23. ifg program kitapçığı - İFG 23

Transkript

23. İstatistiksel Fizik Günleri (İFG23)
İdris Yamantürk Konferans Salonu
Elektrik-Elektronik Fakültesi
Ayazağa Yerleşkesi, İ.T.Ü., İstanbul
Fizik Mühendisliği Bölümü, Fen-Edebiyat Fakültesi, İstanbul Teknik Üniversitesi
23-24 Haziran 2016
23. İstatistiksel Fizik Günleri (İFG23)
23-24 Haziran 2016
Fizik Mühendisliği Bölümü, Fen-Edebiyat Fakültesi, İstanbul Teknik Üniversitesi
http://ifg23.itu.edu.tr
Bilim Kurulu
Prof. Dr. Zehra AKDENİZ Piri Reis Üniversitesi
Prof. Dr. Canan ATILGAN Sabancı Üniversitesi
Prof. Dr. Nihat BERKER Sabancı Üniversitesi
Prof. Dr. Can Fuat DELALE Mef Üniversitesi
Prof. Dr. A. Levent DEMİREL Koç Üniversitesi
Prof. Dr. Gülay DERELİ Koç Üniversitesi
Prof. Dr. Sondan Durukanoğlu FEYİZ Sabancı Üniversitesi
Doç. Dr. Zafer GEDİK Sabancı Üniversitesi
Doç. Dr. Gül GÜLPINAR Dokuz Eylül Üniversitesi
Prof. Dr. Avadis HACINLIYAN Yeditepe Üniversitesi
Doç. Dr. Alkan KABAKÇIOĞLU Koç Üniversitesi
Prof. Dr. Mustafa KESKİN Erciyes Üniversitesi
Doç. Dr. Muhittin MUNGAN Boğaziçi Üniversitesi
Prof. Dr. Özgür MÜSTECAPLIOĞLU Koç Üniversitesi
Doç. Dr. Sevtap Yıldız ÖZBEK İstanbul Teknik Üniversitesi
Doç. Dr. A.Levent SUBAŞI İstanbul Teknik Üniversitesi
Prof. Dr. Bilal TANATAR Bilkent Üniversitesi
Prof. Dr. Uğur TIRNAKLI Ege Üniversitesi
Prof. Dr. Cemal YALABIK Bilkent Üniversitesi
Danışma Kurulu
Prof. Dr. Ayşe ERZAN İstanbul Teknik Üniversitesi
Prof. Dr. Mehmet ERBUDAK University of Zurih
Düzenleme Komitesi
Doç. Dr. Sevtap Yıldız ÖZBEK İstanbul Teknik Üniversitesi
Doç. Dr. Ahmet Levent SUBAŞI İstanbul Teknik Üniversitesi
Araş. Gör. Mehmet Can ÇETiNKAYA İstanbul Teknik Üniversitesi
Araş. Gör. Burçin DANACI İstanbul Teknik Üniversitesi
Şenay ÜSTÜNEL İstanbul Teknik Üniversitesi
Program Yürütücüsü
Doç. Dr. Sevtap Yıldız Özbek İstanbul Teknik Üniversitesi
Destekleyen Kurumlar
İstanbul Teknik Üniversitesi
TÜBA – Türkiye Bilimler Akademisi
Bu kitapçık V. Verfaille tarafından geliştirilen LATEX ‘confproc’ paketinin 0.8. sürümü ile oluşturulmuştur.
23. İstatistiksel Fizik Günleri (İFG23), İ.T.Ü., İstanbul, 23-24 Haziran 2016
İFG23’e hoşgeldiniz!
Michael Hinczewski, Ana Konuşmacı
Assistant Professor
Department of Physics
Case Western Reserve University
http://www.phys.cwru.edu/faculty/index.php?mhincz
İstanbul İstatistiksel Fizik Günleri
Prof. Dr. Nihat Berker ve Prof. Dr. Ayşe Erzan’ın önderliğinde başlatılan İstanbul İstatistiksel Fizik Günleri, 1994 yılından bu yana her yıl ülkemizde bu konuda
çalışan araştırmacıları bir araya getirmek amacıyla sürdürülmektedir. Toplantılar,
genellikle, her yıl Haziran ayının sonunda veya Temmuz ayının başında düzenlenmektedir. Bu yılki toplantı, 23-24 Haziran 2016 tarihlerinde, İstanbul Teknik
Üniversitesi’nde yapılacaktır.
Toplantılara, konusunda uluslararası düzeyde tanınmış bir ana konuşmacı davet
edilmektedir. Bunun yanı sıra, katılımcıların ilgisini çekebilecek konularda araştırmalar yapmakta olan 10-15 konuşmacı da yaklaşık 30 dakikalık konuşmalar yapmak üzere toplantıya davet edilmektedir. İngilizce olarak sunulan bu konuşmaların
yanı sıra diğer katılımcılara araştırma çalışmalarını Türkçe olarak sunmaları için
10’ar dakikalık süreler ayrılmaktadır.
