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At least 631 records · Page 35Linked to original sources

arXiv2004

A mathematical model for top-shelf vertigo: the role of sedimenting otoconia in BPPV

Benign Paroxysmal Positional Vertigo (BPPV) is a mechanical disorder of the vestibular system in which calcite particles called otoconia interfere with the mechanical functioning of the fluid-filled semicircular canals normally used to sense rotation. Using hydrodynamic models, we examine the two mechanisms proposed by the medical community for BPPV: cupulolithiasis, in which otoconia attach directly to the cupula (a sensory membrane), and canalithiasis, in which otoconia settle through the canals and exert a fluid pressure across the cupula. We utilize known hydrodynamic calculations and make reasonable geometric and physical approximations to derive an expression for the transcupular pressure $ΔP_c$ exerted by a settling solid particle in canalithiasis. By tracking settling otoconia in a two-dimensional model geometry, the cupular volume displacement and associated eye response (nystagmus) can be calculated quantitatively. Several important features emerge: 1) A pressure amplification occurs as otoconia enter a narrowing duct; 2) An average-sized otoconium requires approximately five seconds to settle through the wide ampulla, where $ΔP_c$ is not amplified, which suggests a mechanism for the observed latency of BPPV; and 3) An average-sized otoconium beginning below the center of the cupula can cause a volumetric cupular displacement on the order of 30 pL, with nystagmus of order $2^\circ$/s, which is approximately the threshold for sensation. Larger cupular volume displacement and nystagmus could result from larger and/or multiple otoconia.

physics.flu-dyn↗

arXiv2003

Distribution of infected mass in disease spreading in scale-free networks

We use scale-free networks to study properties of the infected mass $M$ of the network during a spreading process as a function of the infection probability $q$ and the structural scaling exponent $γ$. We use the standard SIR model and investigate in detail the distribution of $M$, We find that for dense networks this function is bimodal, while for sparse networks it is a smoothly decreasing function, with the distinction between the two being a function of $q$. We thus recover the full crossover transition from one case to the other. This has a result that on the same network a disease may die out immediately or persist for a considerable time, depending on the initial point where it was originated. Thus, we show that the disease evolution is significantly influenced by the structure of the underlying population.

cond-mat.dis-nn↗

arXiv2003

Folding of Proteins in Go Models with Angular Interactions

Molecular dynamics studies of Go models of proteins with the 10-12 contact potential and the bond and dihedral angle terms indicate statistical similarities to other Go models, e.g. with the Lennard-Jones contact potentials. The folding times depend on the protein size as power laws with the exponents depending on the native structural classes. There is no dependence of the folding times on the relative contact order even though the folding scenarios are governed mostly by the contact order.

cond-mat.stat-mech↗

arXiv2003

A layered neural network with three-state neurons optimizing the mutual information

The time evolution of an exactly solvable layered feedforward neural network with three-state neurons and optimizing the mutual information is studied for arbitrary synaptic noise (temperature). Detailed stationary temperature-capacity and capacity-activity phase diagrams are obtained. The model exhibits pattern retrieval, pattern-fluctuation retrieval and spin-glass phases. It is found that there is an improved performance in the form of both a larger critical capacity and information content compared with three-state Ising-type layered network models. Flow diagrams reveal that saddle-point solutions associated with fluctuation overlaps slow down considerably the flow of the network states towards the stable fixed-points.

cond-mat.dis-nn↗

arXiv2003

Information Flow in Social Groups

We present a study of information flow that takes into account the observation that an item relevant to one person is more likely to be of interest to individuals in the same social circle than those outside of it. This is due to the fact that the similarity of node attributes in social networks decreases as a function of the graph distance. An epidemic model on a scale-free network with this property has a finite threshold, implying that the spread of information is limited. We tested our predictions by measuring the spread of messages in an organization and also by numerical experiments that take into consideration the organizational distance among individuals.

cond-mat.stat-mech↗

arXiv2004

Recoiling DNA Molecule: Simulation & Experiment

Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the persistence length of single DNA molecules can also be measured based on the recoil dynamics of these DNA-microsphere complexes if appropriate corrections are made to the friction coefficient of the microsphere in the vicinity of the substrate. Comparison between computer simulated recoil curves, generated from the corresponding Langevin equation, and experimental recoils is used to assure the validity of data analysis.

