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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Multifunctional alginate-based hydrogel with reversible crosslinking for controlled therapeutics delivery(Elsevier, 2020) Ekinci, Duygu; N/A; Department of Chemical and Biological Engineering; Batool, Syeda Rubab; Nazeer, Muhammad Anwaar; Kızılel, Seda; Şahin, Afsun; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; N/A; 28376; 171267Glycan-based alginate hydrogels have great potential in creating new vehicles with responsive behavior and tunable properties for biomedicine. However, precise control and tunability in properties present major barrier for clinical translation of these materials. Here, we report the synthesis of pH responsive anthracene modified glycan-based hydrogels for selective release of therapeutic molecules. Hydrogels were crosslinked through simultaneous photopolymerization of vinyl groups and photodimerization of anthracene. Incorporation of anthracene into these gels leads to reversible control on crosslinking and transition between gel/sol states through dimerization/dedimerization of anthracene groups. Chemotherapeutic drug doxorubicin-loaded hydrogels were then tested in a cancer mimetic microenvironment where 85% of the drug was released from anthracene-conjugated hydrogels at pH 2 for 6 days. Control on gelation with anthracene incorporation was observed through alterations in modulus, where storage modulus was increased two-fold with anthracene conjugation during photopolymerization and photodimerization. Furthermore, cell survival analysis revealed that anthracene conjugation could selectively compromise cancer cell viability without inducing significant toxicity on healthy fibroblasts. This study combines light-induced control of crosslink density due to anthracene and pH-triggered therapeutics delivery with alginate. The approach would be applicable for systems where multiple control is required with high precision.Publication Open Access Compressed training based massive MIMO(Institute of Electrical and Electronics Engineers (IEEE), 2019) Yılmaz, Baki Berkay; Department of Electrical and Electronics Engineering; Erdoğan, Alper Tunga; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 41624Massive multiple-input-multiple-output (MIMO) scheme promises high spectral efficiency through the employment of large scale antenna arrays in base stations. In time division duplexed implementations, co-channel mobile terminals transmit training information such that base stations can estimate and exploit channel state information to spatially multiplex these users. In the conventional approach, the optimal choice for training length was shown to be equal to the number of users, K. In this paper, we propose a new semiblind framework, named as "MIMO Compressed Training," which utilizes information symbols in addition to training symbols for adaptive spatial multiplexing. We show that this framework enables us to reduce (compress) the training length down to a value close to log(2) (K), i.e., the logarithm of the number of users, without any sparsity assumptions on the channel matrix. We also derive a prescription for the required packet length for proper training. The framework is built upon some convex optimization settings that enable efficient and reliable algorithm implementations. The numerical experiments demonstrate the strong potential of the proposed approach in terms of increasing the number of users per cell and improving the link quality.Publication Open Access The noisy channel mode for unsupervised word sense disambiguation(Massachusetts Institute of Technology (MIT) Press, 2010) Department of Computer Engineering; Yüret, Deniz; Yatbaz, Mehmet Ali; Faculty Member; PhD Student; Department of Computer Engineering; College of Engineering; 179996; 192506We introduce a generative probabilistic model, the noisy channel model, for unsupervised word sense disambiguation. In our model, each context C is modeled as a distinct channel through which the speaker intends to transmit a particular meaning S using a possibly ambiguous word W. To reconstruct the intended meaning the hearer uses the distribution of possible meanings in the given context P(S|C) and possible words that can express each meaning P(W|S). We assume P(W|S) is independent of the context and estimate it using WordNet sense frequencies. The main problem of unsupervised WSD is estimating context-dependent P(S|C) without access to any sense-tagged text. We show one way to solve this problem using a statistical language model based on large amounts of untagged text. Our model uses coarse-grained semantic classes for S internally and we explore the effect of using different levels of granularity on WSD performance. The system outputs fine-grained senses for evaluation, and its performance on noun disambiguation is better than most previously reported unsupervised systems and close to the best supervised systems.Publication Open Access BCS theory of time-reversal-symmetric Hofstadter-Hubbard model(American Physical Society (APS), 2017) Umucalılar, Rıfat Onur; Department of Physics; Işkın, Menderes; Faculty Member; Department of Physics; College of Sciences; 29659The competition between the length scales associated with the periodicity of a lattice potential and the cyclotron radius of a uniform magnetic field is known to have dramatic effects on the single-particle properties of a quantum particle, e.g., the fractal spectrum is known as the Hofstadter butterfly. Having this intricate competition in mind, we consider a two-component Fermi gas on a square optical lattice with opposite synthetic magnetic fields for the components, and study its effects on the many-body BCS-pairing phenomenon. By a careful addressing of the distinct superfluid transitions from the semimetal, quantum spin-Hall insulator, or normal phases, we explore the low-temperature phase diagrams of the model, displaying lobe structures that are reminiscent of the well-known Mott-insulator transitions of the Bose-Hubbard model.Publication Open Access A hybrid architecture for federated and centralized learning(Institute of Electrical and Electronics Engineers (IEEE), 2022) Elbir, Ahmet