18,398 research outputs found
Exploring the membrane potential of a simple dual membrane system by using a constant electric field
KInNeSS: A Modular Framework for Computational Neuroscience
Making use of very detailed neurophysiological, anatomical, and behavioral data to build biological-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalabiltiy, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multu-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions of ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further developement of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effecitively collaborate using a modern neural simulation platform.Center for Excellence for Learning Education, Science, and Technology (SBE-0354378); Air Force Office of Scientific Research (F49620-01-1-0397); Office of Naval Research (N00014-01-1-0624
Transport Coefficients for Holographic Hydrodynamics at Finite Energy Scale
We investigate the relations between black hole thermodynamics and
holographic transport coefficients in this paper. The formulae for DC
conductivity and diffusion coefficient are verified for electrically
single-charged black holes. We examine the correctness of the proposed
expressions by taking charged dilatonic and single-charged STU black holes as
two concrete examples, and compute the flows of conductivity and diffusion
coefficient by solving the linear order perturbation equations. We then check
the consistence by evaluating the Brown-York tensor at a finite radial
position. Finally, we find that the retarded Green functions for the shear
modes can be expressed easily in terms of black hole thermodynamic quantities
and transport coefficients.Comment: 33 pages,4 figures,to appear in Advances in High Energy Physic
Hidden Symmetries of M Theory
A worldvolume action for membrane is considered to study the target space
local symmetries. We introduce a set of generators of canonical transformations
to exhibit the target space symmetries such as the general coordinate
transformation and the gauge transformation of antisymmetric tensor field.
Similar results are derived for type IIB string with manifestly
S-duality-invariant worldsheet action.Comment: 17 pages, revtex, no figure
A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins
Membrane proteins constitute a large portion of the human proteome and
perform a variety of important functions as membrane receptors, transport
proteins, enzymes, signaling proteins, and more. The computational studies of
membrane proteins are usually much more complicated than those of globular
proteins. Here we propose a new continuum model for Poisson-Boltzmann
calculations of membrane channel proteins. Major improvements over the existing
continuum slab model are as follows: 1) The location and thickness of the slab
model are fine-tuned based on explicit-solvent MD simulations. 2) The highly
different accessibility in the membrane and water regions are addressed with a
two-step, two-probe grid labeling procedure, and 3) The water pores/channels
are automatically identified. The new continuum membrane model is optimized (by
adjusting the membrane probe, as well as the slab thickness and center) to best
reproduce the distributions of buried water molecules in the membrane region as
sampled in explicit water simulations. Our optimization also shows that the
widely adopted water probe of 1.4 {\AA} for globular proteins is a very
reasonable default value for membrane protein simulations. It gives an overall
minimum number of inconsistencies between the continuum and explicit
representations of water distributions in membrane channel proteins, at least
in the water accessible pore/channel regions that we focus on. Finally, we
validate the new membrane model by carrying out binding affinity calculations
for a potassium channel, and we observe a good agreement with experiment
results.Comment: 40 pages, 6 figures, 5 table
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