TBAE

Publications

2026

Differential conservation analysis identifies residues defining constitutive internalization in beta-adrenergic receptors

Authors: Walker, A.R., Selçuk, B., Erol, I., Durdağı, S., Hanyaloglu, A.C. and Adebali, O.
Yayınlandığı Adres: iScience, 29(3), 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1016/j.isci.2026.115033

Conserved 3D genome reorganization during DNA repair

Authors: Kaya, Veysel Oğulcan, Ogün Adebali, Hanspeter Naegeli, and Michelle N. Yancoskie.
Yayınlandığı Adres: Life Science Alliance 9, no. 2 (2026): e202503498.
Publication Type: Derleme Makale (Review)
Bağlantı: https://doi.org/10.26508/lsa.202503498

MPXV RNA-seq data provide evidence for protection of viral transcripts from APOBEC3 editing

Authors: Lyskova AO, Abasov RK, Pavlova A, Matveev EV, Madorskaya AV, Kazanov FM, Garshina DV, Smolnikova AE, Ponomarev GV, Sharova EI, Ivankov DN, Adebali O, Gelfand MS, Kazanov MD.
Yayınlandığı Adres: MPXV RNA-seq data provide evidence for protection of viral transcripts from APOBEC3 editing. Journal of Virology, 100(2), pp.e02082-25.
Publication Type: Makale
Bağlantı: https://doi.org/10.1128/jvi.02082-25

Digitization of hand-drawn flow charts with deep learning

Authors: Sayar, Ahmet, and Ahmet Fatih Mustacoglu
Yayınlandığı Adres: Signal, Image and Video Processing 20, no. 3 (2026): 134
Publication Type: Makale
Bağlantı: https://doi.org/10.1007/s11760-026-05212-w

Mechanisms of proton and α-particle emission in the Cu reaction at 22 MeV

Authors: G. Ussabayeva, T. Zholdybayev, Z. Mukan, B. Sadykov, A. Temirzhanov, Y. Küçük, …, İsmail Boztosun, et al.
Yayınlandığı Adres: Interactions, 247(1), 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1007/s10751-026-02423-y

New measurement and analysis for the 15N + 11B elastic scattering system

Authors: N. Amangeldi, İsmail Boztosun, D. Soldatkhan, B. Mauyey, K. Makhanov, R. Akhat, A. Anuar, G. Yergaliuly
Yayınlandığı Adres: Turkish Journal of Physics, 50(1), 69–78, 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.55730/1300-0101.2802

First analytic treatment of keV electronic screening via finite-length nanomeshes: Implications for D + D fusion studies

Authors: Ali İhsan Kılıç, E. Kustan, H. Çiftci, Orkun Hasekioğlu
Yayınlandığı Adres: Modern Physics Letters A, 41(17), 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1142/S0217732326500641

Topological engine monitor: persistent homology-based fault detection in finite-time quantum engines

Authors: Kerem Maden, Miraç, Asghar Ullah, Baris Coskunuzer, and Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Quantum Science and Technology 11, no. 4 (2026): 045012.
Publication Type: Makale
Bağlantı: https://doi.org/10.1088/2058-9565/ae98eb

Distribution of Bell State Entanglement in Qubit Networks via Collision Models

Authors: Yunt, Elif, Mert Doğan, Öner Faruk Ödemiş, and Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Physics Letters A (2026): 132139.
Publication Type: Makale
Bağlantı: https://doi.org/10.1016/j.physleta.2026.132139

Dissipation-protected energy storage in interacting multilevel quantum batteries

Authors: Yiğit Perçin, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Physical Review A, 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/ct48-85bk

Non-associativity induced modifications of open-system quantum dynamics: General master equation and a two-qubit Ising case study

Authors: Ekin Sıla Yörük, Özgür E. Müstecaplıoğlu, Zafer Gedik
Yayınlandığı Adres: Journal of Physics A: Mathematical and Theoretical (2026).
Publication Type: Makale
Bağlantı: https://doi.org/10.1088/1751-8121/aea8aa

Collective purification of interacting quantum networks beyond symmetry constraints

Authors: Sur, Saikat, Pritam Chattopadhyay, Arnab Chakrabarti, Nikolaos E. Palaiodimopoulos, Özgür E. Müstecaplıoğlu, Amit Finkler, Durga Bhaktavatsala Rao Dasari, and Gershon Kurizki.
Yayınlandığı Adres: npj Quantum Information, 2026
Publication Type: Makale
Bağlantı: https://www.nature.com/articles/s41534-026-01228-9

Harnessing Floquet dynamics for selective metrology in few-qubit systems

Authors: Asghar Ullah, Hasan Mermer, Melih Özkurt, Igor Lesanovsky, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Physical Review B, 113, 075123, 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/l9ms-79hn

Configuration-dependent precision in magnetometry and thermometry using multiqubit quantum sensors

