Interactions of slow electrons with biomolecules

We report on results of computational studies of the interaction of slow electrons with the purine and pyrimidine bases of DNA, as well as with their associated nucleosides and nucleotides. The calculations focus on characterisation of the π* resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. High-level studies of the π* resonances in pyrazine, a close analogue of the pyrimidine bases, indicate that the higher-energy π* resonances in these bases may in fact contain large admixtures of core-excited character built on low-lying triplet states. Decay into such triplet states may provide a mechanism for damage to DNA

Programming chemistry in DNA-addressable bioreactors

We present a formal calculus, termed the chemtainer calculus, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by state-of-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis

Integrated Electronics for Molecular Biosensing

This thesis, Integrated electronics for molecular biosensing, focuses on different approaches to sense the presence and activity of a specific analyte by using integrated electronic platforms. The aim of the first platform is to detect the enzyme telomerase. Telomerase causes the elongation of telomeres, which are part of the chromosomes, and determines the lifespan of cells. Telomerase expression is a marker of malignity in tumoral cells and its evaluation can be exploited for early diagnosis of many types of cancer cells. To detect the telomerase enzyme, a CMOS (complementary metal-oxide semiconductor) biosensor based on CMFET (Charge-Modulated Field Effect Transistor) able to measure kinetics of DNA replication and telomerase reaction was developed. The sensor can be functionalized by immobilizing single strands of DNA that contain the telomeric sequence, used as probes. If telomerase is present, the probes will be elongated by the enzyme and the charge on the sensing area will change, which reflects in a variation of the output current or voltage. The chip includes three different readout schemes (voltage, current- and time-based), each of which has different measuring ranges and operating conditions. The measured data is then digitized, stored, and can be sent off-chip through SPI (Serial Peripheral Interface) protocol. A total of 1024 biosensors have been integrated in a single chip with a size of 10x10 mm2. Each sensor can be independently addressed and functionalized by an electrochemical procedure using an integrated potentiostat, thus requiring no external equipment. Although the sensors have been tailored and optimized to perform telomerase detection, the sensing areas can be functionalized to be used with different analytes. This feature turns the chip into a complete bioassay platform. The second part of this work rises from the idea that bacteria, like Escherichia coli, can detect analytes in solution even at extremely low concentrations and change their movement through a process called chemotaxis, to move towards chemical gradients in the solution. E. coli moves by rotating its flagella either clockwise (for random tumbles) or counterclockwise (for straight runs, when it senses a chemical it is attracted to). Therefore, observing bacteria flagellar rotation can give enough information on the presence of a specific analyte in the solution. To electronically detect bacteria movement, an active surface covered in electrodes has been designed. By measuring the impedance between each pair of electrodes through an integrated LIA (lock-in amplifier), it is possible to know how a single bacterium is moving. By that, the presence or absence of the analyte can be deduced, thus effectively turning bacteria into chemical sensors

Experimental studies for the detection of protein in trace amounts

Organic cyanine dye for detection of protein in trace amounts - dye reaction mechanism, methods of eliminating inorganic compound reaction with dye, and detection of humic aci

Symbolic computation: systems and applications

The article presents an overview of symbolic computation systems, their classification-in-history, the most popular CAS, examples of systems and some of their applications. Symbolics versus numeric, enhancement in mathematics, computing nature of CAS, related projects, networks, references are discussed

Enclosing the Maximum Likelihood of the Simplest DNA Model Evolving on Fixed Topologies: Towards a Rigorous Framework for Phylogenetic Inference

This issue was undated. The date given is an estimate.14 pages, 1 article*Enclosing the Maximum Likelihood of the Simplest DNA Model Evolving on Fixed Topologies: Towards a Rigorous Framework for Phylogenetic Inference* (Sainudiin, Raazesh) 14 page