Understanding physical chemistry of Ba<sub><i>x<\/i><\/sub>Sr<sub>1−<i>x<\/i><\/sub>TiO<sub>3<\/sub> using ReaxFF molecular dynamics simulations
Physical Chemistry Chemical Physics, Vol. 23, Ekim 2021, ISSN: 1463-9076
AKBARİAN DOOMAN, NAYİR NADİRE, VAN DUİN ADRİ
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Oxidation and hydrogenation of monolayer MoS2 with compositing agent under environmental exposure: The ReaxFF Mo/Ti/Au/O/S/H force field development and applications
Frontiers Media SA, Vol. 4, Ekim 2022, ISSN: 2673-3013
MAO QİAN, ZHANG YUWEİ, NAYİR NADİRE, KOWALİK MALGORZATA, VAN DUİN ADRİ, CHANDROSS MİCHAEL
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The Inhibition Mechanism of Pancreatic Ductal Adenocarcinoma via LXR Receptors: A Multifaceted Approach Integrating Molecular Docking, Molecular Dynamics and Post-MD Inter-Molecular Contact Analysis
Asian Pacific Journal of Cancer Prevention, Vol. 24, No. 12, Aralık 2023, s. 4103-4109, ISSN: 2476-762X
AĞAR SOYKAN, AKKURT BARBAROS, ULUKAYA ENGİN
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Molecular dynamics simulations can predict the optimum drug loading amount in pectin hydrogels for controlled release
Materials Today Communications, Vol. 31, Haziran 2022, ISSN: 2352-4928
KOCAAGA BANU, GÜNER FATMA SENİHA, KÜRKÇÜOĞLU LEVİTAS AYŞE ÖZGE
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Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations
BIOCHEMISTRY, Ocak 2022, s. 12, ISSN: 0006-2960
ÇİÇEK ERDEM, MONARD GERALD, SUNGUR FETHİYE AYLİN
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Hydrogen Storage in Trimetallic Borohydrides: a Crystal Structure Prediction and Ab Initio Molecular Dynamics Simulations Study
American Chemical Society (ACS), Vol. 127, Eylül 2023, ISSN: 1932-7447
DEMİR SAMET, TORKASHVAND MOSTAFA, JOUYBAR SHİRZAD, NİKFARJAM ZAHRA, ZARGARİ FARSHİD, TAFRESHİ SAEEDEH SARABADANİ, TEKİN ADEM
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Molecular dynamics simulations can predict the optimum drug loading amount in pectin hydrogels for controlled release
Materials Today Communications, Vol. 31, Ocak 2022, ISSN: 2352-4928
KOCAAĞA AYŞE BANU, KÜRKÇÜOĞLU LEVİTAS AYŞE ÖZGE, GÜNER FATMA SENİHA
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Using Molecular Dynamics Simulations to Predict the Optimum Drug Concentration in Pectin Hydrogels with Controlled Release
Global Nanobio Technology E-Conference, Florida/AMERİKA BİRLEŞİK DEVLETLERİ, 1 Mart 2021
KOCAAĞA AYŞE BANU, GÜNER FATMA SENİHA, KÜRKÇÜOĞLU LEVİTAS AYŞE ÖZGE
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Drug Re-Positioning Studies for Novel HIV-1 Inhibitors Using Binary QSAR Models and Multi-Target-DrivenIn SilicoStudies
MOLECULAR INFORMATICS, Vol. 40, No. 2, Şubat 2021, ISSN: 1868-1743
DOĞAN BERNA, DURDAĞI SERDAR
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Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing
STRUCTURE, Vol. 29, No. 12, Aralık 2021, s. 1382, ISSN: 0969-2126
DURDAĞI SERDAR, DOĞAN BERNA, DEMİRCİ HASAN
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Omicron BA.1 and BA.2 variants increase the interactions of SARS-CoV-2 spike glycoprotein with ACE2