Authors: Asghar Ullah, Özgür E. Müstecaplıoğlu, Matteo G. A. Paris
Yayınlandığı Adres: Physical Review A, 113(1), 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/zn5v-rcgd

PNcsp+: A Periodic Number-Based Crystal Structure Prediction Method Enhanced by Machine Learning

Authors: Cem Oran, Riccarda Caputo, Pierre Villars, Adem Tekin
Yayınlandığı Adres: Journal of Chemical Theory and Computation, 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1021/acs.jctc.6c00044

Spin-glass phases and multichaos in the Ashkin–Teller model

Authors: Alican Saray, A. Nihat Berker
Yayınlandığı Adres: Chaos, Solitons & Fractals, 202, 117458, 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1016/j.chaos.2025.117458

Blume–Capel model in d= 1 with long-range interactions: Giant reentrance in the finite-temperature tricritical phase diagrams

Authors: E. Can Artun, A. Nihat Berker
Yayınlandığı Adres: Physica A: Statistical Mechanics and its Applications, 688, 131387, 2026
Publication Type: Makale
Bağlantı: https://doi.org/10.1016/j.physa.2026.131387

2025

Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins

Authors: Hakan Alıcı, Vladimir N. Uversky, Orkid Coşkuner-Weber, Orkun Hasekioğlu
Yayınlandığı Adres: Advances in Protein Molecular and Structural Biology Methods (Elsevier/Academic Press), Bölüm 33, s. 551–563, 2022
Publication Type: Kitap Bölümü
Bağlantı: https://doi.org/10.1016/B978-0-323-90264-9.00033-7

A Wireless Enabled IOT Nondestructive Fatigue Damage Sensor for Estimation of Remaining Useful Service (RUL) of Structures Through Artificial Intelligence-Machine Learning Algorithms

Authors: Kaplan, Halit, ORKUN HASEKIOGLU, TARIK OZKUL, HASAN HUSEYIN CAMUZ, and Mohammad Ikhsan Zakaria
Yayınlandığı Adres: Structural Health Monitoring 2025 (IWSHM Proceedings), DEStech Publications, 2025
Publication Type: Konferans Bildirisi
Bağlantı: https://dpi-proceedings.com/index.php/shm2025/article/view/37551

Probing key resonances in the 40Ca(p,γ)41Sc reaction through ANC-constrained DWBA analysis and astrophysical implications

Authors: Kılıç, A. İ., B. Özcan, and O. Hasekioğlu
Yayınlandığı Adres: И ПРИКЛАДНЫЕ ПРОБЛЕМЫ СОВРЕМЕННОЙ ФИЗИКИ FUNDAMENTAL AND APPLIED PROBLEMS OF MODERN PHYSICS, p.80.The Astrophysical Journal, 2025
Publication Type: Makale

A Wireless Enabled Nondestructive Damage Tolerant Inspection Fatigue Sensor for Structural Health Monitoring and Prediction of Remaining Useful Fatigue Life of Aircraft Structures

Authors: Kaplan, Halit, Hasan Hüseyin Camuz, Tarık Özkul, and Orkun Hasekioglu
Yayınlandığı Adres: Structural Health Monitoring 2025 (IWSHM Proceedings), DEStech Publications, 2025
Publication Type: Konferans Bildirisi
Bağlantı: https://dpi-proceedings.com/index.php/shm2025/article/view/37374

Transcription factors, nucleotide excision repair, and cancer: A review of molecular interplay

Authors: Perihan Yağmur Güneri Sözeri, Ogün Adebali
Yayınlandığı Adres: International Journal of Biochemistry and Cell Biology, 179, 2025
Publication Type: Derleme Makale (Review)
Bağlantı: https://doi.org/10.1016/j.biocel.2024.106724

UV-induced reorganization of 3D genome mediates DNA damage response

Authors: Veysel Oğulcan Kaya, Ogün Adebali
Yayınlandığı Adres: Nature Communications, 16, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1038/s41467-024-55724-7

Assessing predictions on fitness effects of missense variants in HMBS in CAGI6

Authors: Jing Zhang, Lisa Kinch, Panagiotis Katsonis, …, Nurdan Kuru, Onur Dereli, Ogün Adebali, …, Qian Cong, Nick V. Grishin
Yayınlandığı Adres: Human Genetics, 144(2–3), 173–189, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1007/s00439-024-02680-3

PHACE: phylogeny-aware detection of molecular coevolution

Authors: Nurdan Kuru, Ogün Adebali
Yayınlandığı Adres: Molecular Biology and Evolution, 42(7), msaf150, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1093/molbev/msaf150

Chromatin context shapes DNA damage formation and nucleotide excision repair dynamics in Caenorhabditis elegans

Authors: Cansu Kose, Cem Azgari, Laura A. Lindsey-Boltz, Ogün Adebali, Aziz Sancar
Yayınlandığı Adres: Nucleic Acids Research, 53(20), 2025
Publication Type: Makale
Bağlantı: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12585911/

Genome-wide strand-specific UV mutagenesis in Escherichia coli is directed by the Mfd translocase

