ends are rotated to generate a braid of a certain number of pitches (or turns), while the other set remains fixed. This model may describe the situation in which the ends of each molecule are attached to a substrate and a magnetic bead; to the latter a pulling force and rotational torque can be applied. We discuss various aspects of our model. Most importantly, an expression for the free energy is given, from which equations, determining the various geometric parameters of the braid, can be obtained. By numerically solving these equations, we give predictions from the model for the external torque needed to produce a braid with a certain number of turns per bending persistence length, as well as the end to end extension of the two molecules for a given pulling force. Other geometric parameters, as well as the lateral force required to keep the ends of the two molecules apart, are also calculated.

cond-mat.soft↗
arXiv2013

Prediction and Dissipation in Biochemical Sensing

Cells sense and predict their environment via energy-dissipating pathways. However, it is unclear whether dissipation helps or harms prediction. Here we study dissipation and prediction for a minimal sensory module of receptors that reversibly bind ligand. We find that the module performs short-term prediction optimally when operating in an adiabatic regime where dissipation vanishes. In contrast, beyond a critical forecast interval, prediction becomes most precise in a regime of maximal dissipation, suggesting that dissipative sensing in biological systems can serve to enhance prediction performance.

q-bio.MN↗
arXiv2013

Optimal shapes and stresses of adherent cells on patterned substrates

We investigate a continuum mechanical model for an adherent cell on two dimensional adhesive micropatterned substrates. The cell is modeled as an isotropic and homogeneous elastic material subject to uniform internal contractile stresses. The build-up of tension from cortical actin bundles at the cell periphery is incorporated by introducing an energy cost for bending of the cell boundary, resulting to a resistance to changes in local curvature. Integrin-based adhesions are modeled as harmonic springs, that pin the cell to adhesive patches of a predefined geometry. Using Monte Carlo simulations and analytical techniques we investigate the competing effects of bulk contractility and cortical bending rigidity in regulating cell shapes on non-adherent regions. We show that the crossover from convex to concave cell edges is controlled by the interplay between contractile stresses and boundary bending rigidity. In particular, the cell boundary becomes concave beyond a critical value of the contractile stress that is proportional to the cortical bending rigidity. Furthermore, the intracellular stresses are found largely concentrated at the concave edge of the cell. The model can be used to generate a cell-shape phase diagram for each specific adhesion geometry.

physics.bio-ph↗
arXiv2013

Cyclic and Coherent States in Flocks with Topological Distance

A simple model of the two dimensional collective motion of a group of mobile agents have been studied. Like birds, these agents travel in open free space where each of them interacts with the first $n$ neighbors determined by the topological distance with a free boundary condition. Using the same prescription for interactions used in the Vicsek model with scalar noise it has been observed that the flock, in absence of the noise, arrives at a number of interesting stationary states. In the `single sink state' the entire flock maintains perfect cohesion and coherence. In the `cyclic state' every agent executes a uniform circular motion, and the entire flock executes a pulsating dynamics i.e., expands and contracts periodically between a minimum and a maximum size of the flock. When refreshing rate of the interaction zone is the fastest, the entire flock gets fragmented into smaller clusters of different sizes. On introduction of scalar noise a crossover is observed when the agents cross over from a ballistic motion to a diffusive motion. Expectedly the crossover time is dependent on the strength of the noise $η$ and diverges as $η\to 0$. In simpler version the translational degrees of freedom of the agents are suppressed but their angular motion are retained. Here agents are the spins, placed at the sites of a square lattice with periodic boundary condition. Every spin interacts with its $n$ = 2, 3 or 4 nearest neighbors. In the stationary state the entire spin pattern moves as a whole when interactions are anisotropic with $n$ = 2 and 3; but it is completely frozen when the interaction is isotropic with $n=4$. These spin configurations have vortex-antivortex pairs whose density increases as the noise $η$ increases and follows an excellent finite-size scaling analysis.

