11 research outputs found
Dynamic self-assembling DNA nanosystems: design and engineering
Over the last thirty years, DNA has proven to be a great candidate for engineering nanoscale architectures. These DNA nanostructures have been applied in areas such as single-molecular analyses, nanopatterning, diagnostics and therapeutics. One of the most commonly-used techniques to engineer DNA-based two- and three-dimensional functional nanostructures is DNA origami, wherein a long single-stranded DNA (called scaffold) is folded into a predetermined shape with the help of a set of shorter oligonucleotides (called staples). This thesis discusses a brief overview of DNA nanotechnology (design, assembly and applications) and three primary projects undertaken in the area of dynamic self-assembling DNA nanosystems: 1, a self-assembly design strategy that vastly expands the utility of DNA origami, 2, a DNA origami-based reconfigurable nanosystem with potential as a force/energy balance and diagnostic tool, and 3, a collaborative initiative on computational analyses and experimental verification for improving efficiency of DNA nanoengineering
Cryptography Based on DNA Using Random key Generation Scheme
With the growth of technological advancements, the threats dealt by a user grow exponentially. The 21st century is a period of information explosion in which information has become a very important strategic resource, and so the task of information security has become increasingly important in data storage and transmission. As traditional cryptographic systems are now vulnerable to attacks, the concept of using DNA Cryptography has been identified as a possible technology that brings forward a new hope for unbreakable algorithms. A new field of cryptography is emerging based on DNA computing due to high storage capacity, vast parallelism and exceptional energy efficiency of biological DNA. This field is in initial stage so a lot of research has to be done yet. This paper analyzes the different approach on DNA Cryptography based on matrix manipulation and secure key generation scheme
Evolución del VIH-1 durante el proceso de recuperación de la eficacia biológica in vitro
Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 18-10-201
Fixed-parameter algorithms for some combinatorial problems in bioinformatics
Fixed-parameterized algorithmics has been developed in 1990s as an approach to solve NP-hard problem optimally in a guaranteed running time. It offers a new opportunity to solve NP-hard problems exactly even on large problem instances.
In this thesis, we apply fixed-parameter algorithms to cope with three NP-hard problems in bioinformatics:
Flip Consensus Tree Problem is a combinatorial problem arising in computational phylogenetics. Using the formulation of the Flip Consensus Tree Problem as a graph-modification problem, we present a set of data reduction rules and two fixed-parameter algorithms with respect to the number of modifications. Additionally, we discuss several heuristic improvements to accelerate the running time of our algorithms in practice. We also report computational results on phylogenetic data.
Weighted Cluster Editing Problem is a graph-modification problem, that arises in computational biology when clustering objects with respect to a given similarity or distance measure. We present one of our fixed-parameter algorithms with respect to the minimum modification cost and describe the idea of our fastest algorithm for this problem and its unweighted counterpart.
Bond Order Assignment Problem asks for a bond order assignment of a molecule graph that minimizes a penalty function. We prove several complexity results on this problem and give two exact fixed-parameter algorithms for the problem. Our algorithms base on the dynamic programming approach on a tree decomposition of the molecule graph. Our algorithms are fixed-parameter with respect to the treewidth of the molecule graph and the maximum atom valence. We implemented one of our algorithms with several heuristic improvements and evaluate our algorithm on a set of real molecule graphs. It turns out that our algorithm is very fast on this dataset and even outperforms a heuristic algorithm that is usually used in practice
Chemical programming to eploit chemical Reaction systems for computation
This thesis is on programming approaches to exploit the computational
capabilities of chemical systems, consisting of two parts.
In the first part, constructive design, research activities on
theoretical development of chemical programming are reported.
As results of the investigations, general programming principles,
named organization-oriented programming, are derived.
The idea is to design reaction networks such that the desired
computational outputs correspond to the
organizational structures within the networks.
The second part, autonomous design, discusses on programming
strategies without human interactions, namely evolution and
exploration.
Motivations for this programming approach include possibilities to
discover novelty without rationalization.
Regarding first the evolutionary strategies, we rather focused on how
to track the evolutionary processes.
Our approach is to analyze these dynamical processes on a higher
level of abstraction, and usefulness of distinguishing organizational
evolution in space of organizations from actual evolution in state
space is emphasized.
As second strategy of autonomous chemical programming,
we suggest an explorative approach, in which an automated system is
utilized to explore the behavior of the chemical reaction system as a
preliminary step.
A specific aspect of the system's behavior becomes ready for a
programmer to be chosen for a particular computational purpose.
In this thesis, developments of autonomous exploration techniques are
reported.
Finally, we discuss combining those two approaches, constructive
design and autonomous design, titled as a hybrid approach.
From our perspective, hybrid approaches are ideal, and cooperation of constructive design
and autonomous design is fruitful
Department of Computer Science Activity 1998-2004
This report summarizes much of the research and teaching activity of the Department of Computer Science at Dartmouth College between late 1998 and late 2004. The material for this report was collected as part of the final report for NSF Institutional Infrastructure award EIA-9802068, which funded equipment and technical staff during that six-year period. This equipment and staff supported essentially all of the department\u27s research activity during that period
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Biomolecular Materials. Report of the January 13-15, 2002 Workshop
Twenty-two scientists from around the nation and the world met to discuss the way that the molecules, structures, processes and concepts of the biological world could be used or mimicked in designing novel materials, processes or devices of potential practical significance. The emphasis was on basic research, although the long-term goal is, in addition to increased knowledge, the development of applications to further the mission of the Department of Energy
Cellular computation and communications using engineered genetic regulatory networks
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.Includes bibliographical references (p. 130-138).In this thesis, I present an engineering discipline for obtaining complex, predictable, and reliable cell behaviors by embedding biochemical logic circuits and programmed intercellular communications into cells. To accomplish this goal, I provide a well-characterized component library, a biocircuit design methodology, and software design tools. I have built and characterized an initial cellular gate library with biochemical gates that implement the NOT, IMPLIES, and AND logic functions in E. coli cells. The logic gates perform computation using DNA-binding proteins, small molecules that interact with these proteins, and segments of DNA that regulate the expression of the proteins. I introduce genetic process engineering, a methodology for modifying the DNA encoding of existing genetic elements to achieve the desired input/output behavior for constructing reliable circuits of significant complexity. I demonstrate the feasibility of digital computation in cells by building several operational in-vivo digital logic circuits, each composed of three gates that have been optimized by genetic process engineering.(cont.) I also demonstrate engineered intercellular communications with programmed enzymatic activity and chemical diffusions to carry messages, using DNA from the Vibrio fischeri lux operon. The programmed communications is essential for obtaining coordinated behavior from cell aggregates. In addition to the above experimental contributions, I have developed BioSPICE, a prototype software tool for biocircuit design. It supports both static and dynamic simulations and analysis of single cell environments and small cell aggregates. Finally, I present the Microbial Colony Language (MCL), a model for programming cell aggregates. The language is expressive enough for interesting applications, yet relies on simple primitives that can be mapped to the engineered biological processes described above.by Ron Weiss.Ph.D