Eighty-Five Ways of Using Apples

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Influences of Excluded Volume of Molecules on Signaling Processes on Biomembrane

We investigate the influences of the excluded volume of molecules on biochemical reaction processes on 2-dimensional surfaces using a model of signal transduction processes on biomembranes. We perform simulations of the 2-dimensional cell-based model, which describes the reactions and diffusion of the receptors, signaling proteins, target proteins, and crowders on the cell membrane. The signaling proteins are activated by receptors, and these activated signaling proteins activate target proteins that bind autonomously from the cytoplasm to the membrane, and unbind from the membrane if activated. If the target proteins bind frequently, the volume fraction of molecules on the membrane becomes so large that the excluded volume of the molecules for the reaction and diffusion dynamics cannot be negligible. We find that such excluded volume effects of the molecules induce non-trivial variations of the signal flow, defined as the activation frequency of target proteins, as follows. With an increase in the binding rate of target proteins, the signal flow varies by i) monotonically increasing; ii) increasing then decreasing in a bell-shaped curve; or iii) increasing, decreasing, then increasing in an S-shaped curve. We further demonstrate that the excluded volume of molecules influences the hierarchical molecular distributions throughout the reaction processes. In particular, when the system exhibits a large signal flow, the signaling proteins tend to surround the receptors to form receptor-signaling protein clusters, and the target proteins tend to become distributed around such clusters. To explain these phenomena, we analyze the stochastic model of the local motions of molecules around the receptor.Comment: 31 pages, 10 figure

Fatally Flawed? : Discursive Evidence from the Movement to Establish Lesbian Studies Programs

While related areas such as Queer Studies and Sexuality Studies have become established as disciplinary formations in North American and British universities, Lesbian Studies has not. This article reports on an analysis of key publications by critics and advocates of Lesbian Studies to explore the possibility that Lesbian Studies was flawed in ways that account for its non-emergence. Charges against Lesbian Studies include naïve essentialism, white middle-classness, separatism, and paranoia. Discourse analysis of books by Lesbian Studies advocates examines evidence of each of these qualities and concludes that Lesbian Studies was above all too lesbian to be successfully integrated into the enduringly heteropatriarchal institution of universities.University of Winnipeghttp://journals.sagepub.com/doi/10.1177/095935351037018

A Didactic Model of Macromolecular Crowding Effects on Protein Folding

A didactic model is presented to illustrate how the effect of macromolecular crowding on protein folding and association is modeled using current analytical theory and discrete molecular dynamics. While analytical treatments of crowding may consider the effect as a potential of average force acting to compress a polypeptide chain into a compact state, the use of simulations enables the presence of crowding reagents to be treated explicitly. Using an analytically solvable toy model for protein folding, an approximate statistical thermodynamic method is directly compared to simulation in order to gauge the effectiveness of current analytical crowding descriptions. Both methodologies are in quantitative agreement under most conditions, indication that both current theory and simulation methods are capable of recapitulating aspects of protein folding even by utilizing a simplistic protein model

Optical Probing of Thermal Lattice Fluctuations in Charge-Density-Wave Condensates

Thermal lattice fluctuations in charge-density-wave (CDW) condensates have been studied by means of optical investigations on the prototype CDW compound K0.3MoO3 and its alloys. The temperature dependence of the CDW gap absorption in the mid-IR frequency range is strongly indicative of the important role played by the thermal lattice fluctuation effects. The latter remove the inverse-square-root singularity, expected for the case of the static distorted lattice. In fact, a considerable broadening (i.e., larger than k(B)T) of the subgap tail absorption is found by increasing the temperature towards T(CDW). Moreover, we find that the phase phonon modes also give an important contribution to the disorder parameter, thus being an essential ingredient for the thermal fluctuation effects

A coil-globule transition of a semiflexible polymer driven by the addition of spherical particles

The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of magnitude larger than the diameter of the polymer. The spherical particles induce a quite long ranged depletion attraction between the segments of the polymer and this induces a continuous coil-globule transition in the polymer. This behaviour gives an indication of the condensing effect of macromolecular crowding on DNA.Comment: 12 pages, 4 figure

Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction

The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model explains qualitatively some of the experimental observations.Comment: 6 pages, 4 figure

Seismology of the Sun : Inference of Thermal, Dynamic and Magnetic Field Structures of the Interior

Recent overwhelming evidences show that the sun strongly influences the Earth's climate and environment. Moreover existence of life on this Earth mainly depends upon the sun's energy. Hence, understanding of physics of the sun, especially the thermal, dynamic and magnetic field structures of its interior, is very important. Recently, from the ground and space based observations, it is discovered that sun oscillates near 5 min periodicity in millions of modes. This discovery heralded a new era in solar physics and a separate branch called helioseismology or seismology of the sun has started. Before the advent of helioseismology, sun's thermal structure of the interior was understood from the evolutionary solution of stellar structure equations that mimicked the present age, mass and radius of the sun. Whereas solution of MHD equations yielded internal dynamics and magnetic field structure of the sun's interior. In this presentation, I review the thermal, dynamic and magnetic field structures of the sun's interior as inferred by the helioseismology.Comment: To be published in the proceedings of the meeting "3rd International Conference on Current Developments in Atomic, Molecular, Optical and Nano Physics with Applications", December 14-16, 2011, New Delhi, Indi

A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation

Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium _Escherichia coli_, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the _in vivo_ MinDE localization dynamics by accounting for the established properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally