SEARCH · Searcharxiv

Results for “physics.bio-ph”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources

arXiv2017

Can Occipital Alpha Neurofeedback Influence LTRCs and Deterministic ERPs without Critical Branching?

Critical branching is a theoretical interaction in-between simple units, such as neuronal elements of the human brain. Zhigalov, Kaplan, and Palva (2016, Clin. Neurophysiol., 127(8), 2882-2889) revealed that neurofeedback flash stimulation locked to the phase of high-amplitude occipital alpha influences stimulus-locked occipital averages in the alpha-band. This feedback also influences the power scaling of long-range temporal correlations in alpha-band amplitude fluctuations. Seemingly, neurofeedback influences critical branching alongside there being an interaction between ongoing neuronal activity and evoked responses. However, the causal relations between these neuronal long-range temporal correlations, sustained attention, and any avalanche dynamics are called into question. Further, uncorrected concerns include false discovery rate and an objective mathematical error in the precedent (Palva et al., 2013, Proc. Nat. Acad. Sci. U.S.A., 110(9), 3585-3590). An alternative set of illustrative mathematical principles offers a preliminary fit to the effects in the data. That is, neurofeedback influences the deterministic contribution to the single-trial event-related potentials, which each flash evokes, separately from the oscillatory alpha gain that those flashes cause. Accordingly, distinct principles of this neurofeedback-related exponential occipital oscillatory alpha gain and deterministic event-related potential generation produce micro-behaviours with macroscale consequences: neurofeedback causally influences power-scaling of long-range temporal correlations without critical branching.

q-bio.NC↗

arXiv2017

Hindrances to precise recovery of cellular forces in fibrous biopolymer networks

How cells move through the three-dimensional extracellular matrix (ECM) is of increasing interest in attempts to understand important biological processes such as cancer metastasis. Just as in motion on flat surfaces, it is expected that experimental measurements of cell-generated forces will provide valuable information for uncovering the mechanisms of cell migration. However, the recovery of forces in fibrous biopolymer networks may suffer from large errors. Here, within the framework of lattice-based models, we explore possible issues in force recovery by solving the inverse problem: how can one determine the forces cells exert to their surroundings from the deformation of the ECM? Our results indicate that irregular cell traction patterns, the uncertainty of local fiber stiffness, the non-affine nature of ECM deformations and inadequate knowledge of network topology will all prevent the precise force determination. At the end, we discuss possible ways of overcoming these difficulties.

physics.bio-ph↗

arXiv2017

Double-temperature ratchet model and current reversal of coupled Brownian motors

On the basis of the transport features and experimental phenomena observed in studies of molecular motors, we proposea double-temperature ratchet model of coupled motors to reveal the dynamical mechanism of cooperative transport of motors with two heads, where the interactions and asynchrony between two motor heads are taken into account. We investigate the collective unidirectional transport of coupled system and find that the direction of motion can be reversed under certain conditions. Reverse motion can be achieved by modulating the coupling strength, coupling free length, and asymmetric coefficient of the periodic potential, which is understood in terms of the effective potential theory. The dependence of the directed current on various parameters is studied systematically. Directed transport of coupled Brownian motors can be manipulated and optimized by adjusting the pulsation period or the phase shift of the pulsation temperature.

physics.class-ph↗

arXiv2016

Surface Treatment of 45S5 Bio-glass using Femtosecond Laser to Achieve Superior Growth of Hydroxyapatite

45S5 Hench bio-glass (BG) has gained interest in research because of its potential clinical applications. Several studies in-vivo and in-vitro have been in progress to improve bio-integration efficiency of this glass. In present contribution, surface modification of Hench BG has been done employing a femtosecond (fs) laser beam, resulting in increased effective surface area of the sample. These surface modified samples were subsequently immersed in simulated body fluid for varying number of days and characterized using Scanning electron microscope, energy dispersive X-ray analysis, X-ray diffraction, and micro-Raman spectroscopy. In-vitro studies indicated superior growth of hydroxyapatite (HAP) layer on the laser treated samples in comparison to the untreated samples. Presence of strong XRD peaks confirmed faster growth of HAP on laser treated samples. Raman peaks, five times more intense and relatively narrower represented higher crystallinity of hydroxyapatite layer on laser treated BG.

