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At least 613 records · Page 34Linked to original sources

arXiv2014

Multibody simulation of adhesion pili

We present a coarse grained rigid multibody model of a subunit assembled helix-like polymer, e.g., adhesion pili expressed by bacteria, that is capable of describing the polymers force-extension response. With building blocks representing individual subunits the model appropriately describes the complex behavior of pili expressed by the gram-negative uropathogenic Escherichia coli bacteria under the action of an external force. Numerical simulations show that the dynamics of the model, which include both the effects of unwinding and rewinding, are in good quantitative agreement with the characteristic force-extension response as observed experimentally for type 1 and P pili. By tuning the model, it is also possible to reproduce the force-extension response in the presence of anti-shaft antibodies, which dramatically changes the mechanical properties. Thus, the model and the results in this work give enhanced understanding of how a pilus unwinds under action of external forces and provide new perspective of the complex bacterial adhesion processes.

physics.bio-ph↗

arXiv2016

A statistical mechanical model of closed loop plectoneme supercoiling and its variational approximation

Presented here, is a technical manuscript that may form the basis of later published work. In it, we develop a statistical mechanical model to describe a closed loop plectoneme, applicable for when the closed loop is sufficiently supercoiled. The model divides the system up into end loops and a braided section; the end loops are assumed to contribute little to the super-coil writhe. Within the braided section, the model incorporates interactions that depend on the structure of the molecule; in particular, we consider those that depend on helical structure. A method for approximating the steric interactions is utilized that we had previously used in other publications. We go on to construct variational approximations for our closed loop plectoneme model in two cases. The first case is where helix dependent interactions are strong, and in the second case they are considered weak. In developing these approximations, we approximate the Fuller-White condition by replacing, in all expressions that depend on twist, writhe with average writhe, valid when the braided section is sufficiently long. How this approximation is made and the conditions when this approximation is valid are also discussed. The approximation allows for a Legendre transformation of the free energy, which with the introduction of moment (or torque), effectively allowing for twist and average writhe to be treated independently in the transformed (Gibbs like) free energy. Next, we then show how one may compute the average writhe of the braided section. Lastly, we discuss how some of the approximations considered may be relaxed, and discuss how the resulting model free energy might be computed by MC simulation.

cond-mat.soft↗

arXiv2014

Studies of protein adsorption on implant materials in relation to biofilm formation I. Activity of Pseudomonas aeruginosa on Polypropylene and High density Polyethylene in presence of serum albumin

The surface of biomaterials used as implants are highly susceptible to bacterial colonization and subsequent infection. The amount of protein adsorption on biomaterials, among other factors, can affect the nature and quality of biofilms formed on them. The variation in the adsorption time of the protein on the biomaterial surface produces a phenotypic change in the bacteria by alteration of the production of EPS (exoplysaccharide) matrix. Knowledge of the effects of protein adsorption on implant infection will be very useful in understanding the chemistry of the biomaterial surfaces, which can deter the formation of biofilms. It is observed that the adsorption of BSA on the biomaterial surfaces increases with time and concentration, irrespective of their type and the nature of the EPS matrix of the bacterial biofilm is dependent on the amount of protein adsorbed on the biomaterial surface. The adsorption of protein (BSA) on the biomaterials, polypropylene (PP) and high density polyethylene (HDPE) has been studied and the formation of the biofilms of Pseudomonas aeruginosa on them has been examined.