physics.bio-ph↗
arXiv2014

Nanosystem Self-Assembly Pathways Discovered via All-Atom Multiscale Analysis

We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an $N$-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the classical Liouville equation. From a reduced statistical framework, rigorous stochastic equations for population levels of beginning, intermediate, and final aggregates are also derived. It is shown that the definition of an assembly type is a self-consistency criterion that must strike a balance between precision and the need for population levels to be slowly varying relative to the time scale of atomic motion. The deductive multiscale approach is complemented by a qualitative notion of multicomponent association and the ensemble of exact atomic-level configurations consistent with them. In processes such as viral self-assembly from proteins and RNA or DNA, there are many possible intermediates, so that it is usually difficult to predict the most efficient assembly pathway. However, in the current study, rates of assembly of each possible intermediate can be predicted. This avoids the need, as in a phenomenological approach, for recalibration with each new application. The method accounts for the feedback across scales in space and time that is fundamental to nanosystem self-assembly. The theory has applications to bionanostructures, geomaterials, engineered composites, and nanocapsule therapeutic delivery systems.

physics.bio-ph↗
arXiv2014

Effect of ionic ordering in conductivity experiments of DNA aqueous solutions

The effects of ionic ordering in DNA water solutions are studied by conductivity experiments. The conductivity measurements are performed for the solutions of DNA with KCl salt in the temperature range from 28 to 70 C. Salt concentration vary from 0 to 2 M. The conductivity of solutions without DNA but with the same concentration of KCl salt are also performed. The results show that in case of salt free solution of DNA the melting process of the double helix is observed, while in case of DNA solution with added salt the macromolecule denaturation is not featured. For salt concentrations lower than some critical one (0.4 M) the conductivity of DNA solution is higher than the conductivity of KCl water solution without DNA. Starting from the critical concentration the conductivity of KCl solution is higher than the conductivity of DNA solution with added salt. For description of the experimental data phenomenological model is elaborated basing on electrolyte theory. In framework of the developed model a mechanism of counterion ordering is introduced. According to this mechanism under the low salt concentrations electrical conductivity of the system is caused by counterions of DNA ion-hydrate shell. Increasing the amount of salt to the critical concentration counterions condense on DNA polyanion. Further increase of salt concentration leads to the formation of DNA-salt complexes that decreases the conductivity of the system.

q-bio.BM↗
arXiv2014

Cooperativity Can Enhance Cellular Signal Detection

Most sensory cells use surface receptors to detect environmental stimuli and initiate downstream signaling. Cooperative interactions among sensory receptors is known to play a crucial role in enhancing the sensitivity of biochemical processes such as oxygen sensing by hemoglobin, but whether cooperativity enhances the fidelity with which a system with multiple receptors can accurately and quickly detect a signal is poorly understood. We model the kinetics of small clusters of receptors in the presence of ligand, where the receptors act independently or cooperatively. We show that the interaction strength and how it is coupled to the dynamics influences the macroscopic observables. Contrary to recent reports, our analysis shows that receptor cooperativity can increase the signal-to-noise ratio, but this increase depends on the underlying dynamics of the signaling receptor cluster.

q-bio.MN↗
arXiv2014

Communities of dense weighted networks: MicroRNA co-target network as an example

Complex networks are intrinsically modular. Resolving small modules is particularly difficult when the network is densely connected; wide variation of link weights invites additional complexities. In this article we present an algorithm to detect community structure in densely connected weighted networks. First, modularity of the network is calculated by erasing the links having weights smaller than a cutoff $q.$ Then one takes all the disjoint components obtained at $q=q_c,$ where the modularity is maximum, and modularize the components individually using Newman Girvan's algorithm for weighted networks. We show, taking microRNA (miRNA) co-target network of Homo sapiens as an example, that this algorithm could reveal miRNA modules which are known to be relevant in biological context.