physics.bio-ph↗

arXiv2017

Biological implications of possible unattainability of comprehensive, molecular-resolution, real-time, volume imaging of the living cell

Despite the impressive advances in biological imaging, no imaging modality today generates, in a comprehensive manner, high-resolution images of crowded molecules working deep inside the living cell in real time. In this paper, instead of tackling this engineering problem in the hope of solving it, we ask a converse question: What if such imaging is \emph{fundamentally} impossible? We argue that certain decoherence processes could be suppressed because the internal workings of the cell are not being closely "observed" in the quantum mechanical sense, as implied by the assumed impossibility of imaging. It is certainly true that the "wet and warm" living cell should not exhibit quantum behavior merely because of the lack of observation. Despite this, we plow ahead to see what \emph{might} result from such absence of the outward flow of information. We suggest that chaotic dynamics in the cell could be quantum mechanically suppressed --- a known phenomenon in quantum chaology, which is potentially resistant to various mechanisms for the emergence of classicality. We also consider places where experimental evidence for/against such a possibility may be sought.

physics.bio-ph↗

arXiv2016

Nanoparticle-assisted STED nanoscopy with gold nanospheres

We demonstrate stimulated emission depletion (STED) microscopy with 20 nm gold nanospheres coated by fluorescent silica. Compared with previous demonstrations of STED with a hybrid plasmonic fluorescent label, the current implementation offers a substantially smaller label and a better resolution improvement of up to 2.5-fold beyond the diffraction limit of confocal microscopy. This is achieved at approximately 2 times lower intensity than conventional STED based on dyes alone, and in an aqueous environment, demonstrating the relevance to bio-imaging. Finally, we also show, for the first time in this context, a 3-fold reduction in the rate of photobleaching compared to standard dye-based STED, thus, enabling brighter images.

physics.optics↗

arXiv2016

Effect of body deformability on microswimming

In this work we consider the following question: given a mechanical microswimming mechanism, does increased deformability of the swimmer body hinder or promote the motility of the swimmer? To answer this we study a microswimmer model composed of deformable beads connected with springs. We determine the velocity of the swimmer analytically, starting from the forces driving the motion and assuming that the oscillations in the effective radii of the beads are known and are much smaller than the radii themselves. We find that to the lowest order, only the driving frequency mode of the surface oscillations contributes to the swimming velocity, and that this velocity may both rise and fall with the deformability of the beads depending on the spring constant. To test these results, we run immersed boundary lattice Boltzmann simulations of the swimmer, and show that they reproduce both the velocity-promoting and velocity-hindering effects of bead deformability correctly in the predicted parameter ranges. Our results mean that for a general swimmer, its elasticity determines whether passive deformations of the swimmer body, induced by the fluid flow, aid or oppose the motion.

physics.bio-ph↗

arXiv2016

Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments

The equilibrium relative humidity values for a number of the most commonly used precipitants in biological macromolecule crystallisation have been measured using a new humidity control device. A simple argument in statistical mechanics demonstrates that the saturated vapour pressure of a solvent is proportional to its mole fraction in an ideal solution (Raoult's Law). The same argument can be extended to the case where solvent and solute molecules are of different size.

cond-mat.soft↗

arXiv2017

The effects of stochasticity at the single-cell level and cell size control on the population growth

Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the experimentally observed correlations between mother-daughter generation times that are unavoidable when cell size is controlled for - which is essentially always the case. Here, we study population-level growth in the presence of cell size control and corroborate our theory using experimental measurements of single-cell growth rates. We derive a closed formula for the population growth rate and demonstrate that it only depends on the single-cell growth rate variability, not other sources of stochasticity. Our work provides an evolutionary rationale for the narrow growth rate distributions often observed in nature: when single-cell growth rates are less variable but have a fixed mean, the population will exhibit an enhanced population growth rate, as long as the correlations between the mother and daughter cells' growth rates are not too strong.