Authors: Ogün Adebali, Piotr A. Mieczkowski, Aziz Sancar, Christopher P. Selby
Yayınlandığı Adres: Proceedings of the National Academy of Sciences (PNAS), 122(46), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1073/pnas.2523368122

Authors: A. Santago, A. Bagchi, D. Bieler, I. Cernak, A. Erdik, T. Erlich, …, R. Gupta, et al.
Yayınlandığı Adres: ASME Journal of Engineering and Science in Medical Diagnostics and Therapy, 8(4), 041110, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1115/1.4068927

Electromagnetic Interference Shielding Effectiveness Performance of Various Aluminum Foam/Cellular Structures at C-Band: A Numerical and Experimental Investigation

Authors: Kocakuşak, A. Genç, H. Doğan, Levent Turhan, S. Helhel
Yayınlandığı Adres: Advanced Engineering Materials, 27(18), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1002/adem.202500933

Air side thermal and hydraulic performance assessment of skived, louver, offset honeycomb, and metal foam finned mini-channel heat exchangers

Authors: Doğan, M. Öztürk, Levent Turhan
Yayınlandığı Adres: Engineering Science and Technology, an International Journal, 72, 102242, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1016/j.jestch.2025.102242

Prediction of Radio-quiet Gamma-Ray Pulsar Distances Using the Fundamental Plane Relation

Authors: Ekrem Oğuzhan Angüner
Yayınlandığı Adres: The Astrophysical Journal, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.3847/1538-4357/adc914

Galactic transient sources with the Cherenkov Telescope Array Observatory

Authors: K. Abe, S. Abe, E. O. Angüner, et al. (CTAO Consortium)
Yayınlandığı Adres: Monthly Notices of the Royal Astronomical Society, 540(1), 205–238, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1093/mnras/staf655

Statistical analysis and radiological risk assessment of 226Ra, 232Th, 40K, and 137Cs in the sediments of Boğaçay, Antalya

Authors: Özaydın Özkara, İsmail Boztosun, C. Eke
Yayınlandığı Adres: Journal of Radioanalytical and Nuclear Chemistry, 334(10), 7277–7293, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1007/s10967-025-10425-3

One-nucleon transfer reactions in the 20Ne + 76Ge system at Elab=15.3MeV/u

Authors: Linares, E. N. Cardozo, V. A. B. Zagatto, F. Cappuzzello, D. Carbone, M. Cavallaro, İsmail Boztosun, et al. (NUMEN Collaboration)
Yayınlandığı Adres: Physical Review C, 112(3), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/44xl-dkwq

Enhanced alpha decay half-life determination in super-heavy nuclei using a new potential

Authors: Aydın Yıldırım, İsmail Boztosun, Yasemin Küçük, Diana Gusseinova, Dilshod Alimov, Mardan Bakirov
Yayınlandığı Adres: Modern Physics Letters A, 40(26), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1142/S0217732325501007

Status of the NUMEN Construction

Authors: Pierroutsakou, L. Acosta, N. Added, C. Agodi, …, İsmail Boztosun, et al. (NUMEN Collaboration)
Yayınlandığı Adres: EPJ Web of Conferences, 333, 03006, 2025 (46th Symposium on Nuclear Physics, Cocoyoc, Meksika)
Publication Type: Konferans Bildirisi
Bağlantı: https://doi.org/10.1051/epjconf/202533303006

Optical model analyses for the elastic scattering of B, Be and Li with C

Authors: D Gusseinova, I Boztosun, Y Kucuk, E Aciksoz, D Alimov.
Yayınlandığı Adres: Advances in Nuclear Science and Applications 1 (1), 17-24
Publication Type: Makale
Bağlantı: https://doi.org/10.63907/ansa.v1i1.24

New measurements of (p,xp) and (p,xα) reactions on 27Al at 7.0, 22.0 and 30.0 MeV

Authors: Gusseinova, G. Ussabayeva, T. K. Zholdybayev, İsmail Boztosun, Y. Küçük, A. J. Koning, et al.
Yayınlandığı Adres: The European Physical Journal A, 61(6), 133, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1140/epja/s10050-025-01603-8

Multi-port coherence element for quantum information device

Authors: İnanç Adagideli
Yayınlandığı Adres: United States Patent Office, U.S. Patent Application No. 19/113,407. 2025
Publication Type: Patent

Signature of current-induced nuclear spin polarization in (Bi1−xSbx)2Te3

Authors: Sofie Kölling, İnanç Adagideli, Alexander Brinkman
Yayınlandığı Adres: Physical Review B, 112(4), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/tg8q-q456

Non-Ohmic behavior in (Bi1−xSbx)2Te3 by Joule heating

Authors: Sofie Kölling, Daan H. Wielens, İnanç Adagideli, Alexander Brinkman
Yayınlandığı Adres: Physical Review B, 112(4), 045421, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/7wzz-phfk

Current-induced spin polarization on the surface of a topological insulator

Authors: Sofie Kölling, A. Mert Bozkurt, Stijn Roelant de Wit, Feike van Veen, İnanç Adagideli, Alexander Brinkman
Yayınlandığı Adres: 31st Conference of the EPS Condensed Matter Division (CMD-31), Braga, Portekiz, 2025
Publication Type: Konferans Sunumu (Davetli Konuşma)
Bağlantı: https://research.utwente.nl/en/activities/current-induced-spin-polarization-on-the-surface-of-a-topological/

Entropy driven inductive response of topological insulators

Authors: Mert Bozkurt, Sofie Kölling, Alexander Brinkman, İnanç Adagideli
Yayınlandığı Adres: SciPost Physics Core, 8(1), 023, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.21468/SciPostPhysCore.8.1.023

Dataset to 'Crossed Andreev reflection in topological insulator nanowire T junctions'

Authors: Jacob Fuchs, Cosimo Gorini, İnanç Adagideli, Klaus Richter
Yayınlandığı Adres: Universität Regensburg Yayın Sunucusu (epub), 2025
Publication Type: Veri Seti / Doküman
Bağlantı: https://doi.org/10.5283/epub.76898

Implications of Mexican hat-like band structure on thermoelectric properties

Authors: Muhammad Hilal, Oğuz Gülseren
Yayınlandığı Adres: Turkish Journal of Physics 49, no. 4 (2025): 159-168.
Publication Type: Makale
Bağlantı: https://doi.org/10.55730/1300-0101.2782

Analysis of astrophysical 26Mg(n,γ)27Mg reaction via the asymptotic normalization coefficient method

Authors: Ali İhsan Kılıç
Yayınlandığı Adres: Modern Physics Letters A, 39(02), 2350188, 2024
Publication Type: Makale
Bağlantı: https://doi.org/10.1142/S0217732323501882

Direct measurement of the 19F(p,α)16O reaction using the LHASA detector array

Authors: Petruse, G. L. Guardo, D. Lattuada, M. La Cognata, D. L. Balabanski, E. Açıksöz, L. Acosta, …, A. İ. Kılıç, et al.
Yayınlandığı Adres: The European Physical Journal A, 61(1), 4, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1140/epja/s10050-024-01462-9

Analysis of Astrophysical 30Si(n, γ)31Si Reaction via the Asymptotic Normalization Coefficient Method

Authors: Ali İhsan Kılıç
Yayınlandığı Adres: JETP Letters, 122(2), 82–88, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1134/S0021364025605883

Optimal strategies for transient and equilibrium quantum thermometry using Gaussian and non-Gaussian probes

Authors: Asghar Ullah, M. Tahir Naseem, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Physical Review A, 112, 062601, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/62ks-19fs

Optimizing quantum sensing networks via genetic algorithms and deep learning

Authors: Asghar Ullah, Özgür E. Müstecaplıoğlu, Matteo G. A. Paris
Yayınlandığı Adres: Quantum Science and Technology, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1088/2058-9565/ae2d8e

Classical simulation of an all-optical Toffoli gate using soliton scattering through asymmetric potential wells

Authors: Melih Özkurt, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Physical Review A, 112(4), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/y6sc-bzk5

Steady-state entanglement generation via Casimir-Polder interactions
  • Authors: Mohsen Izadyari, Onur Pusuluk, Kanu Sinha, Özgür E. Müstecaplıoğlu
  • Yayınlandığı Adres: Scientific Reports, 15, 37105, 2025
  • Publication Type: Makale
  • Bağlantı: https://doi.org/10.1038/s41598-025-21067-6
Performance Analysis of a Two-Mode Micromaser Quantum Battery

Authors: Kowsar Al-Sadat Mousavitaha, Varinder Singh, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Advanced Quantum Technologies, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1002/qute.202500441

Spin squeezing enhanced quantum magnetometry with nitrogen-vacancy center qutrits

Authors: Lea Gassab, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: New Journal of Physics, 27(8), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1088/1367-2630/adf87b

Quantum thermal machine as a rectifier

Authors: M. Santiago-García, Onur Pusuluk, Özgür E. Müstecaplıoğlu, Barış Çakmak, R. Román-Ancheyta
Yayınlandığı Adres: Quantum Science and Technology, 10(2), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1088/2058-9565/adaee0

Concept for motion sensing using atomic optical memories

Authors: Arash Ahmadi, Yağız Murat, Özgür E. Müstecaplıoğlu, Pei-Chen Kuan, Mustafa Gündoğan, Markus Krutzik
Yayınlandığı Adres: Research Directions: Quantum Technologies, 3, e2, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1017/qut.2024.7

Quantum Models of Consciousness from a Quantum Information Science Perspective

Authors: Lea Gassab, Onur Pusuluk, Marco Cattaneo, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Entropy, 27(3), 243, 2025
Publication Type: Makale (Perspektif)
Bağlantı: https://doi.org/10.3390/e27030243

