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At least 145 records · Page 8Linked to original sources

arXiv2011

Crosstalk between non-processive myosin motors mediated by the actin filament elasticity

Many biological processes involve the action of molecular motors that interact with the cell cytoskeleton. Some processes, such as the transport of cargoes is achieved mainly by the action of individual motors. Other, such as cell motility and division, require the cooperative work of many motors. Collective motor dynamics can be quite complex and unexpected. One beautiful example is the bidirectional ("back and forth") motion of filaments which is induced when the motors within a group exert forces in opposite directions. This review tackles the puzzle emerging from a recent experimental work in which it has been shown that the characteristic reversal times of the bidirectional motion are practically independent of the number of motors. This result is in a striking contradiction with existing theoretical models that predict an exponential growth of the reversal times with the size of the system. We argue that the solution to this puzzle may be the crosstalk between the motors which is mediated by the elastic tensile stress that develops in the cytoskeleton track. The crosstalk does not directly correlate the attachment and detachment of the motors, which work independently of each other. However, it highly accelerates their detachments by making the detachment rates system size dependent.

physics.bio-ph↗

arXiv2012

Let Us Dance Just a Little Bit More --- On the Information Capacity of the Human Motor System

Fitts' law is a fundamental tool in measuring the capacity of the human motor system. However, it is, by definition, limited to aimed movements toward spatially expanded targets. We revisit its information-theoretic basis with the goal of generalizing it into unconstrained trained movement such as dance and sports. The proposed new measure is based on a subject's ability to accurately reproduce a complex movement pattern. We demonstrate our framework using motion-capture data from professional dance performances.

cs.IT↗

arXiv2011

Mechanism of magnetic field effect in cryptochrome

Creatures as varied as mammals, fish, insects, reptiles, and migratory birds have an intriguing `sixth' sense that allows them to distinguish north from south by using the Earth's intrinsic magnetic field. Yet despite decades of study, the physical basis of this magnetic sense remains elusive. A likely mechanism is furnished by magnetically sensitive radical pair reactions occurring in the retina, the light-sensitive part of the eyes. A photoreceptor, cryptochrome, has been suggested to endow birds with magnetoreceptive abilities as the protein has been shown to exhibit the biophysical properties required for an animal magnetoreceptor to operate properly. Here, we propose a concrete light-driven reaction cycle in cryptochrome that lets a magnetic field influence the signaling state of the photoreceptor. The reaction cycle ties together transient absorption and electron-spin-resonance observations with known facts on avian magnetoreception. Our analysis establishes the feasibility of cryptochrome to act as a geomagnetic compass in birds, gives insight into structural and dynamic design features required for optimal detection of the geomagnetic field direction, and suggests further theoretical and experimental studies.

physics.bio-ph↗

arXiv2013

Electro-stimulation of Saccharomyces cerevisiae wine yeasts by Pulsed Electric Field and its effect on fermentation performance

The batch fermentation process, inoculated by pulsed electric field (PEF) treated wine yeasts (S. cerevisiae Actiflore F33), was studied. PEF treatment was applied to the aqueous yeast suspensions (0.12 % wt.) at the electric field strengths of E=100 and 6000 V/cm using the same pulse protocol (number of pulses of n=1000, pulse duration of ti=100 mks, and pulse repetition time of dt=100 ms). Electro-stimulation was confirmed by the observed growth of electrical conductivity of suspensions. The fermentation was running at 30°C for 150 hours in an incubator with synchronic agitation. The obtained results clearly evidence the positive impact of PEF treatment on the batch fermentation process. Electro-stimulation resulted in improvement of such process characteristics as mass losses, consumption of soluble matter content (°Brix) and synthesis of proteins. It also resulted in a noticeable acceleration of consumption of sugars at the initial stage of fermentation in the lag phase. At the end of the lag phase (t=40 hours), consumption of fructose in samples with electrically activated inocula exceeded fructose consumption in samples with control inocula by 2.33 times when it was activated at E=100 V/cm and by 3.98 times after treatment at E=6000 V/cm. At the end of the log phase (120 hours of fermentation), 30% mass reduction was reached in samples with PEF-treated inocula (E=6000 V/cm), whereas the same mass reduction of the control sample required approximately, 20 hours of extra fermentation. The possible mechanisms of electro-stimulation are also discussed in details.