q-bio.PE↗

arXiv2017

Stochastic study of information transmission and population stability in a generic bacterial two-component system

Studies on the role of fluctuations in signal propagation and on gene regulation in monoclonal bacterial population have been extensively pursued based on the machinery of two-component system. The bacterial two-component system shows noise utilisation through its inherent plasticity. The fluctuations propagation takes place using the phosphotransfer module and the feedback mechanism during gene regulation. To delicately observe the noisy kinetics the generic cascade needs stochastic investigation at the mRNA and protein levels. To this end, we propose a theoretical framework to investigate the noisy signal transduction in a generic two-component system. The model shows reliability in information transmission through quantification of several statistical measures. We further extend our analysis to observe the protein distribution in a population of cells. Through numerical simulation, we identify the regime of the kinetic parameter set that generates a stability switch in the steady state distribution of proteins. The results of our theoretical analysis show key features of the network. The noise permeation and information propagation in the autoregulation module is feeble. However, the phosphotransfer module compensates such weakness and plays a significant role in information transmission. The bimodality due to fluctuations pampers the emergence of persistence in an isogenic bacterial pool.

q-bio.MN↗

arXiv2017

Towards a mechanical MPI scanner based on atomic magnetometry

We report on our progress in the development of an atomic magnetometer (AM) based low-frequency magnetic particle imaging (MPI) scanner, expected to be free from Specific Absorption Rate (SAR) and Peripheral Nerve Stimulation (PNS) constraints. We address major challenges in coil and sensor design due to specific AM properties. Compared to our previous work we have changed the AM's mode of operation towards its implementation for detecting weak magnetic nanoparticles (MNP) response fields in the presence of nearby-located strong drive/selection fields. We demonstrate that a pump-probe AM scheme in a buffer gas filled alkali vapour cell can tolerate mT/m gradients while maintaining a sensitivity in the one-digit pT/Hz^(1/2) range over a bandwidth from DC to several kHz. We give a detailed description of the drive/selection coils' geometry and their hardware implementations that provides a field-free-line (FFL) operation, compatible with a best performance AM operation. We estimate the achievable field of view and spatial resolution of the scanner as well as its sensitivity, assuming mechanical scanning of a Resovist sample through the field-free point/line.

physics.ins-det↗

arXiv2017

Dynamic landscape models of coevolutionary games

Players of coevolutionary games may update not only their strategies but also their networks of interaction. Based on interpreting the payoff of players as fitness, dynamic landscape models are proposed. The modeling procedure is carried out for Prisoner's Dilemma (PD) and Snowdrift (SD) games that both use either birth--death (BD) or death--birth (DB) strategy updating. The main focus is on using dynamic fitness landscapes as a mathematical model of coevolutionary game dynamics. Hence, an alternative tool for analyzing coevolutionary games becomes available, and landscape measures such as modality, ruggedness and information content can be computed and analyzed. In addition, fixation properties of the games and quantifiers characterizing the interaction networks are calculated numerically. Relations are established between landscape properties expressed by landscape measures and quantifiers of coevolutionary game dynamics such as fixation probabilities, fixation times and network properties.

q-bio.PE↗

arXiv2016

Tip-enhanced Raman spectroscopic detection of aptamers

Single molecule detection, sequencing and conformational mapping of aptamers are important for improving medical and biosensing technologies and for better understanding of biological processes at the molecular level. We obtain vibrational signals of single aptamers immobilized on gold substrates using tip-enhanced Raman spectroscopy (TERS). We compare topographic and optical signals and investigate the fluctuations of the position-dependent TERS spectra. TERS mapping provides information about the chemical composition and conformation of aptamers, and paves the way to future single-molecule label-free sequencing.

q-bio.BM↗

arXiv2018

Quantifying brain microstructure with diffusion MRI: Theory and parameter estimation