Quantum Thermometry for Ultra-Low Temperatures Using Probe and Ancilla Qubit Chains

Authors: Asghar Ullah, Vipul Upadhyay, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Entropy, 27(2), 204, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.3390/e27020204

Single-qubit probes for temperature estimation in the presence of collective baths

Authors: Asghar Ullah, Marco Cattaneo, Özgür E. Müstecaplıoğlu
Yayınlandığı Adres: Physical Review A, 111(6), 062201, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/PhysRevA.111.062201

Near-surface quantum sensing

Authors: Mohsen Izadyari, Ali Pedram, Lea Gassab, Özgür E. Müstecaplıoğlu, Kanu Sinha
Yayınlandığı Adres: Proceedings of SPIE, Vol. 13392 (Quantum Sensing, Imaging, and Precision Metrology III), 2025
Publication Type: Konferans Bildirisi
Bağlantı: https://doi.org/10.1117/12.3047680

Non-Markovianity and a generalized Landauer bound for a minimal quantum autonomous thermal machine with a work qubit

Authors: Khoudiri, A. El Allati, Özgür E. Müstecaplıoğlu, K. El Anouz
Yayınlandığı Adres: Physical Review E, 111(4), 044124, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/PhysRevE.111.044124

Polaron catastrophe within quantum acoustics

Authors: Alhun Aydın, Joonas Keski-Rahkonen, Anton M. Graf, Shaobing Yuan, Xiao-Yu Ouyang, Özgür E. Müstecaplıoğlu, Eric J. Heller
Yayınlandığı Adres: Proceedings of the National Academy of Sciences (PNAS), 122(23), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1073/pnas.2426518122

Quantum metrology of a structured reservoir

Authors: Youssef Aiache, Asghar Ullah, Özgür E. Müstecaplıoğlu, Abderrahim El Allati
Yayınlandığı Adres: Physical Review A, 111(6), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/ypp6-5bt9

Global dynamics behind enzyme catalysis, evolution, and design

Authors: Burcu Aykaç Fas, Zeynep Ece Akbaş Buz, Türkan Haliloğlu
Yayınlandığı Adres: Current Opinion in Structural Biology, 94, 103131, 2025
Publication Type: Derleme Makale (Mini-review)
Bağlantı: https://doi.org/10.1016/j.sbi.2025.103131

Deciphering Allosteric Disease Mutations Through Intrinsic Dynamics

Authors: Berat Kaşkaloğlu, Özge Duman, Yiğit Kutlu, Türkan Haliloğlu
Yayınlandığı Adres: Journal of Molecular Biology, 437(20), 169326, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1016/j.jmb.2025.169326

Insights into therapeutic discovery through the Kelch domain structure of Keap1 at ambient temperature

Authors: Merve Yılmaz, Serra Tavlı, Belgin Sever, Türkan Haliloğlu, Hasan Demirci, et al.
Yayınlandığı Adres: Turkish Journal of Biology, 49(3), 247–260, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.55730/1300-0152.2742

Computational and experimental mapping of the allosteric network of two manganese ABC transporters

Authors: Özge Duman, Anastasiya Kuznetsova, Nurit Livnat Levanon, Moti Grupper, Ayça Ersoy, Burçin Acar, Amit Kessel, Nir Ben-Tal, Oded Lewinson, Türkan Haliloğlu
Yayınlandığı Adres: Protein Science, 34(2), e70039, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1002/pro.70039

Pseudo-hermiticity, anti-pseudo-hermiticity, and generalized parity-time-reversal symmetry at exceptional points

Authors: Nil İnce, Hasan Mermer, Ali Mostafazadeh
Yayınlandığı Adres: Journal of Mathematical Physics, 66(9), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1063/5.0264120

Low-Frequency Scattering of TE and TM Waves by an Inhomogeneous Medium with Planar Symmetry

Authors: Farhang Loran, Ali Mostafazadeh, Cem Yetişmişoğlu
Yayınlandığı Adres: Journal of Physics A: Mathematical and Theoretical, 58(39), 395202, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1088/1751-8121/ae0848

Dynamical formulation of low-frequency scattering in two and three dimensions

Authors: Farhang Loran, Ali Mostafazadeh
Yayınlandığı Adres: Physical Review A, 111(3), 032215, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/PhysRevA.111.032215

Hydrogen storage in transition metal-loaded MCM-41: an integrated density functional theory and Monte Carlo simulation investigation

Authors: Deniz Karataş, Adem Tekin
Yayınlandığı Adres: Adsorption, 31(8), 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1007/s10450-025-00659-8

Organic Cation Orientation Preferences in Hybrid Lead Halide Perovskites

Authors: Somayyeh Alidoust, Adem Tekin
Yayınlandığı Adres: Advanced Theory and Simulations, 9, e01645, 2026 (çevrimiçi 2025)
Publication Type: Makale
Bağlantı: https://doi.org/10.1002/adts.202501645