q-bio.MN↗
arXiv2013

Anisotropy mapping in rat brains using Intermolecular Multiple Quantum Coherence Effects

This document reports an unconventional and rapidly developing approach to magnetic resonance imaging (MRI) using intermolecular multiple-quantum coherences (iMQCs). Rat brain images are acquired using iMQCs. We detect iMQCs between spins that are 10 μm to 500 μm apart. The interaction between spins is dependent on different directions. We can choose the directions on physical Z, Y and X axis by choosing correlation gradients along those directions. As an important application, iMQCs can be used for anisotropy mapping. In the rat brains, we investigate tissue microstructure. We simulated images expected from rat brains without microstructure. We compare those with experimental results to prove that the dipolar field from the overall shape only has small contributions to the experimental iMQC signal. Because of the underlying low signal to noise ratio (SNR) in iMQCs, this anisotropy mapping method still has comparatively large potentials to grow. The ultimate goal of my project is to develop creative and effective methods of tissue microstructure anisotropy mapping. Recently we found that combining phase data of iMQCs images with phase data of modified-crazed images is very promising to construct microstructure maps. Some information and initial results are shown in this document.

physics.med-ph↗
arXiv2014

Towards plant wires

In experimental laboratory studies we evaluate a possibility of making electrical wires from living plants. In scoping experiments we use lettuce seedlings as a prototype model of a plant wire. We approximate an electrical potential transfer function by applying direct current voltage to the lettuce seedlings and recording output voltage. We analyse oscillation frequencies of the output potential and assess noise immunity of the plant wires. Our findings will be used in future designs of self-growing wetware circuits and devices, and integration of plant-based electronic components into future and emergent bio-hybrid systems.

cs.ET↗
arXiv2014

Hyperbolic statistics and entropy loss in the description of gene distributions

Zipf's law implies the statistical distributions of hyperbolic type, which can describe the properties of stability and entropy loss in linguistics. We present the information theory from which follows that if the system is described by distributions of hyperbolic type it leads to the possibility of entropy loss. We present the number of repetitions of genes in tne genomes for some bacteria, as Borelia burgdorferi and Escherichia coli. Distributions of repetitions of genes in genome appears to be represented by distributions of hyperbolic type.

physics.bio-ph↗
arXiv2014

Characterization of load bearing metrological parameters in reptilian exuviae in comparison to precision finished cylinder liner surfaces

Design of precise functional surfaces is essential for many future applications. In the technological realm, the accumulated experience with the construction of such surfaces is not sufficient. Nature provides many examples of dynamic surfaces worthy of study and adoption, at least as a concept, within human engineering. In this work, we probe load-bearing features of the ventral skin of snake surfaces. We examine the structure of two snake species that mainly move by rectilinear locomotion. These are Python regius (pythonidae) and Bittis gabonica (Vipridae). To this end, we focus on the load bearing characteristics of the ventral skin surface (i.e. the Rk family of parameters). Therefore, we draw detailed comparison between the reptilian surfaces and two sets of technological data. The first set pertains to an actual commercial cylinder liner, whereas, the second set is a summary of recommended surface finish metrological values for several commercial cylinder liner manufacturers. The results highlight several similarities between the two types of surfaces. In particular, we show that there is a striking correspondence between the sense of texture engineering within both surfaces (although that their construction evolved along entirely different paths). We also show that reptilian surfaces manifest a high degree of specialization with respect to habitat constraints on wear resistance and adhesive effects.

physics.bio-ph↗
arXiv2014

Conformation characters of gel sheets with rotational symmetry: the role of boundary