We review, systematize and discuss models of diffusion in neuronal tissue, by putting them into an overarching physical context of coarse-graining over an increasing diffusion length scale. From this perspective, we view research on quantifying brain microstructure as occurring along the three major avenues. The first avenue focusses on the transient, or time-dependent, effects in diffusion. These effects signify the gradual coarse-graining of tissue structure, which occurs qualitatively differently in different brain tissue compartments. We show that studying the transient effects has the potential to quantify the relevant length scales for neuronal tissue, such as the packing correlation length for neuronal fibers, the degree of neuronal beading, and compartment sizes. The second avenue corresponds to the long-time limit, when the observed signal can be approximated as a sum of multiple non-exchanging anisotropic Gaussian components. Here the challenge lies in parameter estimation and in resolving its hidden degeneracies. The third avenue employs multiple diffusion encoding techniques, able to access information not contained in the conventional diffusion propagator. We conclude with our outlook on the future directions which can open exciting possibilities for designing quantitative markers of tissue physiology and pathology, based on methods of studying mesoscopic transport in disordered systems.

physics.bio-ph↗

arXiv2016

New Insights into the Dynamics of Swarming Bacteria: A Theoretical Study

In the present work we simulate the basic two-dimensional dynamics of swarming E. coli bacteria on the surface of a moderately soft agar plate. Individual bacteria are modelled by self-propelled ridged bodies (agents), which interact with each other only through inelastic collision and with the highly viscous environment through damping forces. The motion of single agents is modelled closely corresponding to the behaviour of swimming bacteria. The dynamics of the model were adjusted to reproduce the experimental measurements of swimming E. coli K 12. Accordingly, simulations with loosely packed agents (p=0) show typical run-and-tumble statistics. In contrast, simulations with densely packed agents (p=0.3-0.7) are dominated by interactions (collisions) between agents which lead to the emergence of swarming behaviour. In addition, we model the motion of single agents on the base of modified run-and-tumble dynamics, where the bacteria do not turn actively during the tumble. We show that simulations with densely packed modified agents lead as well the emergence of swarming behaviour, if rotational diffusion is considered.

cond-mat.soft↗

arXiv2018

Performance limits and trade-offs in entropy-driven biochemical computers

The properties and fundamental limits of chemical computers have recently attracted significant interest as a model of computation, an unifying principle of cellular organisation and in the context of bio-engineering. As of yet, research in this topic is based on case-studies. There exists no generally accepted criterion to distinguish between chemical processes that compute and those that do not. Here, the concept of entropy driven computer (EDC) is proposed as a general model of chemical computation. It is found that entropy driven computation is subject to a trade-off between accuracy and entropy production, but unlike many biological systems, there are no trade-offs involving time. The latter only arise when it is taken into account that the observation of the state of the EDC is not energy neutral, but comes at a cost. The significance of this conclusion in relation to biological systems is discussed. Three examples of biological computers, including an implementation of a neural network as an EDC are given.

physics.bio-ph↗

arXiv2017

Electrostatics of non-neutral biological microdomains

Voltage and charge distributions in cellular microdomains regulate communications, excitability, and signal transduction. We report here new electrical laws in a cell, which follow from a nonlinear electro-diffusion model. These newly discovered relations derive from the geometrical cell-membrane properties, such as membrane curvature, volume, and surface area. These electro-diffusion laws can now be used to predict and interpret voltage distribution in cellular microdomains.

physics.bio-ph↗

arXiv2017

Force percolation of contractile active gels

Cells and tissues exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, which includes an active gel of actin filaments, crosslinks, and myosin molecular motors. Although individual motors are only a few nm in size and exert minute forces of a few pN, cells spatially integrate the activity of an ensemble of motors to produce larger contractile forces (order nN and greater) on cellular, tissue, and organismal length scales (order 10 $μ$m and greater). Experimental studies of reconstituted active-network model systems have long suggested that a mechanical interplay between the network's connectivity and motor activity dominates contractile behavior. Recent theoretical models indicate that this interplay can be understood in terms of percolation models, where the network connectivity is influenced by motor activity. Here we review experimental and theoretical studies of model contractile active gels and propose a state diagram that unites a large body of experimental and theoretical observations based on concepts from percolation theory.

cond-mat.soft↗