Human sperm accumulation near surfaces: a simulation study

A hybrid boundary integral/slender body algorithm for modelling flagellar cell motility is presented. The algorithm uses the boundary element method to represent the ‘wedge-shaped’ head of the human sperm cell and a slender body theory representation of the flagellum. The head morphology is specified carefully due to its significant effect on the force and torque balance and hence movement of the free-swimming cell. The technique is used to investigate the mechanisms for the accumulation of human spermatozoa near surfaces. Sperm swimming in an infinite fluid, and near a plane boundary, with prescribed planar and three-dimensional flagellar waveforms are simulated. Both planar and ‘elliptical helicoid’ beating cells are predicted to accumulate at distances of approximately 8.5–22 μm from surfaces, for flagellar beating with angular wavenumber of 3π to 4π. Planar beating cells with wavenumber of approximately 2.4π or greater are predicted to accumulate at a finite distance, while cells with wavenumber of approximately 2π or less are predicted to escape from the surface, likely due to the breakdown of the stable swimming configuration. In the stable swimming trajectory the cell has a small angle of inclination away from the surface, no greater than approximately 0.5°. The trapping effect need not depend on specialized non-planar components of the flagellar beat but rather is a consequence of force and torque balance and the physical effect of the image systems in a no-slip plane boundary. The effect is relatively weak, so that a cell initially one body length from the surface and inclined at an angle of 4°–6° towards the surface will not be trapped but will rather be deflected from the surface. Cells performing rolling motility, where the flagellum sweeps out a ‘conical envelope’, are predicted to align with the surface provided that they approach with sufficiently steep angle. However simulation of cells swimming against a surface in such a configuration is not possible in the present framework. Simulated human sperm cells performing a planar beat with inclination between the beat plane and the plane-of-flattening of the head were not predicted to glide along surfaces, as has been observed in mouse sperm. Instead, cells initially with the head approximately 1.5–3 μm from the surface were predicted to turn away and escape. The simulation model was also used to examine rolling motility due to elliptical helicoid flagellar beating. The head was found to rotate by approximately 240° over one beat cycle and due to the time-varying torques associated with the flagellar beat was found to exhibit ‘looping’ as has been observed in cells swimming against coverslips

Energy Storage in a Hamiltonian System in Partial Contact with a Heat Bath

To understand the mechanism allowing for the long-term storage of excess energy in proteins, we study a Hamiltonian system consisting of several coupled pendula in partial contact with a heat bath. It is found that energy storage is possible when the motion of each pendulum switches between oscillatory (vibrational) and rotational (phase-slip) modes. The storage time increases almost exponentially to the square root of the injected energy. The relevance of our mechanism to protein motors is discussed.Comment: 8 pages, 4 figures, to appear in J.Phys.Soc.Jp

Spontaneous Oscillations of Collective Molecular Motors

We analyze a simple stochastic model to describe motor molecules which cooperate in large groups and present a physical mechanism which can lead to oscillatory motion if the motors are elastically coupled to their environment. Beyond a critical fuel concentration, the non-moving state of the system becomes unstable with respect to a mode with angular frequency omega. We present a perturbative description of the system near the instability and demonstrate that oscillation frequencies are determined by the typical timescales of the motors.Comment: 11 pages, Revtex, 4 pages Figure

A comprehensive and comparative study of elastic electron scattering from OCS and CS2 in the energy region from 1.2 to 200 eV