physics.bio-ph↗

arXiv2016

Motion of an elastic capsule in a constricted microchannel

We study the motion of an elastic capsule through a microchannel characterized by a localized constriction. We consider a capsule with a stress-free spherical shape and impose its steady state configuration in an infinitely long straight channel as the initial condition for our calculations. We report how the capsule deformation, velocity, retention time, and maximum stress of the membrane are affected by the capillary number, Ca, and the constriction shape. We estimate the deformation by measuring the variation of the three-dimensional surface area and a series of alternative quantities easier to extract from experiments. These are the Taylor parameter, the perimeter and the area of the capsule in the spanwise plane. We find that the perimeter is the quantity that reproduces the behavior of the three-dimensional surface area the best. We observe that, in general, area-deformation correlated quantities grow linearly with Ca, while velocity-correlated quantities saturate for large Ca but display a steeper increase for small Ca. The velocity of the capsule divided by the velocity of the flow displays, surprisingly, two different qualitative behaviors for small and large capillary numbers. Finally, we report that longer constrictions and spanwise wall bounded (versus spanwise periodic) domains cause larger deformations and velocities. If the deformation and velocity in the spanwise wall bounded domains are rescaled by the initial equilibrium deformation and velocity, their behavior is undistinguishable from that in a periodic domain. In contrast, a remarkably different behavior is reported in sinusoidally shaped and smoothed rectangular constrictions indicating that the capsule dynamics is particularly sensitive to abrupt changes in the cross section. In a smoothed rectangular constriction larger deformations and velocities occur over a larger distance.

physics.flu-dyn↗

arXiv2014

Disorder and Power-law Tails of DNA Sequence Self-Alignment Concentrations in Molecular Evolution

The self-alignment concentrations, $c(x)$, as functions of the length, $x$, of the identically matching maximal segments in the genomes of a variety of species, typically present power-law tails extending to the largest scales, i.e., $c(x) \propto x^α$, with similar or apparently different negative $α$s ($<-2$). The relevant fundamental processes of molecular evolution are segmental duplication and point mutation, and that recently the stick fragmentation phenomenology has been used to account the neutral evolution. However, disorder is intrinsic to the evolution system and, by freezing it in time (quenching) for the setup of a simple fragmentation model, we obtain decaying, steady-state and the general full time-dependent solutions, all $\propto x^α$ for $x\to \infty$, which is in contrast to the only power-law solution, $x^{-3}$ for $x\to 0$ of the pure model (without disorder). %Other algebraic terms may dominate at intermediate scales, which seems to be confirmed by some species, such as rice. We also present self-alignment results showing more than one scaling regimes, consistent with the theoretical results of the existence of more than one algebraic terms which dominate at different regimes.

q-bio.PE↗

arXiv2014

High-throughput screening for modulators of cellular contractile force

When cellular contractile forces are central to pathophysiology, these forces comprise a logical target of therapy. Nevertheless, existing high-throughput screens are limited to upstream signaling intermediates with poorly defined relationship to such a physiological endpoint. Using cellular force as the target, here we screened libraries to identify novel drug candidates in the case of human airway smooth muscle cells in the context of asthma, and also in the case of Schlemm's canal endothelial cells in the context of glaucoma. This approach identified several drug candidates for both asthma and glaucoma. We attained rates of 1000 compounds per screening day, thus establishing a force-based cellular platform for high-throughput drug discovery.

physics.bio-ph↗

arXiv2014

A semiclassical non-adiabatic theory for elementary chemical reactions

Electron Transfer (ET) reactions are modeled by the dynamics of a quantum two-level system (representing the electronic state) coupled to a thermalized bath of classical harmonic oscillators (representing the nuclei degrees of freedom). Unlike for the standard Marcus theory, the complex amplitudes of the electronic state are chosen as reaction coordinates. Then, the dynamical equations at non vanishing temperature become those of an effective Hamiltonian submitted to damping terms and their associated Langevin random forces. The advantage of this new formalism is to extend the original theory by taking into account both ionic and covalent interactions. The standard theory is recovered only when covalent interactions are neglected. Increasing these covalent interactions from zero, the energy barrier predicted by the standard theory first depresses, next vanish (or almost vanish) and for stronger covalent interactions, covalent bond formation takes place of ET. In biochemistry, the standard Marcus theory often fails to explain the enzymatic reactions especially those with non Arrhenius behavior which are barrierless and also dissipate little heat. We claim that this improved theory should yield an interesting tool for understanding them.

physics.chem-ph↗

arXiv2014

Biological effects of pulsating magnetic fields: role of solitons

In this paper, we analyze biological effects produced by magnetic fields in order to elucidate the physical mechanisms, which can produce them. We show that there is a chierarchy of such mechanisms and that the mutual interplay between them can result in the synergetic outcome. In particular, we analyze the biological effects of magnetic fields on soliton mediated charge transport in the redox processes in living organisms. Such solitons are described by nonlinear systems of equations and represent electrons that are self-trapped in alpha-helical polypeptides due to the moderately strong electron-lattice interaction. They represent a particular type of disssipativeless large polarons in low-dimensional systems. We show that the effective mass of solitons in the is different from the mass of free electrons, and that there is a resonant effect of the magnetic fields on the dynamics of solitons, and, hence, on charge transport that accompanies photosynthesis and respiration. These effects can result in non-thermal resonant effects of magnetic fields on redox processes in particular, and on the metabolism of the organism in general. This can explain physical mechanisms of therapies based on applying magnetic fields.

