Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A 16-bit parallel processing in a molecular assembly.

ABSTRACT: A machine assembly consisting of 17 identical molecules of 2,3,5,6-tetramethyl-1-4-benzoquinone (DRQ) executes 16 instructions at a time. A single DRQ is positioned at the center of a circular ring formed by 16 other DRQs, controlling their operation in parallel through hydrogen-bond channels. Each molecule is a logic machine and generates four instructions by rotating its alkyl groups. A single instruction executed by a scanning tunneling microscope tip on the central molecule can change decisions of 16 machines simultaneously, in four billion (4(16)) ways. This parallel communication represents a significant conceptual advance relative to today's fastest processors, which execute only one instruction at a time.

SUBMITTER: Bandyopadhyay A

PROVIDER: S-EPMC2268776 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A 16-bit parallel processing in a molecular assembly.

Bandyopadhyay Anirban A Acharya Somobrata S

Proceedings of the National Academy of Sciences of the United States of America 20080310 10

A machine assembly consisting of 17 identical molecules of 2,3,5,6-tetramethyl-1-4-benzoquinone (DRQ) executes 16 instructions at a time. A single DRQ is positioned at the center of a circular ring formed by 16 other DRQs, controlling their operation in parallel through hydrogen-bond channels. Each molecule is a logic machine and generates four instructions by rotating its alkyl groups. A single instruction executed by a scanning tunneling microscope tip on the central molecule can change decisi ...[more]

PMID: 18332437

Similar Datasets

Bit-parallel sequence-to-graph alignment.

Project description:MotivationGraphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction and variant calling with respect to a variation graph.ResultsWe generalize two linear sequence-to-sequence algorithms to graphs: the Shift-And algorithm for exact matching and Myers' bitvector algorithm for semi-global alignment. These linear algorithms are both based on processing w sequence characters with a constant number of operations, where w is the word size of the machine (commonly 64), and achieve a speedup of up to w over naive algorithms. For a graph with |V| nodes and |E| edges and a sequence of length m, our bitvector-based graph alignment algorithm reaches a worst case runtime of O(|V|+⌈mw⌉|E| log w) for acyclic graphs and O(|V|+m|E| log w) for arbitrary cyclic graphs. We apply it to five different types of graphs and observe a speedup between 3-fold and 20-fold compared with a previous (asymptotically optimal) alignment algorithm.Availability and implementationhttps://github.com/maickrau/GraphAligner.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC6761980 | biostudies-literature

BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm.

Project description:MotivationMapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice.ResultsWe have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7-25 times faster than a standard iterative algorithm.Availability and implementationSource code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html. BitPAl is implemented in C and runs on all major operating systems.Contactjloving@bu.edu or yhernand@bu.edu or gbenson@bu.eduSupplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC4221118 | biostudies-literature

Molecular cloning, sequence, expression, and processing of the interleukin 16 precursor.

Project description:Interleukin 16 (IL-16) has been shown to function as chemoattractant factor, as a modulator of T-cell activation, and as an inhibitor of immunodeficiency virus replication. The recent identification of inconsistencies in published IL-16 cDNA nucleotide sequences led to the proposal that IL-16 is synthesized in the form of a large precursor protein (pro-IL-16). To identify the true transcriptional start of the IL-16 mRNA rapid amplification of cDNA ends methods were applied. The complete pro-IL-16 cDNA was subsequently molecularly cloned, sequenced, and expressed in COS-7 cells. We report here that pro-IL-16 is most likely synthesized as a 67-kDa protein and is encoded from a major 2.6-kb transcript. Recombinant pro-IL-16 polypeptides are specifically cleaved in lysates of CD8(+) cells, suggesting that the naturally secreted bioactive form of IL-16 is smaller than the originally published 130 amino acids fragment. Moreover, in contrast to other interleukins such as IL-15, IL-16 mRNA expression is almost exclusively limited to lymphatic tissues underlining the potential of IL-16 as an immune regulatory molecule.

| S-EPMC24668 | biostudies-literature

A 16-bit Coherent Ising Machine for One-Dimensional Ring and Cubic Graph Problems.