We report absolute differential cross sections (DCSs) for elastic electron scattering from OCS (carbonyl sulphide) and CS₂ (carbon disulphide) in the impact energy range of 1.2-200 eV and for scattering angles from 10° to 150°. Above 10 eV, the angular distributions are found to agree quite well with our present calculations using two semi-phenomenological theoretical approaches. One employs the independent-atom model with the screening-corrected additivity rule (IAM-SCAR), while the other uses the continuum-multiple-scattering method in conjunction with a parameter-free exchange-polarization approximation. Since OCS is a polar molecule, further dipole-induced rotational excitation cross sections have been calculated in the framework of the first Born approximation and incoherently added to the IAM-SCAR results. In comparison with the calculated DCS for the S atom, atomic-like behavior for the angular distributions in both the OCS and CS₂ scattering systems is observed. Integrated elastic cross sections are obtained by extrapolating the experimental measurements, with the aid of the theoretical calculations, for those scattering angles below 10° and above 150°. These values are then compared with the available total cross sections.The present work has been supported by the Japanese Ministry of Education, Sport, Culture and Technology and the Australian Research Council through its Centers of Excellence program. PL-V acknowledges his Visiting Professor position at Sophia University, Tokyo, Japan and also the Portuguese PEst-OE/FIS/UI0068/2011 grant. This work forms part of the EU/ESF COST Action CM0805 programme “The Chemical Cosmos.” M.J.B. and S.J.B. acknowledge the JSPS for provision of a Senior Fellowship, and the University of Malaya for their hospitality as Visiting Professor F. Blanco and Professor G. García acknowledge partial financial support of the Spanish Ministerio de Economia y Competitividad through Project No. FIS2009-10245 as well as the EU/ESF COST Action MP1002

Self-organization and Mechanical Properties of Active Filament Bundles

A phenomenological description for active bundles of polar filaments is presented. The activity of the bundle results from crosslinks, that induce relative displacements between the aligned filaments. Our generic description is based on momentum conservation within the bundle. By specifying the internal forces, a simple minimal model for the bundle dynamics is obtained, capturing generic dynamic behaviors. In particular, contracted states as well as solitary and oscillatory waves appear through dynamic instabilities. The introduction of filament adhesion leads to self-organized persistent filament transport. Furthermore, calculating the tension, homogeneous bundles are shown to be able to actively contract and to perform work against external forces. Our description is motivated by dynamic phenomena in the cytoskeleton and could apply to stress-fibers and self-organization phenomena during cell-locomotion.Comment: 19 pages, 10 figure

Constraining N2O emissions since 1940 using firn air isotope measurements in both hemispheres

N2O is currently the third most important anthropogenic greenhouse gas in terms of radiative forcing and its atmospheric mole fraction is rising steadily. To quantify the growth rate and its causes over the past decades, we performed a multi-site reconstruction of the atmospheric N2O mole fraction and isotopic composition using new and previously published firn air data collected from Greenland and Antarctica in combination with a firn diffusion and densification model. The multi-site reconstruction showed that while the global mean N2O mole fraction increased from (290±1)nmolmol-1 in 1940 to (322±1)nmolmol-1 in 2008, the isotopic composition of atmospheric N2O decreased by (-2.2±0.2)% for δ15Nav, (-1.0±0.3)% for δ18O, (-1.3±0.6)% for δ15Nα, and (-2.8±0.6)% for δ15Nβ over the same period. The detailed temporal evolution of the mole fraction and isotopic composition derived from the firn air model was then used in a two-box atmospheric model (comprising a stratospheric box and a tropospheric box) to infer changes in the isotopic source signature over time. The precise value of the source strength depends on the choice of the N2O lifetime, which we choose to fix at 123 years. The average isotopic composition over the investigated period is δ15Nav Combining double low line (-7.6±0.8)% (vs. air-N2), δ18O Combining double low line (32.2±0.2)% (vs. Vienna Standard Mean Ocean Water-VSMOW) for δ18O, δ15Nα Combining double low line (-3.0±1.9)% and δ15Nβ Combining double low line (-11.7±2.3)%. δ15Nav, and δ15Nβ show some temporal variability, while for the other signatures the error bars of the reconstruction are too large to retrieve reliable temporal changes. Possible processes that may explain trends in 15N are discussed. The 15N site preference (Combining double low line δ15Nα-δ15Nβ) provides evidence of a shift in emissions from denitrification to nitrification, although the uncertainty envelopes are large

Technical Note: Latitude-time variations of atmospheric column-average dry air mole fractions of CO_2, CH_4 and N_2O

We present a comparison of an atmospheric general circulation model (AGCM)-based chemistry-transport model (ACTM) simulation with total column measurements of CO_2, CH_4 and N_2O from the Total Carbon Column Observing Network (TCCON). The model is able to capture observed trends, seasonal cycles and inter hemispheric gradients at most sampled locations for all three species. The model-observation agreements are best for CO_2, because the simulation uses fossil fuel inventories and an inverse model estimate of non-fossil fuel fluxes. The ACTM captures much of the observed seasonal variability in CO_2 and N_2O total columns (~81 % variance, R>0.9 between ACTM and TCCON for 19 out of 22 cases). These results suggest that the transport processes in troposphere and stratosphere are well represented in ACTM. Thus the poor correlation between simulated and observed CH4 total columns, particularly at tropical and extra-tropical sites, have been attributed to the uncertainties in surface emissions and loss by hydroxyl radicals. While the upward-looking total column measurements of CO_2 contains surface flux signals at various spatial and temporal scales, the N_2O measurements are strongly affected by the concentration variations in the upper troposphere and stratosphere

Force and Motion Generation of Molecular Motors: A Generic Description

We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical reaction. We analyze the essential features of force and motion generation and discuss the general properties of single motors in the framework of two-state models. Systems which contain large numbers of motors such as muscles and flagella motivate the study of many interacting motors within the framework of simple models. In this case, collective effects can lead to new types of behaviors such as dynamic instabilities of the steady states and oscillatory motion.Comment: 29 pages, 9 figure

TransCom N2O model inter-comparison - Part 2:Atmospheric inversion estimates of N2O emissions

This study examines N2O emission estimates from five different atmospheric inversion frameworks based on chemistry transport models (CTMs). The five frameworks differ in the choice of CTM, meteorological data, prior uncertainties and inversion method but use the same prior emissions and observation data set. The posterior modelled atmospheric N2O mole fractions are compared to observations to assess the performance of the inversions and to help diagnose problems in the modelled transport. Additionally, the mean emissions for 2006 to 2008 are compared in terms of the spatial distribution and seasonality. Overall, there is a good agreement among the inversions for the mean global total emission, which ranges from 16.1 to 18.7 TgN yr(-1) and is consistent with previous estimates. Ocean emissions represent between 31 and 38% of the global total compared to widely varying previous estimates of 24 to 38%. Emissions from the northern mid- to high latitudes are likely to be more important, with a consistent shift in emissions from the tropics and subtropics to the mid- to high latitudes in the Northern Hemisphere; the emission ratio for 0-30A degrees N to 30-90A degrees N ranges from 1.5 to 1.9 compared with 2.9 to 3.0 in previous estimates. The largest discrepancies across inversions are seen for the regions of South and East Asia and for tropical and South America owing to the poor observational constraint for these areas and to considerable differences in the modelled transport, especially inter-hemispheric exchange rates and tropical convective mixing. Estimates of the seasonal cycle in N2O emissions are also sensitive to errors in modelled stratosphere-to-troposphere transport in the tropics and southern extratropics. Overall, the results show a convergence in the global and regional emissions compared to previous independent studies

A comprehensive and comparative study of elastic electron scattering from OCS and CS2 in the energy region from 1.2 to 200 eV

We report absolute differential cross sections (DCSs) for elastic electron scattering from OCS (carbonyl sulphide) and CS2 (carbon disulphide) in the impact energy range of 1.2–200 eV and for scattering angles from 10◦ to 150◦. Above 10 eV, the angular distributions are found to agree quite well with our present calculations using two semi-phenomenological theoretical approaches. One employs the independent-atom model with the screening-corrected additivity rule (IAM-SCAR), while the other uses the continuum-multiple-scattering method in conjunction with a parameter-free exchange-polarization approximation. Since OCS is a polar molecule, further dipole-induced rotational excitation cross sections have been calculated in the framework of the first Born approximation and incoherently added to the IAM-SCAR results. In comparison with the calculated DCS for the S atom, atomic-like behavior for the angular distributions in both the OCS and CS2 scattering systems is observed. Integrated elastic cross sections are obtained by extrapolating the experimental measurements, with the aid of the theoretical calculations, for those scattering angles below 10◦ and above 150◦. These values are then compared with the available total cross sections