Browsing by Subject "Logic gates"

Now showing 1 - 10 of 10

Open Access
Cellular biosensors with engineered genetic circuits
(American Chemical Society, 2018) Saltepe, Behide; Kehribar, Ebru Şahin; Yirmibeşoǧlu, Side Selin Su; Şeker, Urartu Özgür Şafak
An increasing interest in building novel biological devices with designed cellular functionalities has triggered the search of innovative tools for biocomputation. Utilizing the tools of synthetic biology, numerous genetic circuits have been implemented such as engineered logic operation in analog and digital circuits. Whole cell biosensors are widely used biological devices that employ several biocomputation tools to program cells for desired functions. Up to the present date, a wide range of whole-cell biosensors have been designed and implemented for disease theranostics, biomedical applications, and environmental monitoring. In this review, we investigated the recent developments in biocomputation tools such as analog, digital, and mix circuits, logic gates, switches, and state machines. Additionally, we stated the novel applications of biological devices with computing functionalities for diagnosis and therapy of various diseases such as infections, cancer, or metabolic diseases, as well as the detection of environmental pollutants such as heavy metals or organic toxic compounds. Current whole-cell biosensors are innovative alternatives to classical biosensors; however, there is still a need to advance decision making capabilities by developing novel biocomputing devices.
Open Access
Design and fabrication of CSWAP gate based on nano-electromechanical systems
(Springer, Cham, 2016) Yüksel, Mert; Erbil, Selçuk Oğuz; Arı, Atakan B.; Hanay, M. Selim
In order to reduce undesired heat dissipation, reversible logic offers a promising solution where the erasure of information can be avoided to overcome the Landauer limit. Among the reversible logic gates, Fredkin (CSWAP) gate can be used to compute any Boolean function in a reversible manner. To realize reversible computation gates, Nano-electromechanical Systems (NEMS) offer a viable platform, since NEMS can be produced en masse using microfabrication technology and controlled electronically at high-speeds. In this work-in-progress paper, design and fabrication of a NEMS-based implementation of a CSWAP gate is presented. In the design, the binary information is stored by the buckling direction of nanomechanical beams and CSWAP operation is accomplished through a mechanism which can selectively allow/block the forces from input stages to the output stages. The gate design is realized by fabricating NEMS devices on a Silicon-on-Insulator substrate. © Springer International Publishing Switzerland 2016.
Open Access
Fabrication of 100 nm pMOSFETS With Hybrid AFW / STM lithography
(IEEE, 1997-06) Soh, H. T.; Wilder, K.; Atalar, Abdullah; Quate, C. F.
Scanning probe lithography (SPL) is an emerging area of research in which the scanning tunneling microscope (STM) or atomic force microscope (AFM) is used to pattern nanometer-scale features. Four factors will dictate the viability of SPL as a patterning technology for the semiconductor industry: 1) resolution, 2) alignment accuracy, 3) reliability, and 4) throughput. We present a new SPL technique-a hybrid between the AFM and STMto address these issues. We demonstrate its capabilities and its compatibility with semiconductor processing by fabricating a pMOSFET with an effective channel length (L,ff) of 100 nm and report the device characteristics.
Open Access
From virtual to physical: Integration of chemical logic gates
(2011) Guliyev, R.; Ozturk, S.; Kostereli, Z.; Akkaya, E. U.
Integration by parts: Advanced information processing at the molecular level requires integrated logic gates, which has to date been possible only virtually. Now, two independently working AND molecular logic gates are brought together by "click" chemistry to form integrated logic gates which respond exactly as predicted from such an integration scheme (see picture, EET=excitation energy transfer).
Open Access
Making the next generation of therapeutics: mRNA meets synthetic biology
(American Chemical Society, 2023-09-15) Hınçer, Ahmet; Ahan, Recep Erdem; Aras, Ebru; Şeker, Urartu Özgür Şafak
The development of mRNA-based therapeutics centers around the natural functioning of mRNA molecules to provide the genetic information required for protein translation. To improve the efficacy of these therapeutics and minimize side effects, researchers can focus on the features of mRNA itself or the properties of the delivery agent to achieve the desired response. The tools considered for mRNA manipulation can be improved in terms of targetability, tunability, and translatability to medicine. While ongoing studies are dedicated to improving conventional approaches, innovative approaches can also be considered to unleash the full potential of mRNA-based therapeutics. Here, we discuss the opportunities that emerged from introducing synthetic biology to mRNA therapeutics. It includes a discussion of modular self-assembled mRNA nanoparticles, logic gates on a single mRNA molecule, and other possibilities.
Open Access
Modular logic gates: cascading independent logic gates via metal ion signals
(Royal Society of Chemistry, 2014) Ecik, E. T.; Atilgan, A.; Guliyev, R.; Uyar, T. B.; Gumus, A.; Akkaya, E. U.
Systematic cascading of molecular logic gates is an important issue to be addressed for advancing research in this field. We have demonstrated that photochemically triggered metal ion signals can be utilized towards that goal. Thus, independent logic gates were shown to work together while keeping their identity in more complex logic designs. Communication through the intermediacy of ion signals is clearly inspired from biological processes modulated by such signals, and implemented here with ion responsive molecules.
Open Access
Photosensitizers for photodynamic action and synthesis of modules for a molecular demultiplexer
(2014) Durgut, Tuğçe
Photodynamic therapy (PDT) is a new therapeutic methodology that uses light as a distinguishing tool for the treatment of diseased cells. In recent years PDT has become one of the most preferred therapies because it is innocent for the healthy cells and tissues while diagnosing and curing the malignant cells and tissues. Bodipy is one of the most favorite fluorophore in this field due to its excellent chemical and physical properties. Logic gates are widely used in modern technology as the fundamentals of logical operations for the development of science. The progressive advances leads to the emergence and growth of molecular logic gates. Molecular logic gates can be used for the diagnosis and therapies of disease which are originated from the heredity. In addition, they occupy an important place in the theoretical and practical use of photodynamic therapy. In the first part of my thesis, we designed and synthesized a calix[4]arene-Bodipy conjugate molecule as a carrier for the photodynamic therapy agents. It is an amphiphilic delivery molecule that is utilized for the curing of tumor tissues. In the second part, we synthesized modules for molecular logic gate function, DEMUX (demultiplexer), serving as a theranostic device which selects either singlet oxygen channel or energy transfer between the modules depending on the inputs. The superiority of the project is that it serves a realistic pathway for the PDT.
Open Access
Physical integration of chemical logic gates
(2012) Öztürk, Şeyma
Recent research in molecular logic gates produced molecular equivalence of highly complex digital designs. Advanced data processing at the molecular level requires a considerable degree of integration (concatenation) between molecular logic gates. So far, almost all the integration reported in the literature has been “virtual”, meaning that the outputs at various channels are determined first and then an integrated set of logic gates is proposed to be operating on inputs to produce those outputs. Nevertheless, there is no doubt that at some point there has to be methods to physically connect one molecular logic gate to the other one, for a rational design and implementation. In this study, we synthesized a few derivatives of the well known fluorophore “Bodipy” and then proposed two methodologies to concatenate separately existing and functioning Bodipy-based chemical logic gates. In one instance, we coupled a photochromicity-based AND gate to an ion-responsive Bodipy-based AND gate, making use of the modulation of inner filter effect. In the other example, we coupled two ion-responsive Bodipy-based AND gates through the increased efficiency of energy transfer and “click” chemistry. We are certain that these methodologies are highly promising and our studies are in progress to demonstrate more complex examples of physical integration.
Open Access
Selective manipulation of ICT and PET processes in styryl-bodipy derivatives: Applications in molecular logic and fluorescence sensing of metal ions
(2010) Bozdemir, O. A.; Guliyev, R.; Buyukcakir, O.; Selcuk, S.; Kolemen, S.; Gulseren, G.; Nalbantoglu, T.; Boyaci, H.; Akkaya, E. U.
Remarkably versatile chemistry of Bodipy dyes allows the design and straightforward synthesis of multivalent-multitopic derivatives, which, with judicious selection of metal ion-ligand pairs based on known affinities, affords control and manipulation of photoinduced electron transfer and internal charge transfer processes as desired. We have demonstrated that metal ions acting as modulators (or inputs, in digital design parlance) can generate absorbance changes in accordance with the operation of a half-adder. In addition, an AND logic gate in the emission mode was delivered using a different binucleating arrangement of ligands. A molecular equivalent of a three-input AND logic gate was also obtained exploiting differential binding affinities of metal ions for different ligands. The results suggest that different metal ions can be used as nonannihilating inputs, selectively targeting various ligands incorporated within a single fluorophore, and with careful design, diverse photophysical processes can be selectively modulated, resulting in a range of signals, useful in molecular logic design, and offering an enticing potential for multianalyte chemosensors.
Open Access
Two-nanometer laser synthesized Si-nanoparticles for low power memory applications
(Springer International Publishing, 2016) El-Atab, N.; Okyay, Ali Kemal; Nayfeh, A.
Current flash memory devices are expected to face two major challenges in the near future: density and voltage scaling. The density of the memory is related to the gate length scaling which is constrained by the gate stack, namely, the tunnel oxide thickness. In fact, the gate length is required to be commensurate with the gate stack in order to maintain a good gate control and to avoid short channel effects. However, in conventional flash memories, the tunnel oxide thickness has a lower limit of 6-7 nm (depending on NOR or NAND structure) in order to avoid back-tunneling and thus leakage of charges which destroys the necessary retention characteristic of the memory (>10 years). The second problem which needs to be solved is the high program and erase operating voltages. Once again, the limitation to operating voltage scaling is the inability to reduce gate stack thickness. Therefore, it is imperative to find novel structures and materials to be incorporated in the memory cells which would allow tunnel oxide and voltage scaling. In this study, MOSFET- and MOSCAP-based memory devices are investigated along with the use of 2-nm silicon nanoparticles (Si-NPs) for charge storage. Atomic layer deposition is used to deposit the active layer of the memory and the spin coating is performed to deliver the Si-nanoparticles across the sample.