Downloads & Free Reading Options - Results

The application of computational mathematics and information science to biology has aided in the understanding of biological systems. Today biology can now aid information science. This research activity addresses this new and potentially symbiotic relationship between biology and information. In this report, a biocomputational analysis of a biologically represented network is demonstrated. A report on new DNA aqueous laboratory computing techniques is also given.

This item represents a case in PACER, the U.S. Government's website for federal case data. If you wish to see the entire case, please consult PACER directly.

A microscopy system was acquired for molecular detection using molecular motor-driven nanodevices. This state of the art system incorporates a motorized stage that can move to successive adjacent fields of view, and stitch the digital color photos for analysis. The detection system utilizes the molecular motor attached to a slide and a gold nanorod that is visible by darkfield microscopy. Assembly of each nanodevice is dependent upon the presence of one molecule of target that bridges between motor and nanorod. Zeptomole sensitivity of target DNA is achieved without PCR or other means of amplification via molecular motor-dependent rotation. We have now demonstrated simultaneous, multiplexed detection of sequence specific DNA, RNA, and proteins unique to MRSA on the same platform with three separate colors of gold nanorods each having a different functionalization. We have also demonstrated the ability to differentiate between Staphylococcus aureus and MRSA as well as detection of target from crude cell lysate. We have written algorithms that can analyze the stitched digital photos of fields of view, correctly identify red, green, and yellow nanorods used to detect DNA, RNA, and proteins, respectively, then rapidly quantify the amount of each target present. Assembly of a commercial prototype of the detection device is underway.

This report examines the potential and limitations of DNA computing. In particular the report examines some of the costs and problems of using DNA computing an large scale problems.

This report examines the potential and limitations of DNA computing. In particular the report examines some of the costs and problems of using DNA computing an large scale problems.

This report examines the potential and limitations of DNA computing. In particular the report examines some of the costs and problems of using DNA computing an large scale problems.

We construct codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$ with $u^2=0$. These code are designed for use in DNA computing applications. The codes obtained satisfy the reverse complement constraint, the $GC$ content constraint and avoid the secondary structure. they are derived from the cyclic complement reversible codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$. We also construct an infinite family of BCH DNA codes.

We construct codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$ with $u^2=0$. These code are designed for use in DNA computing applications. The codes obtained satisfy the reverse complement constraint, the $GC$ content constraint and avoid the secondary structure. they are derived from the cyclic complement reversible codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$. We also construct an infinite family of BCH DNA codes.

We construct codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$ with $u^2=0$. These code are designed for use in DNA computing applications. The codes obtained satisfy the reverse complement constraint, the $GC$ content constraint and avoid the secondary structure. they are derived from the cyclic complement reversible codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$. We also construct an infinite family of BCH DNA codes.

The primary goal of this research was the development of an enabling technology for DNA computing. It focused on the development of two distinct DNA-based nanotechnologies, aqueous computing and DNA arrays. Once merged, these DNA-based nanotechnologies serve as a platform for a hybrid silicon-DNA computing architecture. The aqueous side is where the computing happens and the array side is where the results are preprocessed. The array information passes to an electronic computer for signal processing type decoding. The intent was to develop a computing basis to overcome the exponential time complexity of many discrete mathematical problems so that they can be solved in linear real time. This research addresses needs of the Air Force because computationally hard (NP) problems are critical to logistics, scheduling and national security. Moreover, the DNA nanotechnologies developed in this research has the potential to enhance Biotaggants which provide environmental awareness in the field.

Future advances in computing technology require exploration of next generation strategies. Approaches that use the ultra-parallel processing of bio-molecular procedures are one of the most intriguing strategies for new computing paradigms. These strategies provide for the solution of many algorithms in a linear number of steps compared to an exponential number of steps with traditional computing. Using DNA as the memory register in a fluid environment like water is a strategy called aqueous computing. It has been used to achieve successful solution of simple algorithms based on a restriction enzyme writing procedure. While the proof of concept for this approach has been achieved a number of challenges have been identified including the long time required. For this grant another strategy for writing on DNA was investigated using sequence specific DNA methylation and this strategy was used to solve a 4-variable SAT problem.