Journal of Molecular Graphics and Modelling, Vol. 117, Aralık 2022, ISSN: 1093-3263
GÖLCÜK MERT, YILDIZ AHMET, GÜR MERT
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SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity
Journal of Chemical Information and Modeling, Vol. 62, Mayıs 2022, ISSN: 1549-9596
GÖLCÜK MERT, HACISÜLEYMAN AYSİMA, YILMAZ SEMA ZEYNEP, TAKA ELHAN, YILDIZ AHMET, GÜR MERT
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Optimization of seed-induced lateral liquid beam epitaxy growth of germanium on insulator by molecular dynamics
Collaborative Conference on 3D and Materials Research (CC3DMR-2015), 15 Haziran 2015
NAYİR NADİRE, TAŞCI EMRE, ÖZYURT İREM, YERCİ SELÇUK, ERKOÇ ŞAKİR
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Atomic-scale probing of defect-assisted Ga intercalation through graphene using ReaxFF Molecular Dynamics Simulations
Carbon, Nisan 2022, ISSN: 0008-6223
NAYİR NADİRE, SENGUL MERT, COSTİNE ANNA, REİNKE PETRA, RAJABPOUR SİAVASH, BANSAL ANUSHKA, KOZHAKHMETOV AZİMKHAN, ROBİNSON JOSHUA, REDWİNG JOAN, VAN DUİN ADRİ
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Fmoc-PEG Coated Single-Wall Carbon Nanotube Carriers by Non-covalent Functionalization: An Experimental and Molecular Dynamics Study
Frontiers in Bioengineering and Biotechnology, Vol. 9, No. 648366, Mayıs 2021, ISSN: 2296-4185
YENİYURT YEŞİM, KILIÇ SILA, GÜNER YILMAZ O. ZEYNEP, BOZOĞLU SERDAR, MERAN MEHDİ, BAYSAK ELİF, KÜRKÇÜOĞLU LEVİTAS AYŞE ÖZGE, HIZAL GÜRKAN, YAVUZ NİLGÜN, BATIREL SAİME, GÜNER FATMA SENİHA
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Design and molecular dynamics of multifunctional sulfonated poly(dimethylaminoethyl methacrylate)/mica hybrid cryogels through freezing-induced gelation
SOFT MATTER, Vol. 15, No. 35, Eylül 2019, s. 7043-7062, ISSN: 1744-683X
ÖKTEN BEŞLİ NUR SENA, KAYA BERİL, ORAKDÖĞEN NERMİN
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Exploring Allosteric Signaling in the Exit Tunnel of the Bacterial Ribosome by Molecular Dynamics Simulations and Residue Network Model
Frontiers in Molecular Biosciences, Vol. 7, Eylül 2020, ISSN: 2296-889X
GÜZEL PELİN,YILDIRIM HATİCE ZEYNEP,YÜCE MERVE,KÜRKÇÜOĞLU LEVİTAS AYŞE ÖZGE
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Exploring the binding mechanisms of nanobodies targeting SARS-CoV-2 spike glycoprotein using molecular dynamics simulations
2021 ACS Fall Meeting., Atlanta/AMERİKA BİRLEŞİK DEVLETLERİ, 22 Ağustos 2021
GÖLCÜK MERT, HACISÜLEYMAN AYSİMA, ERMAN BURAK, YILDIZ AHMET, GÜR MERT
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Molecular dynamics simulations of apo holo and inactivator bound GABA at reveal the role of active site residues in PLP dependent enzymes
Proteins: Structure, Function, and Bioinformatics, Vol. 84, No. 7, Temmuz 2016, s. 875-891, ISSN: 08873585
GÖKCAN HATİCE,MONARD GERALD,SUNGUR FETHİYE AYLİN
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Molecular dynamics simulation of size, temperature, heating and cooling rates on structural formation of Ag-Cu-Ni ternary nanoparticles (Ag34-Cu33-Ni33)
COMPUTATIONAL MATERIALS SCIENCE, Vol. 183, Ekim 2020, s. 109842, ISSN: 0927-0256
SAFALTIN ŞERZAT,GÜRMEN SEBAHATTİN
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