physics.bio-ph↗

arXiv2013

In Silico Design, Extended Molecular Dynamic Simulations and Binding Energy Calculations for a New Series of Dually Acting Inhibitors against EGFR and HER2

Starting from the lead structure we have identified in our previous works, we are extending our insight understanding of its potential inhibitory effect against both EGFR and HER2 receptors. Herein and using extended molecular dynamic simulations and different scoring techniques, we are providing plausible explanations for the observed inhibitory effect. Also, we are comparing the binding mechanism in addition to the dynamics of binding with two other approved inhibitors against EGFR (Lapatinib) and HER2 (SYR). Based on this information, we are also designing and in silico screening new potential inhibitors sharing the same scaffold of the lead structure. We have chosen the best scoring inhibitor for additional in silico investigation against both the wild-type and T790M mutant strain of EGFR. It seems that certain substitution pattern guarantees the binding to the conserved water molecule commonly observed with kinase crystal structures. Also, the new inhibitors seem to form a stable interaction with the mutant strain as a direct consequence of their enhanced ability to form additional interactions with binding site residues.

q-bio.BM↗

arXiv2013

One and Two-individual Movements of Fish after Chemical Exposure

Movement behavior of an indicator species, zebrafish (Danio rerio), was analyzed with one- and two-individual groups before and after treatment with a toxic chemical, formaldehyde, at a low concentration (1 ppm). After the boundary area had been determined based on experimental data, intermittency was defined as the probability distributions of the shadowing time during which data were above a pre-determined threshold and were obtained from experimental time-series data on forces and the inter-distances for one and two individuals. Overall intermittencies were similar in the boundary and central areas. However, the intermittencies were remarkably different between the one- and the two-individual groups: the single line was used to fit the data for the one-individual group whereas two phases were observed with breakpoints (approximately 10 seconds in logarithm) in the exponential fitting curves for the two-individual group. A difference in the probability distributions of shadowing time was observed "before" and "after" treatment for different areas. Intermittency patterns before and after treatment were contrasted in the center for the one-individual group whereas the difference was observed in the boundary for two-individual group. The intermittencies for the inter-distances of two individuals in the boundary and central areas were markedly different before and after treatment. When the differences between the intermittencies in the boundary and the central areas and between "before" and "after" treatment are considered, the distribution patterns of the shadowing time (scaling behaviors or intermittency patterns) should be a useful means of bio-monitoring to detect contaminants in the environment.

physics.bio-ph↗

arXiv2013

Slime mould tactile sensor

Slime mould P. polycephalum is a single cells visible by unaided eye. The cells shows a wide spectrum of intelligent behaviour. By interpreting the behaviour in terms of computation one can make a slime mould based computing device. The Physarum computers are capable to solve a range of tasks of computational geometry, optimisation and logic. Physarum computers designed so far lack of localised inputs. Commonly used inputs --- illumination and chemo-attractants and -repellents --- usually act on extended domains of the slime mould's body. Aiming to design massive-parallel tactile inputs for slime mould computers we analyse a temporal dynamic of P. polycephalum's electrical response to tactile stimulation. In experimental laboratory studies we discover how the Physarum responds to application and removal of a local mechanical pressure with electrical potential impulses and changes in its electrical potential oscillation patterns.

cs.ET↗

arXiv2013

Diagnosing Heterogeneous Dynamics in Single Molecule/Particle Trajectories with Multiscale Wavelets

We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large datasets generated in single molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw data to locally match dynamics of interest. This is accomplished using statistically adaptive universal thresholding, whose advantage is to avoid a single arbitrary threshold that might conceal individual variability across populations. How to implement this multiscale method is described, focusing on local confined diffusion separated by transient transport periods or hopping events, with 3 specific examples: in cell biology, biotechnology, and glassy colloid dynamics. This computationally-efficient method can run routinely on hundreds of millions of data points analyzed within an hour on a desktop personal computer.

physics.data-an↗

arXiv2013

Searching with and against the stream: Levy or Brown?