Discovering novel lead-free mixed cation hybrid halide perovskites via machine learning

Authors: Fatemeh Jamalinabijan, Somayyeh Alidoust, Gözde İniş Demir, Adem Tekin
Yayınlandığı Adres: Physical Chemistry Chemical Physics, 27(14), 7389–7398, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1039/d4cp04218b

6-point tripled Ashkin–Teller global phase diagrams in two and three dimensions

Authors: Deniz İpek Zeynioğlu, A. Nihat Berker
Yayınlandığı Adres: Physica A: Statistical Mechanics and its Applications, 680, 131049, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1016/j.physa.2025.131049

Multiplicity of algebraic order from fixed lines of potential surfaces: XY-Ashkin-Teller in spatial dimension d=2

Authors: Can Artun, A. Nihat Berker
Yayınlandığı Adres: Physical Review E, 112, 024126, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1103/32g1-nvbt

XY-Ashkin–Teller phase diagram in d=3

Authors: Alpar Türkoğlu, A. Nihat Berker
Yayınlandığı Adres: Physica A: Statistical Mechanics and its Applications, 674, 130715, 2025
Publication Type: Makale
Bağlantı: https://doi.org/10.1016/j.physa.2025.130715

Entropy driven inductive response of topological insulators

Authors: A. Mert Bozkurt, Sofie Kölling, Alexander Brinkman, İnanç Adagideli
Place of Publication: SciPost Phys.
Publication Type: Journal Article

2024

Factors Affecting the Electron Conductivity in Single Crystal Li7La3Zr2O12 and Li7P3S11

Authors: Samet Demir, Adem Tekin, Yu-Te Chan, Christoph Scheurer, Karsten Reuter, Alan C. Luntz and Johannes Voss
Place of Publication: New Journal of Physics
Publication Type: Journal Article

Signature of topology via heat transfer analysis in the Su-Schrieffer-Heeger (SSH) model

Authors: Vipul Upadhyay, M. Tahir Naseem, Özgür E. Müstecaplıoğlu and Rahul Marathe
Place of Publication: New Journal of Physics
Publication Type: Journal Article

Prospects for γ-ray observations of the Perseus galaxy cluster with the Cherenkov Telescope Array

Authors: Abe, Koya, et al.
Place of Publication: Journal of cosmology and astroparticle physics
Publication Type: Journal Article

Mixing thermal coherent states for precision and range enhancement in quantum thermometry

Authors: Asghar Ullah, M. Tahir Naseem and Özgür E. Müstecaplıoğlu
Place of Publication: Quantum Science and Technology
Publication Type: Journal Article

Prospects for a survey of the galactic plane with the Cherenkov Telescope Array

Authors: Abe, Shinsuke, et al.
Place of Publication: Journal of Cosmology and Astroparticle Physics
Publication Type: Journal Article

PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting

Authors: Onur Dereli, Nurdan Kuru, Emrah Akkoyun, Aylin Bircan, Oznur Tastan, Ogün Adebali
Place of Publication: Molecular Biology and Evolution
Publication Type: Journal Article

Conditions on detecting tripartite entangled state in psychophysical experiments

Authors: Lea Gassab, Ali Pedram and Özgür E. Müstecaplıoğlu
Place of Publication: EPJ Plus
Publication Type: Journal Article

Light-Harvesting Lead-Free Mixed Cation Hybrid Halide Perovskites: A Density Functional Theory-Based Computational Screening Study

Authors: Somayyeh Alidoust, Fatemeh Jamalinabijan, Adem Tekin
Place of Publication: ACS Applied Energy Materials
Publication Type: Journal Article

Cross-species investigation into the requirement of XPA for nucleotide excision repair

Authors: Cansu Kose, Xuemei Cao, Evan B Dewey, Mustafa Malkoç, Ogün Adebali, Jeff Sekelsky, Laura A. Lindsey-Boltz, Aziz Sancar
Place of Publication: Nucleic Acids Research
Publication Type: Journal Article

Phase Prediction via Crystal Structure Similarity in the Periodic Number Representation

Authors: Cem Oran, Riccarda Caputo, Pierre Villars, Hasan Bilal Özcü, Feraye Hatice Canbaz, Adem Tekin
Place of Publication: Inorganic Chemistry
Publication Type: Journal Article

Quantum estimation of the stokes vector rotation for a general polarimetric transformation

Authors: Ali Pedram, Vira R Besaga, Lea Gassab, Frank Setzpfandt and Özgür E. Müstecaplıoğlu
Place of Publication: New Journal of Physics
Publication Type: Journal Article

Dynamics of transcription-coupled repair of cyclobutane pyrimidine dimers and (6-4) photoproducts in Escherichia coli

Authors: Ogϋn Adebali, Aziz Sancar, and Christopher P. Selby
Place of Publication: PNAS
Publication Type: Journal Article