İFG23-iii
İFG23-iv
T OPLANTI P ROGRAMI
1. Gün - 23 Haziran 2016 Perşembe
08:30-09:00 Karşılama ve kayıt
09:00-10:30 1. Oturum
1 Michael Hinczewski
The ties that bind us together: the statistical mechanics of cell adhesion proteins
2 Sofia Piepoli
Target specific Transcription Activator-Like Effectors: How We Analyze And Explain Intermolecular Stability
10:30-10:50 Ara
10:50-13:00 2. Oturum
3 Alper Kiraz
Quantum dot optofluidic lasers and their prospects for biochemical sensing
4 Sevilay Sevinçli
Controlling optical properties of the Rydberg-EIT medium
5 Yusuf Yüksel, Ümit Akıncı, Musa Atlıhan, Gülşen Karakoyun, Numan Şarlı, Emir Haliki, Dicle Yağmur Özdemir
Kısa Konuşmalar-A
13:00-14:10 Ara
14:10-15:40 3. Oturum
14 Aşkın Kocabaş
Controlling and imaging the dynamics of complex neural networks
15 G. Çiğdem Yalçın
Severely contracted configuration space and q-statistics in rank distributions
16 Özgür Afşar
Probability distributions and scaling relations for low dimensional dynamical systems in the vicinity of chaos
15:40-16:00 Ara
16:00-17:50 4. Oturum
17 Göktuğ Karpat
Controlling entropic uncertainty bound through memory effects
18 Caroline Ross, Tandaç Furkan Güçlü, Erol Kurt, Mine Konuk, Dicle Yağmur Özdemir, Berk Onat, Melihat
Madran, Elif Peksu
Kısa Konuşmalar-B
İFG23-v
2. Gün - 24 Haziran 2016 Cuma
08:30-09:00 Çay ve kahve
09:00-10:30 1. Oturum
28 Michael Hinczewski
The price of information: thermodynamics and the limits of signaling in living systems
29 Hande Toffoli
Polarized dipolar fermions in a two-dimensional harmonic trap
10:30-10:50 Ara
10:50-13:00 2. Oturum
30 Ümit Akbey
NMR Supported Structural Biology: With a focus on Functional Amyloids from Bacterial Biofilms
31 Gül Bekçioğlu
Solvation-Dependent Latency of Photoacid Dissociation and Transient IR Signatures of Protonation Dynamics
32 Nihat Berker, Gül Gülpınar, Gülşen Akın Evingür, Barış Pekerten, Numan Şarlı, Ali Asgharpour, İbrahim Ethem
Özyiğit, Haleh Abdizadeh
Kısa Konuşmalar-C
13:00-14:10 Ara
14:10-15:40 3. Oturum
40 Çağdaş Allahverdi
Investigation of Physical Properties of AII-BVI Quantum Dots: Synthesis Techniques, Optical Properties and
Applications
41 Özgür Akarsu
Contemporary cosmology and power-law inflation without a scalar field
42 Birses Debir
Post Newtonian Approximation of Black Hole Entropy
15:40-16:00 Ara
16:00-17:30 4. Oturum
43 Enis Doko, Bilal Tanatar, Menderes Işkın, Alimet Sema Özen, İskender Yalçınkaya, Ayşe Ferhan Yeşil, Barış
Çakmak, Ferdi Altıntaş
Kısa Konuşmalar-D
İFG23-vi
Konuşma Özeti, 23. İstatistiksel Fizik Günleri (İFG23), İ.T.Ü., İstanbul, 23-24 Haziran 2016
THE TIES THAT BIND US TOGETHER:
THE STATISTICAL MECHANICS OF CELL ADHESION PROTEINS
Michael Hinczewski
Case Western Reserve University, Cleveland, Ohio, USA
ABSTRACT
For complex multicellular organisms to function, individual cells need mechanisms to bind to each other.
In humans, cell-to-cell adhesion maintains the architecture of tissues, drives the response of the immune
system, and allows for wound healing. All of the contacts involved in these processes are made through
specialized molecules on the surface of cells known as adhesion proteins. These are particularly interesting from the perspective of statistical physics, since protein bonds are never permanent, but constantly
rupture and reform in a stochastic manner. The distribution of bond lifetimes is intimately related to
the thermal fluctuations in the shape of the protein, and the magnitude of mechanical tension under
which the contact exists. Experiments in the last fifteen years have provided a wealth of data, including
careful measurements of single protein bonds breaking under force. However the data often introduces
as many questions as it answers, revealing strange, counterintuitive phenomena like ”catch bonding”,
where increasing tension strengthens a bond, prolonging its lifetime. My talk explores the ways in
which nonequilibrium statistical mechanics can help us model and predict adhesion protein dynamics,
exploiting simple, analytically solvable theories of diffusion on multidimensional energy landscapes.
The theory gives us a surprisingly detailed perspective on the molecular interactions that underlie bonding, and highlights the critical role of randomness in biological functions.
İFG23-1
TARGET SPECIFIC TRANSCRIPTION ACTIVATOR-LIKE EFFECTORS (TALES):
HOW WE ANALYZE AND EXPLAIN INTERMOLECULAR STABILITY
S. Piepoli, C. Atılgan, B. