Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework

Knowing the location of a protein within the cell is important for understanding its function, role in biological processes, and potential use as a drug target. Much progress has been made in developing computational methods that predict single locations for proteins, assuming that proteins localize to a single location. However, it has been shown that proteins localize to multiple locations. While a few recent systems have attempted to predict multiple locations of proteins, they typically treat locations as independent or capture inter-dependencies by treating each locations-combination present in the training set as an individual location-class. We present a new method and a preliminary system we have developed that directly incorporates inter-dependencies among locations into the multiple-location-prediction process, using a collection of Bayesian network classifiers. We evaluate our system on a dataset of single- and multi-localized proteins. Our results, obtained by incorporating inter-dependencies are significantly higher than those obtained by classifiers that do not use inter-dependencies. The performance of our system on multi-localized proteins is comparable to a top performing system (YLoc+), without restricting predictions to be based only on location-combinations present in the training set.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Comparative studies of the solution properties of vinyl aromatic polymers Final report

Viscosity and nuclear magnetic resonance studies of vinyl aromatic polymer solution

Study of solution properties of block copolymers Final report

Solution properties of polybutadiene and polystyrene block copolymer

Broadband boundary effects on Brownian motion

Brownian motion of particles in confined fluids is important for many applications, yet the effects of the boundary over a wide range of time scales are still not well understood. We report high-bandwidth, comprehensive measurements of Brownian motion of an optically trapped micrometer-sized silica sphere in water near an approximately flat wall. At short distances we observe anisotropic Brownian motion with respect to the wall. We find that surface confinement not only occurs in the long time scale diffusive regime but also in the short time scale ballistic regime, and the velocity autocorrelation function of the Brownian particle decays faster than that of a particle in bulk fluid. Furthermore, at low frequencies the thermal force loses its color due to the reflected flow from the no-slip boundary. The power spectrum of the thermal force on the particle near a no-slip boundary becomes flat at low frequencies. This detailed understanding of boundary effects on Brownian motion opens a door to developing a 3D microscope using particles as remote sensors.Sid W. Richardson FoundationR. A. Welch Foundation F-1258Physic

Design optimization of natural laminar flow bodies in compressible flow

An optimization method has been developed to design axisymmetric body shapes such as fuselages, nacelles, and external fuel tanks with increased transition Reynolds numbers in subsonic compressible flow. The new design method involves a constraint minimization procedure coupled with analysis of the inviscid and viscous flow regions and linear stability analysis of the compressible boundary-layer. In order to reduce the computer time, Granville's transition criterion is used to predict boundary-layer transition and to calculate the gradients of the objective function, and linear stability theory coupled with the e(exp n)-method is used to calculate the objective function at the end of each design iteration. Use of a method to design an axisymmetric body with extensive natural laminar flow is illustrated through the design of a tiptank of a business jet. For the original tiptank, boundary layer transition is predicted to occur at a transition Reynolds number of 6.04 x 10(exp 6). For the designed body shape, a transition Reynolds number of 7.22 x 10(exp 6) is predicted using compressible linear stability theory coupled with the e(exp n)-method

Low temperature thermal expansivities of polyethylene, polypropylene and their mixtures

Low temperature measurements of length- temperature curves of polyethylene, polypropylene, mixtures of polyethylene and polypropylene, and copolymer

Effects of forebody geometry on subsonic boundary-layer stability

As part of an effort to develop computational techniques for design of natural laminar flow fuselages, a computational study was made of the effect of forebody geometry on laminar boundary layer stability on axisymmetric body shapes. The effects of nose radius on the stability of the incompressible laminar boundary layer was computationally investigated using linear stability theory for body length Reynolds numbers representative of small and medium-sized airplanes. The steepness of the pressure gradient and the value of the minimum pressure (both functions of fineness ratio) govern the stability of laminar flow possible on an axisymmetric body at a given Reynolds number. It was found that to keep the laminar boundary layer stable for extended lengths, it is important to have a small nose radius. However, nose shapes with extremely small nose radii produce large pressure peaks at off-design angles of attack and can produce vortices which would adversely affect transition

Unsteady Stokes flow near boundaries: the point-particle approximation and the method of reflections

Problems of particle dynamics involving unsteady Stokes flows in confined geometries are typically harder to solve than their steady counterparts. Approximation techniques are often the only resort. Felderhof (see e.g. 2005, 2009b) has developed a point-particle approximation framework to solve such problems, especially in the context of Brownian motion. Despite excellent agreement with past experiments, this framework has an inconsistency which we address in this work. Upon implementing our modifications, the framework passes consistency checks that it previously failed. Further, it is not obvious that such an approximation should work for short time-scale motion. We investigate its validity by deriving it from a general formalism based on integral equations through a series of systematic approximations. We also compare results from the point-particle framework against a calculation performed using the method of reflections, for the specific case of a sphere near a full-slip plane boundary. We find from our analysis that the reasons for the success of the point-particle approximation are subtle and have to do with the nature of the unsteady Oseen tensor. Finally, we provide numerical predictions for Brownian motion near a full-slip and a no-slip plane wall based on the point-particle approximation as used by Felderhof, our modified point-particle approximation, and the method of reflections. We show that our modifications to Felderhof's framework would become significant for systems of metallic nanoparticles in liquids.Comment: 40 page draft submitted for review to the Journal of Fluid Mechanic