physics.bio-ph↗

arXiv2015

Swimming in a Crystal:

We study catalytic Janus swimmers and Escherichia coli bacteria swimming in a two-dimensional colloidal crystal. The Janus swimmers orbit individual colloids and hop between colloids stochastically, with a hopping rate that varies inversely with fuel (hydrogen peroxide) concentration. At high fuel concentration, these orbits are stable for 100s of revolutions, and the orbital speed oscillates periodically as a result of hydrodynamic, and possibly also phoretic, interactions between the swimmer and the six neighbouring colloids. Motile E.~coli bacteria behave very differently in the same colloidal crystal: their circular orbits on plain glass are rectified into long, straight runs, because the bacteria are unable to turn corners inside the crystal.

cond-mat.soft↗

arXiv2014

Holographic imaging of unlabelled sperm cells for semen analysis: a review

Male reproductive health in both humans and animals is an important research field in biological study. In order to characterize the morphology, the motility and the concentration of the sperm cells, which are the most important parameters to feature them, digital holography demonstrated to be an attractive technique. Indeed, it is a labelfree, non-invasive and high-resolution method that enables the characterization of live specimen. The review is intended both for summarize the state-of-art on the semen analysis and recent achievement obtained by means of digital holography and for exploring new possible applications of digital holography in this field.

physics.bio-ph↗

arXiv2014

Shape reconstruction and height fluctuations of red blood cells using defocusing microscopy

In this paper the bright-field defocusing microscopy (DM) technique is presented. DM is able to obtain quantitative information of each plane/surface of pure phase objects, as live unlabeled cells, and its application to red blood cells (RBCs) is demonstrated. Based on contrast, simple methods to obtain thickness profile and three dimensional (3D) total reconstruction of RBCs are proposed and the actual height profiles of upper and lower surface-membranes (lipid bilayer$/$cytoskeleton) of discocyte and stomatocyte red cells are presented as examples. In addition, using the mean square contrast fluctuation and modeling the RBC membranes fluctuations spectra as dependent of a bending modulus $(κ_c)$, a surface tension $(σ)$ and a confining potential $(γ)$ term, slowly varying quantities along the cell radius, a genetic algorithm (GA) is used and the radial height fluctuations of each surface-membrane are accessed, separately. The radial behaviors of $κ_c$, $σ$ and $γ$ are also obtained, allowing the discussion of physical aspects of the RBC membrane.

physics.bio-ph↗

arXiv2016

The inductive theory of natural selection: summary and synthesis

The theory of natural selection has two forms. Deductive theory describes how populations change over time. One starts with an initial population and some rules for change. From those assumptions, one calculates the future state of the population. Deductive theory predicts how populations adapt to environmental challenge. Inductive theory describes the causes of change in populations. One starts with a given amount of change. One then assigns different parts of the total change to particular causes. Inductive theory analyzes alternative causal models for how populations have adapted to environmental challenge. This chapter emphasizes the inductive analysis of cause.

q-bio.PE↗

arXiv2014

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignment

Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition is still an unsolved puzzle. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular electrostatic ones. In this proposed mechanism, sequences having the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts; the difference termed the recognition energy. Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding was termed the recognition well. We find that there is recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations, and consider more rigorously the optimization of the orientations of the fragments about their long axes. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. However when torsional flexibility of the DNA molecules is introduced, we find excellent agreement between analytical approximation and simulation.

physics.bio-ph↗

arXiv2014

Theory of cargo and membrane trafficking

Endocytosis underlies many cellular functions including signaling and nutrient uptake. The endocytosed cargo gets redistributed across a dynamic network of endosomes undergoing fusion and fission. Here, a theoretical approach is reviewed which can explain how the microscopic properties of endosome interactions cause the emergent macroscopic properties of cargo trafficking in the endosomal network. Predictions by the theory have been tested experimentally and include the inference of dependencies and parameter values of the microscopic processes. This theory could also be used to infer mechanisms of signal-trafficking crosstalk. It is applicable to in vivo systems since fixed samples at few time points suffice as input data.

q-bio.SC↗

arXiv2014

Non-constrictive bead immobilization leading to decreased and uniform shear stress in microfluidic bead-based ELISA

Microfluidic biosensors have been utilized for sensing a wide range of antigens using numerous configurations. Bead based microfluidic sensors have been a popular modality due to the plug and play nature of analyte choice and the favorable geometry of spherical sensor scaffolds. While constriction of beads against fluid flow remains a popular method to immobilize the sensor, it results in poor fluidic regimes and shear conditions around sensor beads that can affect sensor performance. We present an alternative means of sensor bead immobilization using poly-carbonate membrane. This system results in several orders of magnitude lower variance of flow radially around the sensor bead. Shear stress experienced by our non-constrictive immobilized bead was three orders of magnitude lower. We demonstrate ability to quantitatively sense EpCAM protein, a marker for cancer stem cells and operation under both far-red and green wavelengths with no auto-fluorescence.

physics.bio-ph↗

arXiv2014

New oil modified acrylic polymer for pH sensitive drug release: Experimental results and statistical analysis

We report results of an experimental study, complemented by detailed statistical analysis of the experimental data, on the development of a more effective control method of drug delivery using a pH sensitive acrylic polymer. New copolymers based on acrylic acid and fatty acid are constructed from dodecyl castor oil and a tercopolymer based on methyl methacrylate, acrylic acid and acryl amide were prepared using this new approach. Water swelling characteristics of fatty acid, acrylic acid copolymer and tercopolymer respectively in acid and alkali solutions have been studied by a step-change method. The antibiotic drug cephalosporin and paracetamol have also been incorporated into the polymer blend through dissolution with the release of the antibiotic drug being evaluated in bacterial stain media and buffer solution. Our results show that the rate of release of paracetamol getss affected by the pH factor and also by the nature of polymer blend. Our experimental data have later been statistically analyzed to quantify the precise nature of polymer decay rates on the pH density of the relevant polymer solvents. The time evolution of the polymer decay rates indicate a marked transition from a linear to a strictly non-linear regime depending on the whether the chosen sample is a general copolymer (linear) or a tercopolymer (non-linear). Non-linear data extrapolation techniques have been used to make probabilistic predictions about the variation in weight percentages of retained polymers at all future times, thereby quantifying the degree of efficacy of the new method of drug delivery.

physics.bio-ph↗

arXiv2014

Alternative statistical methods for cytogenetic radiation biological dosimetry

The paper presents alternative statistical methods for biological dosimetry, such as the Bayesian and Monte Carlo method. The classical Gaussian and robust Bayesian fit algorithms for the linear, linear-quadratic as well as saturated and critical calibration curves are described. The Bayesian model selection algorithm for those curves is also presented. In addition, five methods of dose estimation for a mixed neutron and gamma irradiation field were described: two classical methods, two Bayesian methods and one Monte Carlo method. Bayesian methods were also enhanced and generalized for situations with many types of mixed radiation. All algorithms were presented in easy-to-use form, which can be applied to any computational programming language. The presented algorithm is universal, although it was originally dedicated to cytogenetic biological dosimetry of victims of a nuclear reactor accident.

stat.ME↗

arXiv2014

Single-enzyme kinetics with branched pathways: exact theory and series expansion

The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on the substrate concentration [S] is one of the fundamental challenges in single molecule enzymology. The distribution of the times of dwell of a molecular motor at the successive positions on its track is an analogous quantity. We derive approximate series expansions for the [ATP]-dependence of the first two moments of the dwell time distributions of motors that catalyze hydrolysis of ATP to draw input energy. Comparison between our results for motors with branched pathways and the corresponding expressions reported earlier for linear enzymatic pathways provides deep insight into the effects of the branches. Such insight is likely to help in discovering the most general form of [S]-dependence of these fundamental distributions.

physics.chem-ph↗