Quantum scars and caustics in Majorana billiards

Authors: R. Johanna Zijderveld, A. Mert Bozkurt, Michael Wimmer, Inanc Adagideli
Place of Publication: SciPost Physics
Publication Type: Journal Article

Nonlocality Enhanced Precision in Quantum Polarimetry via Entangled Photons

Authors: Ali Pedram, Vira R. Besaga, Frank Setzpfandt, Ozgur E. Müstecaplioglu
Place of Publication: Advanced Quantum Technologies
Publication Type: Journal Article

Optimization of CHARMM force field parameters for ryanodine receptor inhibitory drug dantrolene using FFTK and FFParam

Authors: Saliha Nur Uludag, Cemil Can Saylan, Adem Tekin & Sefer Baday
Place of Publication: Journal of Molecular Modeling
Publication Type: Journal Article

The expected potential of hadronic PeVatron searches with spectral γ-ray data from the Southern Wide-field Gamma-ray Observatory

Authors: Ekrem Oğuzhan Angüner, Tülün Ergin
Place of Publication: Astroparticle Physics
Publication Type: Journal Article

Pybkgmodel - a background modeling toolbox for the CTA

Authors: Strzys, Marcel C., et al
Place of Publication: 38th International Cosmic Ray Conference
Publication Type: Conference Article

Engineering Four-Qubit Fuel States for Protecting Quantum Thermalization Machine from Decoherence

Authors: Fatih Ozaydin, Ramita Sarkar, Veysel Bayrakci, Cihan Bayindir, Azmi Ali Altintas and Ozgur E. Müstecaplioglu
Place of Publication: Information 2024
Publication Type: Journal Article

Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations

Authors: Aylin Bircan, Nurdan Kuru, Onur Dereli, Berkay Selçuk, Ogün Adebali
Place of Publication: PLOS Computational Biology
Publication Type: Journal Article

Fundamentals and Applications of Heat Currents in Quantum Systems

Authors: Naseem, M. Tahir, and Ozgur E. Müstecaplioglu
Place of Publication: International Conference on Frontiers of Fundamental Physics
Publication Type: Conference Article

2023

On the role of initial coherence in the spin phase-space entropy production rate

Authors: Giorgio Zicari, Baris Cakmak, Ozgur Esat Müstecaplioglu and Mauro Paternostro
Place of Publication: New Journal of Physics
Publication Type: Journal Article

A quantum Otto engine with shortcuts to thermalization and adiabaticity

Authors: A. Pedram, S. C. Kadıoğlu, A. Kabakçıoğlu and Ö. E. Müstecaplıoğlu
Place of Publication: New Journal of Physics
Publication Type: Journal Article

A compendious review of majorization-based resource theories: quantum information and quantum thermodynamics

Authors: Gökhan Torun, Onur Pusuluk, Özgür Esat Müstecaplıoğlu
Place of Publication: Turkish Journal of Physics
Publication Type: Journal Article

Coherence, superposition, and Löwdin symmetric orthogonalization

Authors: Gökhan Torun
Place of Publication: Journal of Physics A: Mathematical and Theoretical
Publication Type: Journal Article

Experimental and Ab-Initio Investigation of the Electrical Conductivity of Emeraldine Salt

Authors: Zeynep Ergönenç Yavas, Duygu Cevher, Hasan Töre Silis, Ali Cirpan, Oğuz Gülseren, Cesare Franchini
Place of Publication: The Journal of Physical Chemistry C
Publication Type: Journal Article

Exploring the high energy frontiers of the Milky Way with ground-based gamma-ray astronomy: PeVatrons and the quest for the origin of Galactic cosmic-rays

Authors: Ekrem Oğuzhan Angüner
Place of Publication: Turkish Journal of Physics
Publication Type: Journal Article

Hydrogen Storage in Trimetallic Borohydrides: a Crystal Structure Prediction and Ab Initio Molecular Dynamics Simulations Study

Authors: Samet Demir, Mostafa Torkashvand, Shirzad Jouybar, Zahra Nikfarjam, Farshid Zargari, Saeedeh Sarabadani Tafreshi, Adem Tekin
Place of Publication: The Journal of Physical Chemistry C
Publication Type: Journal Article

Sensitivity of the Cherenkov Telescope Array to TeV photon emission from the Large Magellanic Cloud

Authors: Acharyya, Atreya, et al.
Place of Publication: Monthly Notices of the Royal Astronomical Society
Publication Type: Journal Article

Deciphering the dynamic codes: Advances in biomolecular modeling and simulation

Authors: Gregory A Voth, Turkan Haliloglu
Place of Publication: Current opinion in structural biology
Publication Type: Journal Article

Stable and metastable crystal structures and ammonia dynamics in strontium chloride ammines

Authors: Samet Demir, Gözde İniş Demir, Mehmet Çankaya, Adem Tekin
Place of Publication: Physical Chemistry Chemical Physics
Publication Type: Journal Article