We study the efficiency of search processes based on Levy flights (LFs) with power-law distributed jump lengths in the presence of an external drift. While LFs turn out to be efficient search processes when relative to the starting point the target is upstream, in the downstream scenario regular Brownian motion turns out to be advantageous. This is caused by the occurrence of leapovers of LFs, due to which LFs typically overshoot a point in space. We establish criteria when the combination of the external stream and the initial distance between the starting point and the target favors LFs over regular Brownian search. Contrary to the common belief that LFs with a stable index alpha=1 are optimal, we find that the optimal alpha may range in the entire interval (1,2) and even include Brownian motion as the overall most efficient search strategy.

cond-mat.stat-mech↗

arXiv2013

Forster Resonance Energy Transfer and Laser Fluorescent Analysis of Defects in DNA Double Helix

Real time laser induced fluorescence spectroscopy usage for microanalysis of DNA double helix defects is shown. The method is based on Forster resonance energy transfer (FRET) in intercalator-donor pair (acridine orange as a donor and ethidium bromide as an acceptor). Transition metal ions such as Cu(II), Cu(I), Ag(I), silver nanoparticles (AgNPs), photo- and thermo effects were used to cause double helix defects in DNA. FRET radii were experimentally estimated in background electrolyte solution (0.01 M NaNO3) and proved to be 3.9 +- 0.3 nm and the data are in satisfactory agreement with the theoretically calculated value Ro = 3.5 +- 0.3 nm. Concentration of DNA sites, exposed to Cu(II), Cu(I), Ag(I) ions, AgNPs impact as well as laser irradiation (λ = 457 nm) and temperature, which are applicable for intercalation, were estimated in relative units. FRET method allows to estimate the concentration of double helix areas with high quality stability applicable for intercalation in DNA after it was subjected to stress effect. It gives the opportunity to compare DNAs of 1) different origin; 2) with various damage degrees; 3) being in various functional state.

physics.bio-ph↗

arXiv2013

Activity and Steady-State Kinetics of One-Dimensional Kinetic Ising Model

In this work we focused on the kinetics of a one-dimensional Ising system (1DIS) with constant nearest-neighbor interaction (NNI). The exact solution of both thermodynamics and kinetics of this system under quasi-chemical approximation (QCA) had been shown in the literature, and the equilibrium solution was exact. In this work, it was discussed why QCA applied the best in the case of 1DIS with constant NNI. Furthermore, extension had been made to discuss that due to this special reason, perhaps the kinetics of the system under QCA is the correct steady-state kinetics. Inspired by this observation, the activity and activity coefficients of the system was studied closely to re-examine the form of the equation of motion under QCA. A novel concept---the instantaneous activities and the corresponding instantaneous activity coefficients---was introduced, and in terms of these quantities the kinetics seemed to be much simpler and physically more meaningful. The chevron plot of this system was also discussed and new way of looking at the \emph{rollover} of chevron plots was presented.

physics.bio-ph↗

arXiv2014

Non-Newtonian Rheology in Blood Circulation

Blood is a complex suspension that demonstrates several non-Newtonian rheological characteristics such as deformation-rate dependency, viscoelasticity and yield stress. In this paper we outline some issues related to the non-Newtonian effects in blood circulation system and present modeling approaches based mostly on the past work in this field.

physics.flu-dyn↗

arXiv2013

Free energy barrier for melittin reorientation from a membrane-bound state to a transmembrane state