Future advances in computing technology require exploration of next generation strategies. Approaches that use the ultra-parallel processing of bio-molecular procedures are one of the most intriguing strategies for new computing paradigms. These strategies provide for the solution of many algorithms in a linear number of steps compared to an exponential number of steps with traditional computing. Using DNA as the memory register in a fluid environment like water is a strategy called aqueous computing. It has been used to achieve successful solution of simple algorithms based on a restriction enzyme writing procedure. While the proof of concept for this approach has been achieved a number of challenges have been identified including the long time required. For this grant another strategy for writing on DNA was investigated using sequence specific DNA methylation and this strategy was used to solve a 4-variable SAT problem.

Future advances in computing technology require exploration of next generation strategies. Approaches that use the ultra-parallel processing of bio-molecular procedures are one of the most intriguing strategies for new computing paradigms. These strategies provide for the solution of many algorithms in a linear number of steps compared to an exponential number of steps with traditional computing. Using DNA as the memory register in a fluid environment like water is a strategy called aqueous computing. It has been used to achieve successful solution of simple algorithms based on a restriction enzyme writing procedure. While the proof of concept for this approach has been achieved a number of challenges have been identified including the long time required. For this grant another strategy for writing on DNA was investigated using sequence specific DNA methylation and this strategy was used to solve a 4-variable SAT problem.

Future advances in computing technology require exploration of next generation strategies. Approaches that use the ultra-parallel processing of bio-molecular procedures are one of the most intriguing strategies for new computing paradigms. These strategies provide for the solution of many algorithms in a linear number of steps compared to an exponential number of steps with traditional computing. Using DNA as the memory register in a fluid environment like water is a strategy called aqueous computing. It has been used to achieve successful solution of simple algorithms based on a restriction enzyme writing procedure. While the proof of concept for this approach has been achieved a number of challenges have been identified including the long time required. For this grant another strategy for writing on DNA was investigated using sequence specific DNA methylation and this strategy was used to solve a 4-variable SAT problem.

Future advances in computing technology require exploration of next generation strategies. Approaches that use the ultra-parallel processing of bio-molecular procedures are one of the most intriguing strategies for new computing paradigms. These strategies provide for the solution of many algorithms in a linear number of steps compared to an exponential number of steps with traditional computing. Using DNA as the memory register in a fluid environment like water is a strategy called aqueous computing. It has been used to achieve successful solution of simple algorithms based on a restriction enzyme writing procedure. While the proof of concept for this approach has been achieved a number of challenges have been identified including the long time required. For this grant another strategy for writing on DNA was investigated using sequence specific DNA methylation and this strategy was used to solve a 4-variable SAT problem.

Perma.cc archive of https://interestingengineering.com/what-is-dna-computing-how-does-it-work-and-why-its-such-a-big-deal created on 2022-05-16 14:05:16.341964+00:00.

DNA Self-Assembly has emerged as an interdisciplinary field with many intriguing applications such DNA bio-sensor, DNA circuits, DNA storage, drug delivery etc. Tile assembly model of DNA has been studied for various computational primitives such as addition, subtraction, multiplication, and division. Xuncai et. al. gave computational DNA tiles to perform division of a number but the output had integer quotient. In this work, we simply modify their method of division to improve its compatibility with further computation and this modification has found its application in computing rational numbers, both recurring and terminating, with computational tile complexity of $\mathcal{O} (1)$ and $\mathcal{O} (h)$ respectively. Additionally, we also propose a method to compute square-root of a number with computational tile complexity of $\mathcal{O} (n)$ for an n bit number. Finally, after combining tiles of division and square-root, we propose a simple way to compute the ubiquitously used irrational number, $\pi$, using its infinite series.

This project validated the generation of DNA sequences called a DNA (n,d) code. Fifteen strands of 16 nucleotides each were designed such that a code strand would hybridize only with its reverse-complement and would not cross- hybridize or miss-pair with any other strand in the set. The code was designed using principles from nearest-neighbor studies and the thermodynamics of base stacking. All possible combinations of strands were tested for their potential to miss-pair. Hybridizations of the sequences representing junctions of strands were also tested. Strands were tested for their potential to cross-hybridize by measuring fluorescence over varying temperatures in the presence of SYBR Green Strands were tested in pools to show that hybridization between Watson-Crick complements is still thermodynamically favorable even when all strands are present. Nearly all twenty strands and 56 junction sequences showed suitable preference for their direct complement and did not appreciably miss-pair with any other strand in the code. The general properties and modes of binding of SYBR Green I were explored. The experiments indicate that SYBR Green I is positively-charged and binds to DNA predominantly via electrostatic interactions and groove binding. Its fluorescence increases with the number of base pairs in a predictable manner.