Prototype Open Event Reconstruction Pipeline for the Cherenkov Telescope Array

Authors: Maximilian Linhoff, Lukas Beiske, Noah Biederbeck, Stefan Fröse, Karl Kosack and Lukas Nicke
Place of Publication: 38th International Cosmic Ray Conference
Publication Type: Conference Article

Dynamical spin-orbit-based spin transistor

Authors: Fahriye N. Gürsoy, P. Reck, C. Gorini, K. Richter, I. Adagideli
Place of Publication: SciPost Phys.
Publication Type: Journal Article

Terrestrial Very-Long-Baseline Atomic Interferometry: Workshop Summary

Authors: Abend, S., et al.
Place of Publication: Theoretical Physics Group
Publication Type: Journal Article

Search for the Galactic accelerators of cosmic rays up to the knee with the Pevatron test statistic

Authors: Ekrem Oğuzhan Angüner, Gerrit Spengler, Elena Amato, Sabrina Casanova
Place of Publication: Monthly Notices of the Royal Astronomical Society
Publication Type: Journal Article

The interplay of 3D genome organization with UV-induced DNA damage and repair

Authors: Ümit Akköse, Ogün Adebali
Place of Publication: JBC Communication
Publication Type: Journal Article

The Mfd protein is the transcription-repair coupling factor (TRCF) in Mycobacterium smegmatis

Authors: Ogun Adebali, Yanyan Yang, Pradeep Neupane, Nneka I. Dike, Julia L. Boltz, Cansu Kose, Miriam Braunstein, Christopher P. Selby, Aziz Sancar, Laura A. Lindsey-Boltz
Place of Publication: Journal of Biological Chemistry
Publication Type: Journal Article

Downregulated NPAS4 in multiple brain regions is associated with major depressive disorder

Authors: Berkay Selcuk, Tuana Aksu, Onur Dereli & Ogun Adebali
Place of Publication: Scientific Reports
Publication Type: Journal Article

2022

Classical and quantum orbital correlations in molecular electronic states

Authors: Onur Pusuluk, Mahir H Yeşiller, Gökhan Torun, Özgür E Müstecaplıoğlu, Ersin Yurtsever and Vlatko Vedral
Place of Publication: New Journal of Physics
Publication Type: Journal Article

2D-FFCASP-A New Approach for 2D Structure Prediction Applied to Self-Assemblies of DNA Bases

Authors: Gözde İniş Demir, Samet Demir, Adem Tekin
Place of Publication: Advanced Theory and Simulations
Publication Type: Journal Article

Equiatomic binary phases of Copper-Rare Earth Elements. An overview of monocuprides from first-principles calculations

Authors: Prof. Dr. Riccarda Caputo, Cem Oran, Prof. Dr. Adem Tekin, Dr. Pierre Villars
Place of Publication: ChemPhysChem
Publication Type: Journal Article

Engineering entanglement between resonators by hot environment

Authors: M. Tahir Naseem and Özgür E. Müstecaplıoğlu
Place of Publication: Quantum Science and Technology
Publication Type: Journal Article

Quantum signatures in a quadratic optomechanical heat engine with an atom in a tapered trap

Authors: Mohsen Izadyari, Mehmet Öncü, Kadir Durak, and Özgür E. Müstecaplioğlu
Place of Publication: Journal of the Optical Society of America B
Publication Type: Journal Article

Environment-Assisted Modulation of Heat Flux in a Bio-Inspired System Based on Collision Model

Authors: Ali Pedram, Baris Cakmak and Ozgur E. Müstecaplioglu
Place of Publication: Entropy 2022
Publication Type: Journal Article

A novel phylogeny-dependent coevolution algorithm

Authors: Kuru, Nurdan and Adebali, Ogun
Place of Publication: 15th International Symposium on Health Informatics and Bioinformatics HIBIT'22
Publication Type: Conference Article

Reproducible and scalable data analysis on high performance computing

Authors: Akkoyun Emrah, Kuru Nurdan, Dereli Onur, Bircan Aylin, Taştan Öznur and Adebali Ogün
Place of Publication: 15th International Symposium on Health Informatics and Bioinformatics HIBIT'22
Publication Type: Conference Article

Effects of replication domains on genome-wide UV-induced DNA damage and repair

Authors: Yanchao Huang, Cem Azgari, Mengdie Yin, Yi-Ying Chiou, Laura A. Lindsey-Boltz, Aziz Sancar, Jinchuan Hu, Ogun Adebali
Place of Publication: PLoS genetics
Publication Type: Journal Article

2021

Crystal Structure Prediction and Dehydrogenation Mechanism of LiMg(BH4)3(NH3)2

Authors: Gözde İniş Demir, Riccarda Caputo, Samet Demir, Adem Tekin
Place of Publication: The Journal of Physical Chemistry C
Publication Type: Journal Article

FFCASP: A Massively Parallel Structure Prediction Algoritrystal Shm

Authors: Samet Demir, Adem Tekin
Place of Publication: Journal of Chemical Theory and Computation
Publication Type: Journal Article

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