physics.bio-ph↗

arXiv2003

Control of cardiac alternans in a mapping model with memory

We investigate a map-based model of paced cardiac muscle in the presence of closed-loop feedback control. The model relates the duration of an action potential to the preceding diastolic interval as well as the preceding action potential duration and thus has some amount of `memory.' We find that the domain of control depends on this memory, independently of the specific functional form of the map. The memory-dependent domain of control can encompass large feedback gains, thus providing the first possible explanation of the recent experimental results of Hall et al. [Phys. Rev. Lett, 88, 198102 (2002)] on controlling alternans in small pieces of rapidly-paced cardiac muscle.

physics.bio-ph↗

arXiv1999

Pathways in Two-State Protein Folding

The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that folding is guided. We reconcile these two seemingly contradictory observations quantitatively in a schematic model of protein folding. We propose a new dynamical transition temperature which is lower than the thermodynamic one, in qualitative agreement with in vivo measurement of protein stability using E.coli. Finally we demonstrate that our framework is easily generalized to encompass cold unfolding, and make predictions that relate the sharpness of the cold and hot unfolding transitions.

cond-mat↗

arXiv2001

Heat Capacity of Protein Folding

We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal dipoles that are ordered around the unfolded surfaces, where the influence of these surfaces, covered with an ``ice-like'' shell of water, is represented by an effective field that directs the water dipoles. An intermolecular pair interaction between water molecules is also introduced. The heat capacity of the model exhibits the common feature of small globular proteins, two peaks corresponding to cold and warm unfolding, respectively. By introducing vibrational modes, we obtain quantitatively good accordance with experiments.

cond-mat↗

arXiv2001

The binding dynamics of tropomyosin on actin

We discuss a theoretical model for the cooperative binding dynamics of tropomyosin to actin filaments. Tropomyosin binds to actin by occupying seven consecutive monomers. The model includes a strong attraction between attached tropomyosin molecules. We start with an empty lattice and show that the binding goes through several stages. The first stage represents fast initial binding and leaves many small vacancies between blocks of bound molecules. In the second stage the vacancies annihilate slowly as tropomyosin molecules detach and re-attach. Finally the system approaches equilibrium. Using a grain-growth model and a diffusion-coagulation model we give analytical approximations for the vacancy density in all regimes.

cond-mat.soft↗

arXiv2002

Interaction of proteins in solution from small angle scattering: a perturbative approach

In this work, an improved methodology for studying interactions of proteins in solution by small-angle scattering, is presented. Unlike the most common approach, where the protein-protein correlation functions $g_{ij}(r)$ are approximated by their zero-density limit (i.e. the Boltzmann factor), we propose a more accurate representation of $g_{ij}(r)$ which takes into account terms up to the first order in the density expansion of the mean-force potential. This improvement is expected to be particulary effective in the case of strong protein-protein interactions at intermediate concentrations. The method is applied to analyse small angle X-ray scattering data obtained as a function of the ionic strength (from 7 to 507 mM) from acidic solutions of $β$-Lactoglobuline at the fixed concentration of 10 $\rm g L^{-1}$. The results are compared with those obtained using the zero-density approximation and show a significant improvement particularly in the more demanding case of low ionic strength.

cond-mat.stat-mech↗

arXiv2002

Solvation model dependency of helix-coil transition in polyalanine

Helix-coil transitions in poly-alanine molecules of length 10 are studied by multicanonical Monte Carlo simulations. The solvation effects are included by either a distance-dependent dielectric permittivity or by a term that is proportional to the solvent-accessible surface area of the peptide. We found a strong dependence of the characteristics of the helix-coil transition from the details of the solvation model.

physics.bio-ph↗

arXiv2003

Growth Velocities of Branched Actin Networks

The growth of an actin network against an obstacle that stimulates branching locally is studied using several variants of a kinetic rate model based on the orientation-dependent number density of filaments. The model emphasizes the effects of branching and capping on the density of free filament ends. The variants differ in their treatment of side vs. end branching and dimensionality, and assume that new branches are generated by existing branches (autocatalytic behavior) or independently of existing branches (nucleation behavior). In autocatalytic models, the network growth velocity is rigorously independent of the opposing force exerted by the obstacle, and the network density is proportional to the force. The dependence of the growth velocity on the branching and capping rates is evaluated by a numerical solution of the rate equations. In side-branching models, the growth velocity drops gradually to zero with decreasing branching rate, while in end-branching models the drop is abrupt. As the capping rate goes to zero, it is found that the behavior of the velocity is sensitive to the thickness of the branching region. Experiments are proposed for using these results to shed light on the nature of the branching process.

physics.bio-ph↗

arXiv2017

Perfect and near perfect adaptation in a model of bacterial chemotaxis

The signaling apparatus mediating bacterial chemotaxis can adapt to a wide range of persistent external stimuli. In many cases, the bacterial activity returns to its pre-stimulus level exactly and this "perfect adaptability" is robust against variations in various chemotaxis protein concentrations. We model the bacterial chemotaxis signaling pathway, from ligand binding to CheY phosphorylation. By solving the steady-state equations of the model analytically, we derive a full set of conditions for the system to achieve perfect adaptation. The conditions related to the phosphorylation part of the pathway are discovered for the first time, while other conditions are generalization of the ones found in previous works. Sensitivity of the perfect adaptation is evaluated by perturbing these conditions. We find that, even in the absence of some of the perfect adaptation conditions, adaptation can be achieved with near perfect precision as a result of the separation of scales in both chemotaxis protein concentrations and reaction rates, or specific properties of the receptor distribution in different methylation states. Since near perfect adaptation can be found in much larger regions of the parameter space than that defined by the perfect adaptation conditions, their existence is essential to understand robustness in bacterial chemotaxis.

physics.bio-ph↗

arXiv2002

Nucleosome repositioning via loop formation

Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail the energetics and dynamics of DNA-loop-mediated nucleosome repositioning, as previously proposed by Schiessel et al. (H. Schiessel, J. Widom, R. F. Bruinsma, and W. M. Gelbart. 2001. {\it Phys. Rev. Lett.} 86:4414-4417). The surprising outcome of the present study is the inherent nonlocality of nucleosome motion within this model -- being a direct physical consequence of the loop mechanism. On long enough DNA templates the longer jumps dominate over the previously predicted local motion, a fact that contrasts simple diffusive mechanisms considered before. The possible experimental outcome resulting from the considered mechanism is predicted, discussed and compared to existing experimental findings.

physics.bio-ph↗

arXiv2002

Entropy loss in long-distance DNA looping

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the entropy loss for a given configuration. Numerical values obtained for some examples suggest that the entropy loss encountered in loop closure in typical genetic switches may become a relevant factor which has to be overcome by the released bond energy between the looping contact sites.

cond-mat.stat-mech↗

arXiv2003

Two adaptation processes in auditory hair cells together can provide an active amplifier

The hair cells of the vertebrate inner ear convert mechanical stimuli to electrical signals. Two adaptation mechanisms are known to modify the ionic current flowing through the transduction channels of the hair bundles: a rapid process involves calcium ions binding to the channels; and a slower adaptation is associated with the movement of myosin motors. We present a mathematical model of the hair cell which demonstrates that the combination of these two mechanisms can produce `self-tuned critical oscillations', i.e. maintain the hair bundle at the threshold of an oscillatory instability. The characteristic frequency depends on the geometry of the bundle and on the calcium dynamics, but is independent of channel kinetics. Poised on the verge of vibrating, the hair bundle acts as an active amplifier. However, if the hair cell is sufficiently perturbed, other dynamical regimes can occur. These include slow relaxation oscillations which resemble the hair bundle motion observed in some experimental preparations.

physics.bio-ph↗

arXiv2003

Instabilities in the transient response of muscle

We investigate the isometric transient response of muscle using a quantitative stochastic model of the actomyosin cycle based on the swinging lever-arm hypothesis. We first consider a single pair of filaments, and show that when values of parameters such as the lever-arm displacement and the crossbridge elasticity are chosen to provide effective energy transduction, the T2 curve (the tension recovered immediately after a step displacement) displays a region of negative slope. If filament compliance and the discrete nature of the binding sites are taken into account, the negative slope is diminished, but not eliminated. This implies that there is an instability in the dynamics of individual half-sarcomeres. However, when the symmetric nature of whole sarcomeres is taken into account, filament rearrangement becomes important during the transient: as tension is recovered, some half-sarcomeres lengthen while others shorten. This leads to a flat T2 curve, as observed experimentally. In addition, we investigate the isotonic transient response and show that for a range of parameter values the model displays damped oscillations, as recently observed in experiments on single muscle fibers. We conclude that it is essential to consider the collective dynamics of many sarcomeres, rather than the dynamics of a single pair of filaments, when interpreting the transient response of muscle.

physics.bio-ph↗