Asymmetric Lee Distance Codes for DNA-Based Storage

We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a quaternary alphabet, although the results carry over to other alphabet sizes; furthermore, symbol confusability is dictated by their underlying binary representation. Our contributions are two-fold. First, we demonstrate that the new distance represents a linear combination of the Lee and Hamming distance and derive upper bounds on the size of the codes under this metric based on linear programming techniques. Second, we propose a number of code constructions which imply lower bounds

A New Cell Association Scheme In Heterogeneous Networks

Cell association scheme determines which base station (BS) and mobile user (MU) should be associated with and also plays a significant role in determining the average data rate a MU can achieve in heterogeneous networks. However, the explosion of digital devices and the scarcity of spectra collectively force us to carefully re-design cell association scheme which was kind of taken for granted before. To address this, we develop a new cell association scheme in heterogeneous networks based on joint consideration of the signal-to-interference-plus-noise ratio (SINR) which a MU experiences and the traffic load of candidate BSs1. MUs and BSs in each tier are modeled as several independent Poisson point processes (PPPs) and all channels experience independently and identically distributed ( i.i.d.) Rayleigh fading. Data rate ratio and traffic load ratio distributions are derived to obtain the tier association probability and the average ergodic MU data rate. Through numerical results, We find that our proposed cell association scheme outperforms cell range expansion (CRE) association scheme. Moreover, results indicate that allocating small sized and high-density BSs will improve spectral efficiency if using our proposed cell association scheme in heterogeneous networks.Comment: Accepted by IEEE ICC 2015 - Next Generation Networking Symposiu

Optical Gravitational Lensing Experiment. OGLE-1999-BUL-19: The First Multi-Peak Parallax Event

We describe a highly unusual microlensing event, OGLE-1999-BUL-19, which exhibits multiple peaks in its light curve. The Einstein radius crossing time for this event is approximately one year, which is unusually long. We show that the motion of the Earth induces these multiple peaks in the light curve, since the relative transverse velocity of the lens projected into the observer plane is very small (v = 12.5 km/s). This is the lowest velocity so far published and we believe that this is the first multiple-peak parallax event ever observed. We also believe that this event may be exhibiting slight binary-source signatures in addition to these parallax-induced multiple peaks. With spectroscopic observations it is possible to test this `parallax plus binary-source' hypothesis and (if this hypothesis turns out to be correct) to simultaneously fit both models and obtain a measurement of the lens mass. Furthermore, spectroscopic observations could also supply information regarding the lens properties, possibly providing another avenue for determining the lens mass. We found that most of the I-band blending is probably caused by light from the lens or a binary companion to the source. However, in the V-band, there appears to be a second blended source 0.35" away from the lensed source. HST observations will be very useful for understanding the nature of the blends. We also suggest that a radial velocity survey of all parallax events will be very useful for further constraining the lensing kinematics and understanding the origins of these events and the excess of long events toward the bulge.Comment: 36 pages, 7 figures. Accepted for publication in MNRA

Primary Structure and Solution Conditions Determine Conformational Ensemble Properties of Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) are a class of proteins that do not exhibit well-defined three-dimensional structures. The absence of structure is intrinsic to their amino acid sequences, which are characterized by low hydrophobicity and high net charge per residue compared to folded proteins. Contradicting the classic structure-function paradigm, IDPs are capable of interacting with high specificity and affinity, often acquiring order in complex with protein and nucleic acid binding partners. This phenomenon is evident during cellular activities involving IDPs, which include transcriptional and translational regulation, cell cycle control, signal transduction, molecular assembly, and molecular recognition. Although approximately 30% of eukaryotic proteomes are intrinsically disordered, the nature of IDP conformational ensembles remains unclear. In this dissertation, we describe relationships connecting characteristics of IDP conformational ensembles to their primary structures and solution conditions. Using molecular simulations and fluorescence experiments on a set of base-rich IDPs, we find that net charge per residue segregates conformational ensembles along a globule-to-coil transition. Speculatively generalizing this result, we propose a phase diagram that predicts an IDP\u27s average size and shape based on sequence composition and use it to generate hypotheses for a broad set of intrinsically disordered regions (IDRs). Simulations reveal that acid-rich IDRs, unlike their oppositely charged base-rich counterparts, exhibit disordered globular ensembles despite intra-chain repulsive electrostatic interactions. This apparent asymmetry is sensitive to simulation parameters for representing alkali and halide salt ions, suggesting that solution conditions modulate IDP conformational ensembles. We refine the ion parameters using a calibration procedure that relies exclusively on crystal lattice properties. Simulations with these parameters recover swollen coil behavior for acid-rich IDRs, but also uncover a dependence on sequence patterning for polyampholytic IDPs. These contributions initiate an endeavor to elucidate general principles that enable prediction of an IDP\u27s conformational ensemble based on primary structure and solution conditions, a goal analogous to structure prediction for folded proteins. Such principles would provide a molecular basis for understanding the roles of IDPs in physiology and pathophysiology, guide development of agents that modulate their behavior, and enable their rational design from chosen specifications