In this paper, we systemically study the conformation characters of rotational symmetric gel sheets with free boundary and investigate the role of boundary on the equilibrium conformation. In gel sheet the boundary provides a residual strain which leads to re-distribution of stress and impacts the shape of equilibrium conformation accordingly. For sheet with boundary, the in-plane stretching energy is far larger than the bending energy in some cases. It is intrinsic different from closed membrane. In gel sheets, the boundary doesn't only quantitatively amend to the elastic energy. The residual strain on boundary cooperates with bending and stretching to determine the equilibrium conformation rather than just the last two factors. Furthermore, on the boundary of gel sheet, there is an additional energy induced by boundary line tension $γ$. If $γ=0$, there is $10\%$ difference of elastic energy from the experimental result. Finally, we discuss the effects of such line tension $γ$ and propose a way to measure it by the border radius. It redounds to study the physical origination of $γ$.

physics.bio-ph↗
arXiv2014

Kirkwood-Shumaker interactions and general thermal fluctuation forces

We present an extension of the Kirkwood-Shumaker (KS) theory of proton-fluctuation interactions to situations where the perturbation theory, usually invoked to derive these interactions, fails. In order to do that we formulate a generalized theory of fluctuation interactions with non-linear macroion (surface) free energy term that naturally leads to the long-range KS interactions, but can also be straightforwardly generalized to situations where the perturbation expansion ceases to be valid. It also allows for other surface free energy terms to be treated within the same formalism, enabling us to derive the complete fluctuation interaction with monopolar and dipolar fluctuations included, leading to the KS theory as a limiting form.

physics.bio-ph↗
arXiv2014

The Gabor-Einstein Wavelet: A Model for the Receptive Fields of V1 to MT Neurons

Our visual system is astonishingly efficient at detecting moving objects. This process is mediated by the neurons which connect the primary visual cortex (V1) to the middle temporal (MT) area. Interestingly, since Kuffler's pioneering experiments on retinal ganglion cells, mathematical models have been vital for advancing our understanding of the receptive fields of visual neurons. However, existing models were not designed to describe the most salient attributes of the highly specialized neurons in the V1 to MT motion processing stream; and they have not been able to do so. Here, we introduce the Gabor-Einstein wavelet, a new family of functions for representing the receptive fields of V1 to MT neurons. We show that the way space and time are mixed in the visual cortex is analogous to the way they are mixed in the special theory of relativity (STR). Hence we constrained the Gabor-Einstein model by requiring: (i) relativistic-invariance of the wave carrier, and (ii) the minimum possible number of parameters. From these two constraints, the sinc function emerged as a natural descriptor of the wave carrier. The particular distribution of lowpass to bandpass temporal frequency filtering properties of V1 to MT neurons (Foster et al 1985; DeAngelis et al 1993b; Hawken et al 1996) is clearly explained by the Gabor-Einstein basis. Furthermore, it does so in a manner innately representative of the motion-processing stream's neuronal hierarchy. Our analysis and computer simulations show that the distribution of temporal frequency filtering properties along the motion processing stream is a direct effect of the way the brain jointly encodes space and time. We uncovered this fundamental link by demonstrating that analogous mathematical structures underlie STR and joint cortical spacetime encoding. This link will provide new physiological insights into how the brain represents visual information.

q-bio.NC↗
arXiv2014

Quantification of propidium iodide delivery with millisecond electric pulses: A model study

A model study of propidium iodide delivery with millisecond electric pulses is presented; this work is a companion of the experimental efforts by Sadik et al. [1]. Both membrane permeabilization and delivery are examined with respect to six extra-cellular conductivities. The transmembrane potential of the permeabilized regions exhibits a consistent value, which corresponds to a bifurcation point in the pore-radius-potential relation. Both the pore area density and membrane conductance increase with an increasing extra-cellular conductivity. On the other hand, the inverse correlation between propidium iodide delivery and extra-cellular conductivity as observed in the experiments is quantitatively captured by the model. This agreement confirms that this behavior is primarily mediated by electrophoretic transport during the pulse. The results suggest that electrophoresis is important even for the delivery of small molecules such as propidium iodide. The direct comparison between model prediction and experimental data presented in this work helps validate the former as a robust predictive tool for the study of electroporation.

physics.bio-ph↗