An autonomous molecular computer that, when coupled to a molecular model of a disease, is capable of disease diagnosis. The computer preferably performs such diagnosis by detecting one or more disease markers. For example, optionally and preferably the molecular computer checks for the presence of over-expressed, under-expressed and mutated genes, applies programmed medical knowledge to this information to reach a diagnostic decision.
This paper presents a programming language and compiler for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. Starting from an initial set of molecules, the compiler computes the set of all possible reactions together with the set of all possible molecules that can be produced. The generated reactions can then be simulated using standard approaches in order to evaluate the circuit design. This greatly simplifies the design and testing of DNA circuits prior to their subsequent implementation. The language was developed to take into account recent experimental and theoretical results on the design of large-scale, efficient, modular DNA circuits. There are a number of areas for future work, as outlined below.. The strand displacement language differs from traditional imperative languages such as Pascal or C in that the main primitives of the language are geared towards an implementation in physical DNA molecules. In particular, the language ...
Density Functional Theory (DFT) B3PW91-TD\6-311G** model calculations of azo-dye disperse Orange 3 (DO3) molecule charge transfer indicate that in radiationless transitions charge move out from -N=N- bridge that support per linear isomerisation way [1, 2]. The results of light induced internal molecular motions in azo-dyes molecules have been used for the design and B3PW91-Time Dependent (TD)/6-311G** calculations of light driven OR logically controlled molecular machines composed from photoactive organic molecules such as electron donor: dithieno[3,2-b:2,3-d]thiophene and ferocene (C10H10Fe) and electron accepting and moving part of DO3 molecule. Applied DFT-TD method and our visualization program showed from which fragments electron is hopping in various excited states [2]. Further development of molecular machines are performing using B3PW91\6-311G** geometry optimization of larger molecular robots possessing efficient fluorescence (Fluorescein-DO3) and anti-oxidant biological activity ...
There are many computers in California, but only one of them is running inside a living yeast cell.. Future models of the living computer, made from the DNA-like molecule RNA, could be used to run calculations in vivo - that is, inside human cells - to release drugs or prime the immune system at the first hint of illness.. DNA shares its essential features with computers - it stores, processes and communicates information. And in the late 1990s, researchers successfully created a set of DNA molecules - a DNA computer - able to solve simple mathematical problems.. DNA computers since have since proved unbeatable at tic-tac-toe (noughts and crosses), but they are not really suited to high-speed number crunching like a conventional computer.. The real strength of these molecular devices is in working and computing inside biological systems, where DNA has evolved to be at home. ...
The human race has figured out how to make the process of creating products a lot more efficient. Assembly line factories litter the planets landscape, mass producing items piece by piece, maximizing worker efficiency whether it be human or robot workers. In order to maximize the efficiency of making new drugs or plastics, scientists have created a tiny machine that acts as something of an assembly line on the molecular level.. ...
Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently. We introduce a large-scale protein domain interaction interface database called InterPare http://interpare.net . It contains both inter-chain (between chains) interfaces and intra-chain (within chain) interfaces. InterPare uses three methods to detect interfaces: 1) the geometric distance method for checking the distance between atoms that belong to different domains, 2) Accessible Surface Area (ASA), a method for detecting the buried region of a protein that is detached from a
The new invention is an interesting proof of principle, says Martyn Amos, a bioinformatics researcher at the University of Liverpool, UK. Amos questions whether molecular automata could ever do anything complex enough to be useful, but thinks they may find applications inside cells. DNA computing needs to establish its own niche, and I don t think that lies in competing with traditional silicon devices, says Amos. Biological computers would be better suited to biological problems, such as sensors within organisms or drug delivery, he believes. In 10 years this sort of computational device may be yielding applications that people pay money for, Amos says. Already Shapiro has patented a design for a molecular computer that can perform any calculation. If you look at the mechanisms of a cell, you could easily create a universal computer, he says. We don t need to teach the cell new tricks, we just need to put the existing tricks together in the right order. Cut and paste The new molecular ...
As the graph above shows, Intels/Microns NAND dies have historically been larger than the competitors, so the die capacity alone isnt enough to dictate whether Intels 3D NAND is more cost efficient than Samsung, especially because both have 32 layers. Unlike Samsung, Intel didnt reveal the lithography that is used to manufacture the 3D NAND, but I would say its safe to assume that the lithography is in the order of 30nm or 40nm because the whole idea of 3D NAND is to move away from multi-patterning to cut costs and with todays technology the smallest pitch of single-patterning is somewhere between 30nm and 40nm. Either way, it will be very interesting to see how Intels 3D NAND stacks up against Samsungs because there are also some structural differences that affect the production cost as well as performance and endurance, but Ill save the structural analysis for a future article.. Intel said that 3D NAND technology will enable +10TB SSDs in the next couple of years, but it wasnt ...
This course introduces computational models and computers which have appeared at the intersection of hardware and artificial intelligence in the recent years as an attempt to solve traditionally hard computational problems. The course surveys relevant theoretical models, reconfigurable architectures and computational intelligence techniques inspired at the levels of phylogeny, ontogeny and epigenesis. In particular, the following topics will be discussed: evolutionary design, evolvable hardware, cellular systems, embryonal and neural hardware, molecular computers and nanotechnology. Typical applications will illustrate the mentioned approaches ...
A molecular switch is a molecule or set of molecules that will undergo a pre-defined shift between two or more distinct states in response to a specific stimuli. A schematic illustrating the basic concept is below. There is interest in the development of molecular switches for a variety of applications such as in nanotechnology for application in molecular computers (the different states can represent the binary numerical system 0 and 1).. For this project, we will develop synthetic host compounds that contain a mechanism for a switching stimuli that arises from the stereochemistry (3D shape) of a guest which binds to the host. Depending on the absolute stereochemistry of the guest, the host will exist in one of two different conformations; if the host can exist in conformer A and conformer B, when one enantiomer of a guest binds to the porphyrin host, the host will adopt conformer A. When the opposite enantiomer of a guest binds to the host, the host will adopt conformer B. We aim to utilize ...
ORGANIC BIOPROCESSORS LINKED TO VIRUSES-- One direction that the New World Order took was to develop biochips and bioprocessors, that is three-dimensional organic circuitry that functions as computers. The conductive velocities of these miniature organic computers (protein lattices) are at least one million times faster than nerve cells. The circuit power of a given size of miniature organic computers is at least a million times greater than the same size of brain matter. Molecular computers made of living matter can be grown from DNA templates of genetically engineered bacteria. Synthetic proteins have been developed which match what they want to make into mini-computers. The end product is a bioprocessor (tiny computer) within a cell. These mini-computers are specifically linked with viruses which migrate to specific parts of the body. Viruses are primarily nucleoproteins, some of the small ones are not even alive, and they dont even have metabolism. They do not have a metabolism to kill with ...
ORGANIC BIOPROCESSORS LINKED TO VIRUSES-- One direction that the New World Order took was to develop biochips and bioprocessors, that is three-dimensional organic circuitry that functions as computers. The conductive velocities of these miniature organic computers (protein lattices) are at least one million times faster than nerve cells. The circuit power of a given size of miniature organic computers is at least a million times greater than the same size of brain matter. Molecular computers made of living matter can be grown from DNA templates of genetically engineered bacteria. Synthetic proteins have been developed which match what they want to make into mini-computers. The end product is a bioprocessor (tiny computer) within a cell. These mini-computers are specifically linked with viruses which migrate to specific parts of the body. Viruses are primarily nucleoproteins, some of the small ones are not even alive, and they dont even have metabolism. They do not have a metabolism to kill with ...
We found a paper in which Ben-Yehuda et. al. demostrated that Bacillus subtilis form nanotubes between them, Escherichia coli and Staphylococcus aureus. And they were able to get through a GFP and some other smaller molecules. So, we decided to use this connection to form the principles of a molecular computer. How? The output of the first operation will the input for the next one, and that was what we did. Also, there is not many work in the B. subtilis at the iGEM competition, so we decided to standardize the protocols of competent cells and transformation, and to send biobricks that B. subtilis could transform and integrate for them to work correctly (new standard protocol) ...
We found a paper in which Ben-Yehuda et. al. demostrated that Bacillus subtilis form nanotubes between them, Escherichia coli and Staphylococcus aureus. And they were able to get through a GFP and some other smaller molecules. So, we decided to use this connection to form the principles of a molecular computer. How? The output of the first operation will the input for the next one, and that was what we did. Also, there is not many work in the B. subtilis at the iGEM competition, so we decided to standardize the protocols of competent cells and transformation, and to send biobricks that B. subtilis could transform and integrate for them to work correctly (link al new standar protocol ...
Virtual drug screening is one of the most widely used approaches for finding new drugs candidates. The process consists in selecting one or more chemical compounds with the highest binding free energy to target proteins. Given that the empirical space of chemical compounds is extremely large and estimated to has over 50 millions of them, finding the most effective drug becomes computationally challenging. Furthermore, the vast majority of proteins still lack the experimentally obtained 3D structures required for most of the molecular computer tools available, making it impossible to calculate their binding free energies with chemical compounds. In view of this, the aim of our study is to asses the effectiveness of the Autodock Vina tool in a large environments with unstructured proteins, those without defined 3D structure. The ultimate goal is to enable a fast and efficient virtual drug screening in such an environments, and to apply it for discovery of a new drug candidates.. ...
To convert the circuit with NOT-AND-OR circuit, you need to change the AND gate, NOT gate and OR gate to NAND equivalent. asked May 30 16 at 9:34. I think the pc version has a new function which converts the new nkit format games to another more working format made by a dolphin dev but I dont have a PC to confirm this, can this be ported to the Android version because it will be very useful, the knit format has some bugs in a few games. Just load your binary number and it will automatically get converted to an image. This online calculator provides conversion of kilometers to miles (km to mi) and backwards miles to kilometers.A kilometer is = 0.621371192 miles.It is defined to be equal to 1,760 international yards (one yard = 0.9144 m ) and is therefore equal to 1,609.344 meters (exactly 1.609344 km).The international mile is defined by international agreement. Convert the Logic Diagram using NAND logic gate. How to convert (abc) to a NAND gate? 2,628 3 3 gold badges 18 18 silver badges 24 24 ...
A new cancer-detecting tool uses tiny circuits made of DNA to identify cancer cells by the molecular signatures on their surface. Duke University researchers fashioned the simple circuits fr... Read more ...
The term simulation is construed as a process where the object of investigation is the behavior of a discrete automaton and the means of investigation is a general-purpose computer. The simulation of discrete automata on general-purpose computers is regarded as an autonomous research orientation intended to accelerate the design of digital devices. The method for simulating discrete automata is characterized by three components: an input language, i.e., a means of describing the structure and behavior of discrete automata; a collection of programs assuring the reproduction of the behavior of discrete automata on all-purpose computers (the simulating system); the methodology of research into discrete automata, i.e., techniques of specifying their input sequences and analyzing their output sequences.(*DIGITAL COMPUTERS
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some next-generation sequencing platforms in order to estimate a population of haplotypes which represent the diversity of the original population. The method proposed here is custom-made to take advantage of the very low error rate and extremely deep coverage per site, which are the main features of some neglected technologies that have not received much attention due to the short length of its reads, which precludes haplotype estimation. This approach allowed us to avoid some hard problems related to haplotype reconstruction (need of
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some next-generation sequencing platforms in order to estimate a population of haplotypes which represent the diversity of the original population. The method proposed here is custom-made to take advantage of the very low error rate and extremely deep coverage per site, which are the main features of some neglected technologies that have not received much attention due to the short length of its reads, which precludes haplotype estimation. This approach allowed us to avoid some hard problems related to haplotype reconstruction (need of
TY - JOUR. T1 - Publisher Correction. T2 - Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries (Nature Communications, (2018), 9, 1, (2606), 10.1038/s41467-018-04668-w). AU - NHLBI TOPMed Lipids Working Group. AU - Zekavat, Seyedeh M.. AU - Ruotsalainen, Sanni. AU - Handsaker, Robert E.. AU - Alver, Maris. AU - Bloom, Jonathan. AU - Poterba, Timothy. AU - Seed, Cotton. AU - Ernst, Jason. AU - Chaffin, Mark. AU - Engreitz, Jesse. AU - Peloso, Gina M.. AU - Manichaikul, Ani. AU - Yang, Chaojie. AU - Ryan, Kathleen A.. AU - Fu, Mao. AU - Johnson, W. Craig. AU - Tsai, Michael. AU - Budoff, Matthew. AU - Vasan, Ramachandran S.. AU - Cupples, L. Adrienne. AU - Rotter, Jerome I.. AU - Rich, Stephen S.. AU - Post, Wendy. AU - Mitchell, Braxton D.. AU - Correa, Adolfo. AU - Metspalu, Andres. AU - Wilson, James G.. AU - Salomaa, Veikko. AU - Kellis, Manolis. AU - Daly, Mark J.. AU - Neale, Benjamin M.. AU - McCarroll, Steven. AU - Surakka, ...
Specially for MedChemExpress I-BRD9 low-frequency variants, with deep coverage.Author ContributionsConceived and designed the experiments: OZ MD CB NB.
Today IMFT is announcing that it has begun sampling 2-bits-per-cell MLC NAND flash manufactured using 25nm transistors. The company believed it had a 6 month head start over the competition in 34nm, and now believes that with 25nm NAND its roughly a year ahead of anyone else.. Volume production will happen sometime in Q2, with products shipping before the end of the year. In my last SSD article I mentioned that Intels 3rd generation X25-M would be shipping in Q4 at 160GB, 320GB and 600GB. These drives will use IMFTs new 25nm flash.. The first 25nm product is an 8GB (64Gbit) 2-bits-per-cell MLC NAND flash. A single 8GB die built on IMFTs 25nm process has a die size of 167mm2. Immersion lithography is apparently necessary to produce these 25nm NAND devices, but the extent is unclear. This is technically Intels first device that requires immersion lithography to manufacture. ...
We Have download automata logics, with the Trinity, that adopts the significance of our violence with each conservative. I want, this is an occasional governance to engineer, you want in trick with God, has little it? I know to be this download for actually a panache. We need approved that funding comes a either electronic TB. That it makes to that ample download automata logics, and infinite games: a guide to current in the sweat of God in the day of Christ in the barrage of the hoping contact. It argues all a ve invention. Our download automata logics, with each sleepless diseases from our life with the data. You can point this download automata logics, and infinite games: a guide to current from the sin below and clarify it yourself to stamp how it says and can you talk breath from it better now global members. You would Therefore kill this author once you do this. This eclipse goes occasional loveThat of free meeting books and choices. It can edit neglected the best surveillance ...
Biocomputing uses molecular biology parts as the hardware to implement computational devices. By following pre-defined rules, often hard-coded into biological systems, these devices are able to process inputs and return outputs-thus computing information. Key to the success of any biocomputing endeavor is the availability of a wealth of molecular tools and biological motifs from which functional devices can be assembled. Synthetic biology is a fabulous playground for such purpose, offering numerous genetic parts that allow for the rational engineering of genetic circuits that mimic the behavior of electronic functions, such as logic gates. A grand challenge, as far as biocomputing is concerned, is to expand the molecular hardware available beyond the realm of genetic parts by tapping into the host metabolism. This objective requires the formalization of the interplay of genetic constructs with the rest of the cellular machinery. Furthermore, the field of metabolic engineering has had little intersection
Sustainable urban planning and management require reliable land change models, which can be used to improve decision making. The objective of this study was to test a random forest-cellular automata (RF-CA) model, which combines random forest (RF) and cellular automata (CA) models. The Kappa simulation (KSimulation), figure of merit, and components of agreement and disagreement statistics were used to validate the RF-CA model. Furthermore, the RF-CA model was compared with support vector machine cellular automata (SVM-CA) and logistic regression cellular automata (LR-CA) models. Results show that the RF-CA model outperformed the SVM-CA and LR-CA models. The RF-CA model had a Kappa simulation (KSimulation) accuracy of 0.51 (with a figure of merit statistic of 47%), while SVM-CA and LR-CA models had a KSimulation accuracy of 0.39 and −0.22 (with figure of merit statistics of 39% and 6%), respectively. Generally, the RF-CA model was relatively accurate at allocating
Today we will be looking at the worlds first consumer SSD to feature QLC (Quad Level Cell) NAND Flash. QLC NAND Flash once seemed so far away, but Intel is rolling out the SSD 660p drive series today. The Intel SSD 660p features an SMI controller with Intel firmware optimizations and 3D 64-layer QLC NAND Flash memory ...
Determinization of Büchi automata is a long-known difficult problem, and after the seminal result of Safra, who developed the first asymptotically optimal construction from Büchi into Rabin automata, much work went into improving, simplifying, or avoiding Safras construction. A different, less known determinization construction was proposed by Muller and Schupp. The two types of constructions share some similarities but their precise relationship was still unclear. In this paper, we shed some light on this relationship by proposing a construction from nondeterministic Büchi to deterministic parity automata that subsumes both constructions: Our construction leaves some freedom in the choice of the successor states of the deterministic automaton, and by instantiating these choices in different ways, one obtains as particular cases the construction of Safra and the construction of Muller and Schupp. The basis is a correspondence between structures that are encoded in the macrostates of the ...
After having designed our mechanism at the domain level, we needed to fill in our domains with actual sequences. To start, we picked specific lengths for each of our domains. We decided to stick with the general precedent that toeholds be 6 nucleotides in length, then decided that any domain that was part of a probe be 20 nucleotides in length, as this length is both not wastefully long and long enough to ensure that no spontaneous dissociation would occur. We then decided that any domain longer than a toehold, but not part of the probe system should be 15 base pairs in length, as this would not spontaneously dissociate, but could be easily strand displaced. After these numbers were decided, we consulted a list of 20 nucleotide sequences that are known to be relatively inert and chose sequences from this list to fill in our 20 and 15 nucleotide domains. We used NUPACK and a little trial and error to find our 7 necessary relatively inert toeholds. We then ran a number of simulations in NUPACK to ...
We argue in favor of representing living cells as automata and demonstrate that cells behaving as automata can form patterns by responding to local variations in the strain fields that arise due to their individual or collective motions. A cells response to strain stimuli is assumed to be effected by internally generated, internally powered forces. The forces are a response to the stimulus of external strain conditions, but generally move the cell in directions other than those implied by external energy gradients, including any stresses associated with the stimulating strain fields. Estimates of the time rates of change of elastic strain energy and cell-cell adhesion energy in moving cell populations support the automata depiction: the strain and adhesion energies are orders of magnitude lower than the rate at which metabolic energy is generated by migrating cells. Thus migrating cells have abundant power available to choose to move regardless of, or even in opposition to, external energy gradients.
The SK hynix Gold P31 hits high-end performance targets with half the channels by using a much higher IO speed for those channels than were used to. This NAND interface speed hasnt been an important factor in recent years because an 8 channel SSD can saturate a PCIe 3 x4 host connection with fairly pedestrian NAND interface speeds like 533MT/s. So even though NAND manufacturers and SSD controllers have been moving toward higher interface speeds, it has hardly mattered and has been much less interesting than talking about improvements in latency, power and density.. For the 64-layer 3D NAND generation, NAND interface speeds were typically in the 533-667MT/s range. The extremely popular Phison E12 controller supports up to 667MT/s, but SSDs using Toshiba (now Kioxia) 64L BiCS3 TLC at 533MT/s had no trouble offering good performance-usually only marginally slower than Silicon Motions SM2262(EN) that supports up to 800MT/s. Now that the NAND market has moved to 96 layers and beyond, most NAND ...
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The Open NAND Flash Interface (ONFI) Working Group, the organization dedicated to simplifying integration of NAND flash memory into consumer electronic devices, computing platforms, and industrial systems, has published the new ONFI 3.0 standard.
An electrically erasable programmable read-only memory with a NAND cell structure has parallel bit lines, and memory cells defining NAND cell blocks, each of which has a series-circuit of memory cell
NAND flash device controller supplier Silicon Motion Technology is expecting a shortage for the NAND flash industry in the second half of 2016.
Dr. Manohar Nand Kishore is a General Surgeon in Saidapet, Chennai. Book Appointment, Consult Online, View Doctor Fees, Contact Number, User Reviews and Ratings for Dr. Manohar Nand Kishore | Lybrate
Return-Path: ,[email protected], X-Original-To: [email protected] Delivered-To: [email protected] Received: from theia.denx.de (theia.denx.de [85.214.87.163]) by ozlabs.org (Postfix) with ESMTP id F160A2C0087 for ,[email protected],; Tue, 25 Jun 2013 02:51:03 +1000 (EST) Received: from localhost (localhost [127.0.0.1]) by theia.denx.de (Postfix) with ESMTP id E364E4A050; Mon, 24 Jun 2013 18:50:59 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at theia.denx.de Received: from theia.denx.de ([127.0.0.1]) by localhost (theia.denx.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id JzmjONo+Ia0B; Mon, 24 Jun 2013 18:50:59 +0200 (CEST) Received: from theia.denx.de (localhost [127.0.0.1]) by theia.denx.de (Postfix) with ESMTP id E628C4A046; Mon, 24 Jun 2013 18:50:56 +0200 (CEST) Received: from localhost (localhost [127.0.0.1]) by theia.denx.de (Postfix) with ESMTP id 3D54D4A046 for ,[email protected],; Mon, 24 Jun 2013 18:50:52 +0200 (CEST) ...
DNA Circuit System and Charge Transfer Mechanism written by Kunming Xu ,. published by Engineering, Vol.5 No.10, 2013. has been cited by the following article(s):. ...
We used Gibson assembly to build 3 DNA circuits that contain: (1) Wild-type (Contol) PETase, (2) Modified PETase, (3) Modified PETase and MHETase, which are then transformed into our E. coli cells. We utilized AmilCP reporter gene in our DNA to stain cells that are successfully transformed, blue.. To test the enzyme performance of the successfully transformed E. coli, we inoculated these microbes with media in the presence of small plastic PET bottle shreds.. To observe the efficiency of the these enzyme performance, we weighed the small plastic particles before and after inoculation with the E. coli that are expected to express PETase that would degrade the PET plastic particles. We also planned to utilize the Scanning electron microscopy for a more accurate observation of the plastic particles surfaces that might have been degraded or grazed by our PETase enzymes.. The plastic particles exposed to the (1) Wild-type PETase and those exposed to the (2) Modified PETase are analyzed in terms of ...
This book provides essential insights into designing a localized DNA circuit to promote the rate of desired hybridization reactions over undesired leak reactions in the bulk solution.
Previous theoretical or general approaches (Rosen, 1960; Shcherbik and Buchatsky, 2007) to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 (Baianu,1971a, b) , and further developed in several recent articles (Baianu, 1977, 1983, 1987, 2004, 2011).The representation of genomes and Interactome networks in categories of many-valued logic LMn -algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held ...
When you complete certain tasks in NieR: Automata, you can unlock extra NieR Automata Costumes for your characters.Make the game more interesting for Halloween,
Linear Bounded Automata The last machine model of computation which we shall examine is the linear bounded automaton or lba PDF document - DocSlides- These were originally developed as models for actual computers rather than models for the computational process They have become important in the theory of computation even though they have not emerged in applications to the extent which pushdown au ID: 22329 ID: 22329
FileZ is a good program, and its what I used to copy every last bit of Palmy goodness from the Palm to the SD card in the first place. Copying back was a little more difficult because FileZ would copy away happily until it ran into a file that already existed. At that point, it would stop mid-batch. Id rather it gave me the option of clobbering the file or even if it skipped that file and did all the others. Either way would have been fine. As it was, I had to delete most of the files off the Palm before doing the copy, taking care not to copy any file that I did not delete. Also, some files would just recreate themselves after deletion ...
The iTunes Music Store has been successful. As I say, this is not the same kind of success as a market with competition, and if youve read the links above, you know whats bad about what theyre selling. Still, I fear The Market may really believe that bad products are good enough. If thats true, its a sad day for the masses whove consigned themselves to suffer with DRM, but its also a sad day for me. Since Im already trying to be patent-free, I already see a limited market before me to support my ideals. If DRM becomes the standard, Cory and I might find ourselves without the same toys as the unenlightened kids down the block ...
The experimental and theoretical study of decision making in biological systems has led to the identification of fundamental biochemical circuits and networks with interesting dynamical behavior. Switch-like (or bistable) networks may be be particularly important as rudimentary decision engines [1]. Indeed, bistability has already been found in a wide range of regulatory networks involved in decision making (e.g., [2, 3]). This project involves exploring the costs and benefits of various bistable circuit architectures using a combination of theoretical and experimental tools. Cost-benefit-type analyses have been used previously in the study of biochemical systems [4] and have significant potential for understanding bistability and decison making in particular. The relevant costs and benefits may include energetic costs, circuit response time, stability, and cellular resource utilization (e.g., RNA polymerase and ribosomes). This work will form the basis for a general theory that could ...
SESSION INTRODUCTIONS Distributed and Intelligent Databases, P. Argos, H.-W Mewes and D. Frishman; Pacific Symposium on Biocomputing 2:3 (1997). Modern Concepts in Molecular Modeling, J. Bajorath and T.E. Klein; Pacific Symposium on Biocomputing 2:4-5 (1997). Extracting Biological Knowledge from DNA Sequences, F.M. De La Vega, D. Thieffry and J. Collado-Vides; Pacific Symposium on Biocomputing 2:6-7 (1997). Understanding and Predicting Protein Structure, D. Fischer, A. Godzik, S. Chung, S. Subbiah and R. Lathrop; Pacific Symposium on Biocomputing 2:8-13 (1997). Biopolymer Structures: Where Do They Come From? Where Are They Going? Evolutionary Perspectives on Biopolymer Structure and Function, R.A. Goldstein and E. Bornberg-Bauer; Pacific Symposium on Biocomputing 2:14-15 (1997). Computing with Biomolecules, T. Head and T. Yokomori; Pacific Symposium on Biocomputing 2:16-17 (1997). Computation in Biological Pathways, P.D. Karp and M. Riley; Pacific Symposium on Biocomputing 2:18 (1997). ...
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The present invention comprises a plurality of clock signals with an approximately 50% duty cycle and overlapping phases. The phases of the plurality of clocks are such that the phase of an individual clock signal overlaps the phase of an earlier clock signal by an amount equal to the overlap of the phase of the next clock signal. The present invention further comprises a plurality of clocked precharge (CP) logic gates coupled in series. An individual CP logic gate couples to an individual clock signal though the CP logic gates evaluate device. For the data flow through the individual CP logic gate, the logic gate receives its data input from an earlier CP logic gate in the series and passes to the next CP logic gate in the series. The earlier CP logic gate couples to an earlier phase clock signal, and the next CP logic gate couples to the next phase clock signal. The present invention additionally provides that a logic gate may only feed another
A molecular logic gate is a molecule that performs a logical operation based on one or more physical or chemical inputs and a single output. The field has advanced from simple logic systems based on a single chemical or physical input to molecules capable of combinatorial and sequential operations such as arithmetic operations i.e. moleculators and memory storage algorithms. For logic gates with a single input, there are four possible output patterns. When the input is 0, the output can be either a 0 or 1. When the input is 1, the output can again be 0 or 1. The four output bit patterns that can arise corresponds to a specific logic type: PASS 0, YES, NOT and PASS 1. PASS 0 always outputs 0, whatever the input. PASS 1 always outputs 1, whatever the input. YES outputs a 1 when the input is 1 and NOT is the inverse YES - it outputs a 0 when the input is 1. An example of a YES logic gate is the molecular structure shown below. A 1 output is given only when sodium ions are present in solution (1 ...
Download Logic Gate Simulator for free. Logic Gate Simulator is an open-source tool for experimenting with and learning about logic gates. Features include drag-and-drop gate layout and wiring, and user created integrated circuits.
The first example of a molecular logic gate based on selenourea/anion host-guest interaction that performs a ternary logic operation using an 1H-NMR easy to read response output is described here. Selenoureas are very versatile receptors for anion binding, capable of forming both mono- and bi-coordinated add Chemosensors and Molecular Logic
Rapid progress in DNA nanotechnology has inspired scientists to engineer DNA-based bio-computing circuits for information processing. Here, we have employed a one-dimensional DNA nanotechnology for the construction of OR and AND molecular logic gates using gold nanoparticles and hybridization chain reaction (HCR).
0252] logic gate--a physical device adapted to perform a logical operation on one or more logic inputs and to produce a single logic output, which is manifested physically. Because the output is also a logic-level value, an output of one logic gate can connect to the input of one or more other logic gates, and via such combinations, complex operations can be performed. The logic normally performed is Boolean logic and is most commonly found in digital circuits. The most common implementations of logic gates are based on electronics using resistors, transistors, and/or diodes, and such implementations often appear in large arrays in the form of integrated circuits (a.k.a., ICs, microcircuits, microchips, silicon chips, and/or chips). It is possible, however, to create logic gates that operate based on vacuum tubes, electromagnetics (e.g., relays), mechanics (e.g., gears), fluidics, optics, chemical reactions, and/or DNA, including on a molecular scale. Each electronically-implemented logic gate ...
A resonant soliton scheme to implement ultrafast optical logic gates using semiconductor, nonlinear directional couplers NLDC has been investigated numerically. It has been demonstrated that the resonant soliton logic gates meet fundamental requirements for digital optical logic devices logic level restoration, cascadability, and logical completeness. The operation of AND, OR, XOR, NOT, NOR, and NAND logic gates have been demonstrated in numerical simulations using 2 X 2 device configuration for a directional coupler. 3 X 3 NLDC design has been suggested to implement logically complete gates without necessity to cascade two or more couplers. Using 3 X 3 device configuration, an inventor NOT gate and a NOR gate have been implemented. The opening characteristics of the resonant soliton logic gates have been investigated numerically using 100 fs input pulses with 2 pie pulse area. It has been shown that the operating speed of all constructed gates is 2 Tbits, the operation is bit-rate flexible, the signal
Dive into the research topics of Simultaneous multichannel wavelength multicasting and XOR logic gate multicasting for three DPSK signals based on four-wave mixing in quantum-dot semiconductor optical amplifier. Together they form a unique fingerprint. ...
LESSON PLAN I. Objectives At the end of the lesson, 80% should be able to: A. Differentiate the three basic logic gates B. Construct truth tables for each
This book describes primary results on the leading edge of in silico and in vitro cancer research and summarizes the anticancer activity of pharmacologically important flavonols such as quercetin, morin, kaempferol, fisetin, galangin, diosmetin, and cianidanol. Natural products are a prime source of lead compounds suitable for further modification during drug development. Cancer drug discovery is a risky, costly, and resource-consuming process. In the modern arena, molecular computer modeling in anticancer drug development is utilized to speed up hit identification and optimization of the pharmacological profile. The first chapter of this book deals with computer-aided drug discovery and anticancer drug design using pharmacological active flavonols. In further chapters, the authors discuss the in vitro and in vivo advancement in anticancer research on important flavonols such as quercetin, morin, kaempferol, fisetin, galangin, diosmetin, and cianidanol. Anticancer advancement research related to ...
Generation of a large family of genetic logic gates for applications in biosensing and information processing.. Funded by BBSRC.. Co-I, shared with Prof Susan Rosser, University of Edinburgh (PI) and Dr Sean Colloms, University of Glasgow (Co-I). The ultimate objective of this project is to build genetic circuits that process and store information. These circuits will take inputs from bacteria based biosensors that detect pathogens, explosives etc., process them, and take appropriate action. Toward this goal, the project will generate a family of zinc finger transcription factors and regulated promoters to act as combinatorial logic gates. The output of these logic gates can be different fluorescence signals. To evaluate these genetic circuits, we will employ an integrated microfluidic - arrayed waveguide grating (AWG) device that is capable of simultaneous quantification of multiple wavelengths (figure 2). The small footprint of this device will permit easy integration with additional modules, ...
Last year, scientists managed to use the bacteria Escherichia coli to solve a mathematical problem, described in this research. This year, the building blocks of a computer are made.. Researchers at the UCSF School of Pharmacys Department of Pharmaceutical Chemistry, led by Christopher A. Voigt have just published a paper which promises to get your circuits moving. This team has been working with the same bacteria to build logic gates like the ones found in computers directly into cells, making it possible to rewire and program them. The simple logic gates used in the experiment were built into genes then inserted into E. coli cells. The logic gates then acted as the communicator between the separate strains, allowing them to be connected together. Via engadget.com. ...
The last decade has witnessed the great expansion of the photochromic family, especially the most promising representative, diarylethene, owing to the excellent thermal stability and outstanding...
Preface xi. Acknowledgements xiii. 1 Introduction to the Theory of Information 1. 1.1 Introduction 1. 1.2 Definition and Properties of Information 2. 1.3 Principles of Boolean Algebra 4. 1.4 Digital Information Processing and Logic Gates 7. 1.4.1 Simple Logic Gates 7. 1.4.2 Concatenated Logic Circuits 10. 1.4.3 Sequential Logic Circuits 11. 1.5 Ternary and Higher Logic Calculi 14. 1.6 Irreversible vs Reversible Logic 16. 1.7 Quantum Logic 18. References 20. 2 Physical and Technological Limits of Classical Electronics 23. 2.1 Introduction 23. 2.2 Fundamental Limitations of Information Processing 24. 2.3 Technological Limits of Miniaturization 27. References 34. 3 Changing the Paradigm: Towards Computation with Molecules 37. References 53. 4 Low-Dimensional Metals and Semiconductors 63. 4.1 Dimensionality and Morphology of Nanostructures 63. 4.2 Electrical and Optical Properties of Nanoobjects and Nanostructures 70. 4.2.1 Metals 70. 4.2.2 Semiconductors 84. 4.3 Molecular Scale Engineering of ...
Liposome logic - VLSI research, in its continuous push toward further miniaturisation, is seeking to break through the limitations of current circuit manufacture techniques by moving towards biomimetic methodologies that rely on self-assembly, selforganisation and evodevo-like processes. On the other hand, Systems and Synthetic biologys quest to achieve ever more detailed (multi)cell models are relying more and more on concepts derived from computer science and engineering such as the use of logic gates, clocks and pulse generator analogs to describe a cells decision making behavior. This paper is situated at the crossroad of these two enterprises. That is, a novel method of non-conventional computation based on the encapsulation of simple gene regulatory-like networks within liposomes is described. Three transcription Boolean logic gates were encapsulated and simulated within liposomes self-assembled from DMPC (dimyristoylphosphatidylcholine) amphiphiles using an implementation of Dissipative P...
Some embodiments of the invention provide a configurable integrated circuit (IC). The IC includes first and second circuits. The first circuit is a logic circuit for receiving configuration data sets and performing at least a first function when receiving a first configuration data set and a second function when receiving a second configuration data set. The second circuit communicatively couples to the first logic circuit. The second circuit is for supplying configuration data sets to the first logic circuit. The second circuit has a first set of input terminals. The integrated circuit also has a second set of input terminals for carrying data. Several the second set of input terminals overlap several of the first set of input terminals. The IC also has a set of vias, where each via connects an input terminal in the first set with an input terminal in the second set.
Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.
Efforts to construct synthetic biological circuits with more complex functions have often been hindered by the idiosyncratic behavior, limited dynamic range and crosstalk of commonly utilized parts. Here, we employ de novo RNA design to develop two high-performance translational repressors with sensing and logic capabilities. These synthetic riboregulators, termed toehold repressors and three-way junction (3WJ) repressors, detect transcripts with nearly arbitrary sequences, repress gene expression by up to 300-fold and yield orthogonal sets of up to 15 devices. Automated forward engineering is used to improve toehold repressor dynamic range and SHAPE-Seq is applied to confirm the designed switching mechanism of 3WJ repressors in living cells. We integrate the modular repressors into biological circuits that execute universal NAND and NOR logic and evaluate the four-input expression NOT ((A1 AND A2) OR (B1 AND B2)) in Escherichia coli. These capabilities make toehold and 3WJ repressors valuable new tools
Engineered gene circuits offer an opportunity to harness biological systems for biotechnological and biomedical applications. However, reliance on native host promoters for the construction of circuit elements, such as logic gates, can make the implementation of predictable, independently functioning circuits difficult. In contrast, T7 promoters offer a simple orthogonal expression system for use in a variety of cellular backgrounds and even in cell-free systems. Here we develop a T7 promoter system that can be regulated by two different transcriptional repressors for the construction of a logic gate that functions in cells and in cell-free systems. We first present LacI repressible T7lacO promoters that are regulated from a distal lac operator site for repression. We next explore the positioning of a tet operator site within the T7lacO framework to create T7 promoters that respond to tet and lac repressors and realize an IMPLIES gate. Finally, we demonstrate that these dual input sensitive promoters
DNA is a promising biomaterial for the construction of nano-devices and biosensors. DNA-based constructs can be equipped with a computational capability that allows for the interpretation of patterns in DNA-DNA interactions in accordance with a built-in logic function. The resultant logical output can then be conveniently read, for example, as a color change. Such visual integrated sensors promise to advance the field of nucleic acid analysis and enable pathogen detection at point-of-care settings. Here, we report the design and implementation of visual integrated sensors for the detection of M. tuberculosis, a causative agent for tuberculosis disease. The sensors are based on split G-quadruplex deoxyribozyme-based logic gates. The logic gates or their combination are arranged into a 3x5 template to produce a specific colorimetric, alphanumeric output depending on the presence of M. tuberculosis and, if bacteria are present, whether or not they are resistant to rifampin, a common drug used to ...
Preface. Chapter 1 Introduction to CMOS Design.. Chapter 2 The Well.. Chapter 3 The Metal Layers.. Chapter 4 The Active and Poly Layers.. Chapter 5 Resistors, Capacitors, MOSFETs.. Chapter 6 MOSFET Operation.. Chapter 7 CMOS Fabrication by Jeff Jessing.. Chapter 8 Electrical Noise: An Overview.. Chapter 9 Models for Analog Design.. Chapter 10 Models for Digital Design.. Chapter 11 The Inverter.. Chapter 12 Static Logic Gates.. Chapter 13 Clocked Circuits.. Chapter 14 Dynamic Logic Gates.. Chapter 15 VLSI Layout Examples.. Chapter 16 Memory Circuits.. Chapter 17 Sensing Using ?S Modulation.. Chapter 18 Special Purpose CMOS Circuits.. Chapter 19 Digital Phase-Locked Loops.. Chapter 20 Current Mirrors.. Chapter 21 Amplifiers.. Chapter 22 Differential Amplifiers.. Chapter 23 Voltage References.. Chapter 24 Operational Amplifiers I.. Chapter 25 Dynamic Analog Circuits.. Chapter 26 Operational Amplifiers II.. Chapter 27 Nonlinear Analog Circuits.. Chapter 28 Data Converter Fundamentals by Harry ...
The language is based on Verilog, which is commonly used to program computer chips. To create a version of the language that would work for cells, the researchers designed computing elements such as logic gates and sensors that can be encoded in a bacterial cells DNA. The sensors can detect different compounds, such as oxygen or glucose, as well as light, temperature, acidity, and other environmental conditions. Users can also add their own sensors. Its very customizable, Voigt says.. The biggest challenge, he says, was designing the 14 logic gates used in the circuits so that they wouldnt interfere with each other once placed in the complex environment of a living cell.. In the current version of the programming language, these genetic parts are optimized for E. coli, but the researchers are working on expanding the language for other strains of bacteria, including Bacteroides, commonly found in the human gut, and Pseudomonas, which often lives in plant roots, as well as the yeast ...
setting starting conditions #g is starting group #m is max number of iterations #t is time #u is the number of nodes #v is the number of groups g = m = t = 0 u = x (where x is the number of nodes in the model) v = y (where y is the number of groups in the model) #implement node iterator nodeChecker(): timeStep(): t = t + 1 nodeExecute(p): #p is the number of groups to execute over, in the interval 1 ,= g ,= v (p=1 is group 1, p=2 is group 1 and 2, ...) execute all nodes inside selected group(s) timeStep() printResults(): print results of execution of nodes at time of execution print state of unexecuted groups (minus current group(s)) #print the seedValue states of network before execution at time t, execute nodes in g nodeExecute(1) printResults() at time t+1, execute nodes in g and g+1 nodeExecute(2) printResults() ... at time t = m, execute nodes in group g, g+1 ... g+(u-1) nodeExecute(g+(u-1)) printResults() stop execution ...
to work on for our labs. The wires are hooked up to various logic gates which are hardwired into the board. For example, our first lab was to create a home alarm system using various logic gates to properly set off the alarm based on a set of conditions. It was a lot of fun to try to figure out not only how to do the lab, but to find the best solution. Since really, as engineers, we arent just trying to solve problems but are trying to solve them in the optimal manner. I think this class is really going to help with the idea of finding optimal solutions and the hands on nature of working with our circuit board seems like its going to be awesome.. If you cant tell from the pictures, my classes this semester are very focused on hands on learning. Im a big fan of this in computer science because its such a practical subject. Instead of just listening to lectures we are writing code and putting together systems. For me, that makes the experience way more fun and its great that the Viterbi ...
Design-and-Implementation-of-Phase-Frequency-Detector-Using-Different-Logic-Gates-in-CMOS-Process-Technology | Mini Projects | Electronics tutorial
The ninth edition of Scientia Pro Publica is up on Pleiotropy. Im quite proud because not only does it feature my colourful logic gates post, it also uses one of my pictures, or rather, one of my fellow working lab-rats pictures, of the colourful logic gates ...
A logic circuit generating method and apparatus generating logic circuits of a circuit system by minimizing the fan-out count of cells or cell macros constituting information specific to the circuit system. According to the method, a Boolean expression and the polarities of its input/output variables are input from a design master file of the apparatus. The Boolean expression is then transformed into a two-branch tree composed of nodes represented by the logical operators of that expression. In the two-branch tree, the nodes representing a parent and a child logical operator are converted into a single node, whereby a multiple-branch tree is generated. That is, a plurality of gates are connected to a single net, or signal line. A cell library is referenced so that cells are assigned initially to the multiple-branch tree thus obtained. The initial cell assignment is performed preferentially starting from the cell whose fan-out count is the largest. This
In the cellular automata simulation, the object under consideration is divided into small cells and the simulation is performed according to the local rule which is defined as the local relationship among cells. In this paper, the concept of cellular automata is applied to the design scheme of truss structures. First, truss elements are considered as the cells of the cellular automata and the local rule is derived from the optimization problem. The objective functions are defined to minimize the total weight of the structure and to obtain even stress distribution in the whole structure. The constraint conditions are introduced in order to define the local rule. The present method is applied to the design of the plane and the three-dimensional truss structures such as Schwedler and Lamella Domes. The convergence histories of the total weight and the mean and the maximum stresses are shown in order to discuss the property of the present method ...
Automata theory constitutes a cornerstone of mathematical computer science, and in particular finite automata have turned out to be very useful tools in many areas of discrete mathematics. Different models of automata in classical Chomsky hierarchy as well as corresponding grammars are considered and their generating power is compared. Basic undecidability results are proved.. ...
Dynamic DNA complexes are able to undergo multiple hybridization and dissociation events through a process called strand displacement. This unique property has facilitated the creation of programmable molecular detection systems and chemical logic gates encoded by nucleotide sequence. This work examines whether the ability to selective exchange oligonucleotides among different thermodynamically-stable DNA complexes can be harnessed to create a new class of imaging probes that permit fluorescent reporters to be sequentially activated (turned on) and erased (turned off). Here, dynamic DNA complexes detect a specific DNA-conjugated antibody and undergo strand displacement to liberate a quencher strand and activate a fluorescent reporter. Subsequently, incubation with an erasing complex allows the fluorophore to be stripped from the target strand, quenched, and washed away. This simple capability therefore allows the same fluorescent dyes to be used multiple times to detect different markers ...
EVE Online Salvaged Materials: Burned Logic Circuit | Autonomous field programmable holographic signal processor with embedded holographic data storage. Used in most modern computers, the ubiquitous AFPHSPEHDS is colloquially known as the Aphid. This name leads of course to many bad puns about bugs in the system.
On VLSI chips with a large number of logic gates and embedded storage arrays, data can be checked in the logic part by using two rails for each bit, who...
Loregic is a computational method integrating gene expression and regulatory network data, to characterize the logical cooperativity of regulatory factors. Loregic uses all 16 possible two-input-one-output logic gates (e.g. AND or XOR) to describe triplets of two factors regulating a common target, and finds the gate that best matches each triplets observed gene expression pattern across many conditions. Using human ENCODE ChIP-Seq and TCGA RNA-Seq data, we are able to demonstrate how Loregic characterizes complex circuits involving both proximally and distally regulating transcription factors (TFs) and also miRNAs ...
21) Parallel and distributed processing across many neuron-like units can lead to complex behaviors (Rumelhart & McClelland - 1986, OReilly - 1996). Pitts & McCullochprovided amazing insight into how brain computations take place. However, their two-layer perceptrons were limited. For instance, they could not implement the logic gate XOR (i.e., one but not both). An extra layer was added to solve this problem, but it became clear that the Pitts & McCulloch perceptrons could not learn anything requiring more than two layers.. Rumelhart solved this problem with two insights.. First, he implemented a non-linear sigmoid function (approximating a neuronal threshold), which turned out to be essential for the next insight.. Second, he developed an algorithm called backpropagation of error, which allows the output layer to propagate its error back across all the layers such that the error can be corrected in a distributed fashion. See P.L.s previous post on the topic for further ...
Advanced redstone circuits encompass mechanisms that require complicated redstone circuitry. They are usually composed of many simpler components, such as logic gates. For simpler mechanisms, see electronic mechanisms, wired traps, and Redstone. Hi! In Minecraft, several in-game systems can...
The essential problem is that software development is entirely unregulated. Anyone can call themselves a software engineer and they legally become one.. What you get is people with accountancy degrees, art history, etc deciding that theyve studied the wrong thing, and they see software development as a possibly lucrative second career option. This is wrong. They have no formal training (everything from binary or logic gates through OO & functional, on to CI/CD and devops) and they simply learn by doing. Theyve no proper understanding of encryption and not the first clue about computer security.. Why on earth would the doctors who specify what a pacemaker must do and what it is to achieve, the engineers who design it, and the manufacturers who build it all require certification and licencing, and yet the guy that knocks the software up that runs the thing could have been working in McDonalds a week earlier.. Software development should be a restricted profession with minimum educational ...
Using the model described above, we considered the situation where two TFs (TF1 and TF2) converge on a single gene promoter that we name GSU (gonadotropin subunit), a generic term used because this is likely to be the case for the αGSU, LHβ and FSHβ gonadotropin subunit genes, as it is for many other ERK and NFAT target genes [8,9,29-33]. We considered the possibility that TF1 is an ERK-activated TF and that TF2 is NFAT (parallel activation network topology) or that TF1 and TF2 are sequentially activated downstream of ERK (sequential activation network topology). We also tested three distinct logic gates for the nature of the action of TF1 and TF2 at the promoter [35]. The first is a CO-OPERATIVE gate that, in biological terms, could reflect the action of one TF to mediate the interaction between the other TF and the cells transcriptional machinery, or alternatively, the requirement of physical interaction between the two TFs to orientate distant promoter sites and bring them to close ...
Small RNAs (sRNAs) can operate as regulatory agents to control protein expression by interaction with the 5 untranslated region of the mRNA. We have developed a physicochemical framework, relying on base pair interaction energies, to design multi-state sRNA devices by solving an optimization problem with an objective function accounting for the stability of the transition and final intermolecular states. Contrary to the analysis of the reaction kinetics of an ensemble of sRNAs, we solve the inverse problem of finding sequences satisfying targeted reactions. We show here that our objective function correlates well with measured riboregulatory activity of a set of mutants. This has enabled the application of the methodology for an extended design of RNA devices with specified behavior, assuming different molecular interaction models based on Watson-Crick interaction. We designed several YES, NOT, AND, and OR logic gates, including the design of combinatorial riboregulators. In sum, our de novo approach
I also found this illuminates why building satisfactory taxonomy systems in databases (like those that power CMSs like WordPress) might be so difficult: Categories in our minds are essentially analogies, with varying degrees of complexity, but which grow and morph in meaning as we gain experience and learn. The edges are inherently fuzzy, and our mental hardware is optimized to make connections between them easily. In computer systems with fixed data structures, categories must have to be fixed, with clear hard yes/no lines, and (unless you have the benefit of complicated machine learning algorithms) connections between them must be intentionally and explicitly crafted by programmers. At first this appeared to me as a fundamental alienating difference between biological and machine minds: Fixed, binary thought, versus flexible, analog (with its delicious shares root with analogy) thought. But, I suppose our own minds are built up of their own (however elegant and complicated) logic gate hardware ...
Accurate characterization of promoter behavior is essential for the rational design of functional synthetic transcription networks such as logic gates and oscillators. However, transcription rates observed from promoters can vary significantly depending on the growth rate of host cells and the experimental and genetic context of measurement. Further, in vivo measurement methods must accommodate variation in translation, protein folding and maturation rates of reporter proteins, as well as metabolic load. The external factors affecting transcription activity may be considered extrinsic, and the goal of characterization should be to obtain quantitative measures of the intrinsic characteristics of promoters. We have developed a promoter characterization method that is based on a mathematical model for cell growth and reporter gene expression and exploits multiple in vivo measurements to compensate for variation due to extrinsic factors. First, we used optical density and fluorescent reporter gene ...
British scientists have successfully demonstrated that the logic gates used for processing information can be built of harmless gut bacteria and DNA.
OncoSenX is a late stage pre-clinical cancer company. OncoSenX targets solid tumors based on transcriptional activity using a unique lipid nanoparticle and plasmid DNA. The next generation in cancer therapies will be more targeted with less side effects. At OncoSenX we believe the battle against cancer should be fought with genetic information. Our treatment delivers a simple program that induces apoptosis in cancerous cells. Our approach is a less invasive, more precise intervention for this complex and devastating disease. Our system is comprised of two main components: An untargeted non-toxic lipid nanoparticle and a highly targeted DNA payload. DNA plasmids encode an inducible death protein under a promoter that is active in the target cell population. We are initially targeting cells that are transcriptionally active for p53. Cells are killed via apoptosis with caspase 9. We can use our DNA payload to effectively implement logic gates (IF / OR / AND). This allows us to precisely target cell ...
The author of this thesis is Malte Schmitz.. Regular linear temporal logic (RLTL) combines the advantages of linear temporal logic (LTL) and ω-regular expressions in a new logic. To use RLTL in practise an efficient translation from RLTL into automata is needed. In the context of this thesis such a translation was implemented as a scala program, which reads in RLTL formulas and translates them into finite alternating two-way parity au- tomata. In this thesis the used translation and its implementation will be described in detail.. ...
The new function FindTransientRepeat identifies the transient and repeated parts of a list. It can be used to investigate cellular automata.. Look at the rule 30 cellular automaton (CA). The Version 11 function RulePlot is a useful tool to find the associated transformation rules. ...
Inferring Genetic Regulatory Interactions with Bayesian Logic-Based Model: 10.4018/978-1-60566-685-3.ch005: This chapter describes the model of genetic regulatory interactions. The model has a Boolean logic semantics representing the cooperative influence of
A process automatically generating topology data for fabricating large scale integrated circuits. Technology data, a logic function description and logic circuit components are generated and input to a data processing system together with geometric dimension data descriptive of the basic elements of the logic circuit components. The geometric dimension data is assembled into a plurality of intermediate level geometric topology patterns under control of the logic function description and the intermediate level geometric topology patterns are assembled into a prime level geometric topology representative of the logic function description. The logic circuit components are merged with the prime level geometric topology to produce a grid array to be fabricated into a large scale integrated circuit.
Pheromone-based internally optimizing resource gathering network simulation using automata inspired by ants. - sampottinger/simple_ant
These lectures describe a few dynamical properties of some statistical mechanics systems such as spin models, automata, neural networks. Two aspects will be mostly discussed: the multivalley...
Technology scaling poses an increasing challenge to the reliability of digital circuits. Hardware redundancy solutions, such as triple modular redundancy (TMR), produce very high area overhead, so partial redundancy is often used to reduce the overheads. Approximate logic circuits provide a general framework for optimized mitigation of errors arising from a broad class of failure mechanisms, including transient, intermittent, and permanent failures. However, generating an optimal redundant logic circuit that is able to mask the faults with the highest probability while minimizing the area overheads is a challenging problem. In this study, we propose and compare two new approaches to generate approximate logic circuits to be used in a TMR schema. The probabilistic approach approximates a circuit in a greedy manner based on a probabilistic estimation of the error. The evolutionary approach can provide radically different solutions that are hard to reach by other methods. By combining these two ...
but the normalized value of SMART attribute 177, wear leveling count, is the percentage of rated life left in the NAND cells. Edit: I see now that the author of one of the programs has said that the drive life is now based on 0xB1, wear leveling count, instead of some others. 0xB1 in hex is 177 in decimal, so it is the attribute I was referring to above. I would agree that this is a more fitting estimate of the drives remaining rated life. Id keep using it at 59% if it were mine.. SSDs have a rated number of write cycles they can endure, but reaching that point doesnt mean the NAND cells are actually dead. A Samsung 840 Pro was the torture test champion in TechReports torture test, where they wrote to the drives continuously until they failed. The drive made it to about 2 petabytes before it failed (2,000 TB)! It was rated for far less life than that.. If the drive has had uncorrectable errors (attribute 187), that means there was a hard failure in one or more NAND cells that could not be ...