Storage and retrieval of individual genomes

A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tree occupies O(N log N) bits, which very soon inhibits in-memory analyses. Recent advances in full-text self-indexing reduce the space of suffix tree to O(N log σ) bits, where σ is the alphabet size. In practice, the space reduction is more than 10-fold, for example on suffix tree of Human Genome. However, this reduction factor remains constant when more sequences are added to the collection. We develop a new family of self-indexes suited for the repetitive sequence collection setting. Their expected space requirement depends only on the length n of the base sequence and the number s of variations in its repeated copies. That is, the space reduction factor is no longer constant, but depends on N / n. We believe the structures developed in this work will provide a fundamental basis for storage and retrieval of individual genomes as they become available due to rapid progress in the sequencing technologies.

Dark solitons in holographic superfluids

We construct dark soliton solutions in a holographic model of a relativistic superfluid. We study the length scales associated with the condensate and the charge density depletion, and find that the two scales differ by a non-trivial function of the chemical potential. By adjusting the chemical potential, we study the variation of the depletion of charge density at the interface.

AC transport at holographic quantum hall transitions

We compute AC electrical transport at quantum Hall critical points, as modeled by intersecting branes and gauge/gravity duality. We compare our results with a previous field theory computation by Sachdev, and find unexpectedly good agreement. We also give general results for DC Hall and longitudinal conductivities valid for a wide class of quantum Hall transitions, as well as (semi)analytical results for AC quantities in special limits. Our results exhibit a surprising degree of universality; for example, we find that the high frequency behavior, including subleading behavior, is identical for our entire class of theories.

Inhomogeneous Structures in Holographic Superfluids I

We begin an investigation of inhomogeneous structures in holographic superfluids. As a first example, we study domain wall like defects in the 3+1 dimensional Einstein-Maxwell-Higgs theory, which was developed as a dual model for a holographic superconductor. In [1], we reported on such "dark solitons" in holographic superfluids. In this work, we present an extensive numerical study of their properties, working in the probe limit. We construct dark solitons for two possible condensing operators, and find that both of them share common features with their standard superfluid counterparts. However, both are characterized by two distinct coherence length scales (one for order parameter, one for charge condensate). We study the relative charge depletion factor and find that solitons in the two different condensates have very distinct depletion characteristics. We also study quasiparticle excitations above the holographic superfluid, and find that the scale of the excitations is comparable to the soliton coherence length scales.

Holographic Superfluids and Solitons

Superfluidity is perhaps one of the most remarkable observed macroscopic quantum effect. Superfluidity appears when a macroscopic number of particles occupies a single quantum state. Using modern experimental techniques one dark solitons) and vortices. There is a large literature on theoretical work studying the properties of such solitons using semiclassical methods. This thesis describes an alternative method for the study of superfluid solitons. The method used here is a holographic duality between a class of quantum field theories and gravitational theories. The classical limit of the gravitational system maps into a strong coupling limit of the quantum field theory. We use a holographic model of superfluidity to study solitons in these systems. One particularly appealing feature of this technique is that it allows us to take into account finite temperature effects in a large range of temperatures.

Lyophilized disaccharides – the effect of water during storage

Nearly one fourth of new medicinal molecules are biopharmaceutical (protein, antibody or nucleic acid derivative) based. However, the administration of these compounds is not always that straightforward due to the fragile nature of aforementioned domains in GI-tract. In addition, these molecules often exhibit poor bioavailability when administered orally. As a result, parenteral administration is commonly preferred. In addition, shelf-life of these molecules in aqueous environments is poor, unless stored in low temperatures. Another approach is to bring these molecules to anhydrous form via lyophilization resulting in enhanced stability during storage. Proteins cannot most commonly be freeze dried by themselves so some kind of excipients are nearly always necessary. Disaccharides are commonly utilized excipients in freeze-dried formulations since they provide a rigid glassy matrix to maintain the native conformation of the protein domain. They also act as "sink"-agents, which basically mean that they can absorb some moisture from the environment and still help to protect the API itself to retain its activity and therefore offer a way to robust formulation. The aim of the present study was to investigate how four amorphous disaccharides (cellobiose, melibiose, sucrose and trehalose) behave when they are brought to different relative humidity levels. At first, solutions of each disaccharide were prepared, filled into scintillation vials and freeze dried. Initial information on how the moisture induced transformations take place, the lyophilized amorphous disaccharide cakes were placed in vacuum desiccators containing different relative humidity levels for defined period, after which selected analyzing methods were utilized to further examine the occurred transformations. Affinity to crystallization, water sorption of the disaccharides, the effect of moisture on glass transition and crystallization temperature were studied. In addition FT-IR microscopy was utilized to map the moisture distribution on a piece of lyophilized cake. Observations made during the experiments backed up the data mentioned in a previous study: melibiose and trehalose were shown to be superior over sucrose and cellobiose what comes to the ability to withstand elevated humidity and temperature, and to avoid crystallization with pharmaceutically relevant moisture contents. The difference was made evident with every utilized analyzing method. In addition, melibiose showed interesting anomalies during DVS runs, which were absent with other amorphous disaccharides. Particularly fascinating was the observation made with polarized light microscope, which revealed a possible small-scale crystallization that cannot be observed with XRPD. As a result, a suggestion can safely be made that a robust formulation is most likely obtained by utilizing either melibiose or trehalose as a stabilizing agent for biopharmaceutical freeze-dried formulations. On the other hand, more experiments should be conducted to obtain more accurate information on why these disaccharides have better tolerance for elevating humidities than others.