M.; Papazafeiropoulos, Anastasios K.; Kourtessis, Pandelis; Chatzinotas, Symeon; Department of Electrical and Electronics Engineering; Ergen, Sinem Çöleri; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 7211Many of the machine learning tasks rely on centralized learning (CL), which requires the transmission of local datasets from the clients to a parameter server (PS) entailing huge communication overhead. To overcome this, federated learning (FL) has been suggested as a promising tool, wherein the clients send only the model updates to the PS instead of the whole dataset. However, FL demands powerful computational resources from the clients. In practice, not all the clients have sufficient computational resources to participate in training. To address this common scenario, we propose a more efficient approach called hybrid federated and centralized learning (HFCL), wherein only the clients with sufficient resources employ FL, while the remaining ones send their datasets to the PS, which computes the model on behalf of them. Then, the model parameters are aggregated at the PS. To improve the efficiency of dataset transmission, we propose two different techniques: i) increased computation-per-client and ii) sequential data transmission. Notably, the HFCL frameworks outperform FL with up to 20% improvement in the learning accuracy when only half of the clients perform FL while having 50% less communication overhead than CL since all the clients collaborate on the learning process with their datasets.Publication Open Access Macroscopic loop formation in circular DNA denaturation(American Physical Society (APS), 2012) Bar, Amir; Mukamel, David; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T-c and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T-c, with a cusp at the critical point.Publication Open Access A divergence-free parametrization for dynamical dark energy(Institute of Physics (IOP) Publishing, 2015) Vazquez, J. Alberto; Department of Physics; Dereli, Tekin; Akarsu, Özgür; Faculty Member; Department of Physics; College of Sciences; 201358; N/AWe introduce a new parametrization for the dark energy, led by the same idea to the linear expansion of the equation of state in scale factor a and in redshift z, which diverges neither in the past nor future and contains the same number of degrees of freedom with the former two. We present constraints of the cosmological parameters using the most updated baryon acoustic oscillation (BAO) measurements along with cosmic microwave background (CMB) data and a recent reanalysis of Type Ia supernova (SN) data. This new parametrization allowed us to carry out successive observational analyses by decreasing its degrees of freedom systematically until ending up with a dynamical dark energy model that has the same number of parameters with ACDM. We found that the dark energy source with a dynamical equation of state parameter equal 2/3 at the early universe and -1 today fits the data slightly better than A.Publication Open Access Two-band superfluidity and intrinsic Josephson effect in alkaline-earth-metal Fermi gases across an orbital Feshbach resonance(American Physical Society (APS), 2016) Department of Physics; Işkın, Menderes; Faculty Member; Department of Physics; College of Sciences; 29659We first show that the many-body Hamiltonian governing the physical properties of an alkaline-earth Yb-173 Fermi gas across the recently realized orbital Feshbach resonance is exactly analogous to that of two-band s-wave superconductors with contact interactions; i.e., even though the free-particle bands have a tunable energy offset in between and are coupled by a Josephson-type attractive interband pair scattering, the intraband interactions have exactly the same strength. We then introduce two intraband order parameters within the BCS mean-field approximation and investigate the competition between their in-phase and out-of-phase (i.e., the so-called pi-phase) solutions in the entire BCS-BEC evolution at zero temperature.Publication Open Access In situ formation of copper phosphate on hydroxyapatite for wastewater treatment(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Rahmani, Fatemeh; Ghadi, Arezoo; Khaksar, Samad; Doustkhah, Esmail; PhD Student; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM)Here, we control the surface activity of hydroxyapatite (HAp) in wastewater treatment which undergoes peroxodisulfate (PDS) activation. Loading the catalytically active Cu species on HAp forms a copper phosphate in the outer layer of HAp. This modification turns a low active HAp into a high catalytically active catalyst in the dye degradation process. The optimal operational conditions were established to be [Cu-THAp](0) = 1 g/L, [RhB](0) = 20 mg/L, [PDS](0) = 7.5 mmol/L, and pH = 3. The experiments indicate that the simultaneous presence of Cu-THAp and PDS synergistically affect the degradation process. Additionally, chemical and structural characterizations proved the stability and effectiveness of Cu-THAp. Therefore, this work introduces a simple approach to water purification through green and sustainable HAp-based materials.Publication Open Access Discrete-time quantum walk with nitrogen-vacancy centers in diamond coupled to a superconducting flux qubit(American Physical Society (APS), 2013) Xue, Peng; Shikano, Yutaka; Sanders, Barry C.; Department of Physics; Hardal, Ali Ümit Cemal; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 1674We propose a quantum-electrodynamics scheme for implementing the discrete-time, coined quantum walk with the walker corresponding to the phase degree of freedom for a quasimagnon field realized in an ensemble of nitrogen-vacancy centers in diamond. The coin is realized as a superconducting flux qubit. Our scheme improves on an existing proposal for implementing quantum walks in cavity quantum electrodynamics by removing the cumbersome requirement of varying drive-pulse durations according to mean quasiparticle number. Our improvement is relevant to all indirect-coin-flip cavity quantum-electrodynamics realizations of quantum walks. Our numerical analysis shows that this scheme can realize a discrete quantum walk under realistic conditions.