In this project, a synthetic Deoxyribonucleic Acid, DNA-based memory called ComDMems (Combinatorial DNA Memories) was developed. This research focused on the application and implementation of combinatorial based information theory and group testing to create associative DNA memories and to retrieve information stored in these DNA memories by chemical and electro-chemical means. This research demonstrates that this combinatorial method can feasibly yield billions of covert and synthetic DNA memory strands that carry object and process information. A key component of this innovation is the combinatorial method of bio-memory design and detection that encodes item or process information as numerical sequences represented in DNA. This DNA data structure can be read by the wet laboratory method polymerase chain reaction (PCR) and then algorithmically decoded to retrieve virtually an unlimited amount of item or process information that has been stored in the combinatorial memories. ComDMem is a content addressable memory (CAM) as opposed to a standard random access memory (RAM). A standard RAM goes directly to a physical address and returns the contents. ComDMem achieves CAM when multiple parallel PCR probes, specific for certain pieces of information, search the ComDMem for memories that contain these pieces of information. In this way all memories associated with a concept(s) can be retrieved and decoded in parallel.

Large collections of carefully constructed single stranded DNA sequences, called DNA Libraries, can be algorithmically filtered to encode solutions to numerical questions. To date, there has been no simple way to decode theses solutions. One possible decoding method is to further augment or embed the original encoded DNA library strands with synthetic reading strands made from the blueprints of classical superimposed codes. This can make the DNA output readable without complicated chemical separation or isolation protocols.

In this project, a synthetic Deoxyribonucleic Acid, DNA-based memory called ComDMems (Combinatorial DNA Memories) was developed. The research focused on the application and implementation of combinatorial based information theory and group testing to create associative DNA memories and to retrieve information stored in these DNA memories by chemical and electro-chemical means. This research demonstrates that this combinatorial method can feasibly yield billions of covert and synthetic DNA memory strands that carry object and process information. A key component of this innovation is the combinatorial method of bio-memory design and detection that encodes item or process information as numerical sequences represented in DNA. ComDMem is a content addressable memory (CAM) as opposed to a standard random access memory (RAM). A standard RAM goes directly to a physical address and returns the contents. ComDMem achieves CAM when multiple parallel PCR probes, specific for certain pieces of information search, the ComDMem for memories that contain these pieces of information. In this way all memories associated with a concept(s) can be retrieved and decoded in parallel. A visualization model was created and a tiled display system was built to provide high resolution display of large images for verification of probe-strand interactions.

Hyperelliptic Curve Cryptography (HECC) is a Public Key Cryptographic technique which is required for secure transmission. HECC is better than the existing public key cryptography technique such as RSA, DSA, AES and ECC in terms of smaller key size. DNA cryptography is a next generation security mechanism, storing almost a million gigabytes of data inside DNA strands. Existing DNA based Elliptic Curve Cryptographic technique require larger key size to encrypt and decrypt the message resulting in increased processing time, more computational and memory overhead. To overcome the above limitations, DNA strands are used to encode the data to provide first level of security and HECC encryption algorithm is used for providing second level of security. Hence this proposed integration of DNA computing based HECC provides higher level of security with less computational and memory overhead.

S-box is one of the most significant structures used to construct encryption that is strong and resistant to attacks in encryption algorithms. The new 4D-hyper chaotic system and deoxyribonucleic acid (DNA) computing are used in this paper to provide a new dynamic S-box generating approach. The 4D generated numbers are processed to generate a hexadecimal number that will encode using the DNA coding method and using addition, subtraction, and exclusive-or operations to produce the final DNA string decoded to make the S-Box. The dynamic form of s-boxes is represented by a minor change in the initial conditions of the proposed chaotic method that will generate dynamic sequences of numbers. The proposed method enhances the security criteria of the block ciphers. The S-box testing criteria were done like strict avalanche, balanced, and bit independence criteria, in addition to differential approximation probability and linearity approximation probability, to test the security of the new S-Box. The results show that the new S-box has good security and is resistant to attacks.

Perma.cc archive of https://pubsonline.informs.org/do/10.1287/LYTX.2017.05.03/full/ created on 2022-09-12 21:25:05.764117+00:00.