Project description:Many tasks in our modern life, such as planning an efficient travel, image processing and optimizing integrated circuit design, are modeled as complex combinatorial optimization problems with binary variables. Such problems can be mapped to finding a ground state of the Ising Hamiltonian, thus various physical systems have been studied to emulate and solve this Ising problem. Recently, networks of mutually injected optical oscillators, called coherent Ising machines, have been developed as promising solvers for the problem, benefiting from programmability, scalability and room temperature operation. Here, we report a 16-bit coherent Ising machine based on a network of time-division-multiplexed femtosecond degenerate optical parametric oscillators. The system experimentally gives more than 99.6% of success rates for one-dimensional Ising ring and nondeterministic polynomial-time (NP) hard instances. The experimental and numerical results indicate that gradual pumping of the network combined with multiple spectral and temporal modes of the femtosecond pulses can improve the computational performance of the Ising machine, offering a new path for tackling larger and more complex instances.

| S-EPMC5034318 | biostudies-literature

Molecular logic for cellular specializations that initiate the auditory parallel processing pathways

Project description:The cochlear nuclear complex (CN), the starting point for all central auditory processing, comprises a suite of neuronal cell types that are highly specialized for neural coding of acoustic signals, yet molecular logic governing cellular specializations remains largely unknown. By combining single-nucleus RNA sequencing and Patch-seq analysis, we reveal a set of transcriptionally distinct cell populations encompassing all previously observed types and discover multiple new subtypes with anatomical and physiological identity. The resulting complete cell-type taxonomy reconciles anatomical position, morphological, physiological, and molecular criteria, enabling determination of molecular basis of the remarkable cellular phenotypes in the CN. In particular, CN cell-type identity is encoded in a transcriptional architecture that orchestrates functionally congruent expression across a small set of gene families to customize projection patterns, input-output synaptic communication, and biophysical features required for encoding distinct aspects of acoustic signals. This high-resolution account of cellular heterogeneity from the molecular to the circuit level illustrates molecular logic for cellular specializations and enables genetic dissection of auditory processing and hearing disorders with unprecedented specificity.

2024-11-04 | GSE273145 | GEO

Storage-efficient 16-Bit Hybrid IP traceback with Single Packet.

Project description:Since adversaries may spoof their source IPs in the attacks, traceback schemes have been proposed to identify the attack source. However, some of these schemes' storage requirements increase with packet numbers. Some even have false positives because they use an IP header's fragment offset for marking. Thus, we propose a 16-bit single packet hybrid IP traceback scheme that combines packet marking and packet logging with high accuracy and low storage requirement. The size of our log tables can be bounded by route numbers. We also set a threshold to determine whether an upstream interface number is stored in a log table or in a marking field, so as to balance the logging frequency and our computational loads. Because we store user interface information on small-degree routers, compared with current single packet traceback schemes, ours can have the lowest storage requirements. Besides, our traceback achieves zero false positive/negative rates and guarantees reassembly of fragmented packets at the destination.

| S-EPMC4217332 | biostudies-other

ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements.

Project description:Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying parallel and convergent replacements involves multiple steps and computational routines, such as multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, topology tests, and simulation of sequence evolution. Here, we present ProtParCon, a Python 3 package that provides a common interface for users to process molecular data and identify parallel and convergent amino acid replacements in orthologous protein sequences. By integrating several widely used programs for computational biology, ProtParCon implements general functions for handling multiple sequence alignment, ancestral-state reconstruction, maximum-likelihood phylogenetic tree inference, and sequence simulation. ProtParCon also contains a built-in pipeline that automates all these sequential steps, and enables quick identification of observed and expected parallel and convergent amino acid replacements under different evolutionary assumptions. The most up-to-date version of ProtParCon, including scripts containing user tutorials, the full API reference and documentation are publicly and freely available under an open source MIT License via GitHub. The latest stable release is also available on PyPI (the Python Package Index).

| S-EPMC6471834 | biostudies-literature

pUBLically unzipping Parkin: how phosphorylation exposes a ligase bit by bit.

Project description: Not available

| S-EPMC4609180 | biostudies-literature

Massively parallel exon capture and library-free resequencing across 16 genomes.

Project description: Not available

| S-EPMC2703445 | biostudies-literature

Parallel information processing channels created in the retina.

Project description:In the retina, several parallel channels originate that extract different attributes from the visual scene. This review describes how these channels arise and what their functions are. Following the introduction four sections deal with these channels. The first discusses the "ON" and "OFF" channels that have arisen for the purpose of rapidly processing images in the visual scene that become visible by virtue of either light increment or light decrement; the ON channel processes images that become visible by virtue of light increment and the OFF channel processes images that become visible by virtue of light decrement. The second section examines the midget and parasol channels. The midget channel processes fine detail, wavelength information, and stereoscopic depth cues; the parasol channel plays a central role in processing motion and flicker as well as motion parallax cues for depth perception. Both these channels have ON and OFF subdivisions. The third section describes the accessory optic system that receives input from the retinal ganglion cells of Dogiel; these cells play a central role, in concert with the vestibular system, in stabilizing images on the retina to prevent the blurring of images that would otherwise occur when an organism is in motion. The last section provides a brief overview of several additional channels that originate in the retina.

| S-EPMC2951406 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data