Extended-System Adaptively Biased Simulations of Membrane Protein Orientation
نویسندگان
چکیده
منابع مشابه
Adaptively restrained particle simulations.
Interaction potentials used in particle simulations are typically written as a sum of terms which depend on just a few relative particle positions. Traditional simulation methods move all particles at each time step, and may thus spend a lot of time updating interparticle forces. In this Letter we introduce adaptively restrained particle simulations (ARPS) to speed up particle simulations by ad...
متن کاملMembrane-Channel Protein System Mesh Construction for Finite Element Simulations
We present a method of constructing the volume meshes of the membrane-channel protein system for finite element simulation of ion channels. The membrane channel system consists of the solvent region and the membrane-protein region. Our method focuses on labeling the tetrahedra in the solvent and membrane-protein regions and collecting the interface triangles between different regions. It contai...
متن کاملBiased orientation games
We study biased orientation games, in which the board is the complete graph Kn, and OMaker (oriented maker) and OBreaker (oriented breaker) take turns in directing previously undirected edges of Kn. At the end of the game, the obtained graph is a tournament. OMaker wins if the tournament has some property P and OBreaker wins otherwise. We provide bounds on the bias that is required for OMaker’s...
متن کاملMembrane orientation of laminin binding protein.
Earlier we presented several lines of evidence that a 67-kDa laminin binding protein (LBP) in Leishmania donovani, that is different from the putative mammalian 67-kDa laminin receptor, may play an important role in the onset of leishmaniasis, as these parasites invade macrophages in various organs after migrating through the extracellular matrix. Here we describe the membrane orientation of th...
متن کاملExploring the Use of Adaptively Restrained Particles for Graphics Simulations
In this paper, we explore the use of Adaptively Restrained (AR) particles for graphics simulations. Contrary to previous methods, Adaptively Restrained Particle Simulations (ARPS) do not adapt time or space sampling, but rather switch the positional degrees of freedom of particles on and off, while letting their momenta evolve. Therefore, inter-particles forces do not have to be updated at each...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2012
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2011.11.939