An important step in a phospholipid membrane pore formation by melittin antimicrobial peptide is a reorientation of the peptide from a surface into a transmembrane conformation. In this work we perform umbrella sampling simulations to calculate the potential of mean force (PMF) for the reorientation of melittin from a surface-bound state to a transmembrane state and provide a molecular level insight into understanding peptide and lipid properties that influence the existence of the free energy barrier. The PMFs were calculated for a peptide to lipid (P/L) ratio of 1/128 and 4/128. We observe that the free energy barrier is reduced when the P/L ratio increased. In addition, we study the cooperative effect; specifically we investigate if the barrier is smaller for a second melittin reorientation, given that another neighboring melittin was already in the transmembrane state. We observe that indeed the barrier of the PMF curve is reduced in this case, thus confirming the presence of a cooperative effect.

physics.bio-ph↗

arXiv2013

Slimy hairs: Hair sensors made with slime mould

Slime mould Physarum polycephalum is a large single cell visible by unaided eye. We design a slime mould implementation of a tactile hair, where the slime mould responds to repeated deflection of hair by an immediate high-amplitude spike and a prolonged increase in amplitude and width of its oscillation impulses. We demonstrate that signal-to-noise ratio of the Physarum tactile hair sensor averages near six for the immediate response and two for the prolonged response.

cs.ET↗

arXiv2013

Prediction of the effective force on DNA in a nanopore based on density functional theory

We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore was presented, in which density functional theory (DFT) combined with the continuum Navier-Stokes (NS) equations is utilized to investigate electro-osmotic flow and the viscous drag force acting on the DNA inside a nanopore. Surface charge on the walls of the nanopore is also taken into account in our model. The consistence between our calculation and the previous experimental measurement indicates that the present theoretical model is an effective tool to predict the hydrodynamic resistance on DNA. Results show that charge inversion, which cannot be obtained by the Poisson-Boltzmann (PB) model, will reduce electro-osmotic velocity, or even lead to flow reversal for higher salt concentration. This is helpful to raise the effective force profoundly in the overscreening region.

cond-mat.soft↗

arXiv2013

Computational investigations of folded self-avoiding walks related to protein folding

Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are studied computationally in this article. We show that these two sets are equal and correspond to the whole $n$-step self-avoiding walks for $n\leqslant 14$, but that they are different for numerous $n \geqslant 108$, which are common protein lengths. Concrete counterexamples are provided and the computational methods used to discover them are completely detailed. A tool for studying these subsets of walks related to both pivot moves and proteins conformations is finally presented.

q-bio.BM↗

arXiv2013

The remarkable discreteness of being

Life is a discrete, stochastic phenomena : for a biological organism, the time of the two most important events of its life (reproduction and death) is random and these events change the number of individuals of the species by single units. These facts can have surprising, counter-intuitive consequences. I review here three examples where these facts play, or could play, important roles : the spatial distribution of species, the biodiversity and the (Darwinian) evolution of altruistic behavior.

physics.bio-ph↗

arXiv2013

When does TMAO fold a polymer chain and urea unfold it?

Longstanding mechanistic questions about the role of protecting osmolyte trimethylamine N- oxide (TMAO) which favors protein folding and the denaturing osmolyte urea are addressed by studying their effects on the folding of uncharged polymer chains. Using atomistic molecular dynamics simulations, we show that 1-M TMAO and 7-M urea solutions act dramatically differently on these model polymer chains. Their behaviors are sensitive to the strength of the attractive dispersion interactions of the chain with its environment: when these dispersion interactions are high enough, TMAO suppresses the formation of extended conformations of the hydrophobic polymer as compared to water, while urea promotes formation of extended conformations. Similar trends are observed experimentally on real protein systems. Quite surprisingly, we find that both protecting and denaturing osmolytes strongly interact with the polymer, seemingly in contrast with existing explanations of the osmolyte effect on proteins. We show that what really matters for a protective osmolyte is its effective depletion as the polymer conformation changes, which leads to a negative change in the preferential binding coefficient. For TMAO, there is a much more favorable free energy of insertion of a single osmolyte near collapsed conformations of the polymer than near extended conformations. By contrast, urea is preferentially stabilized next to the extended conformation and thus has a denaturing effect.

physics.bio-ph↗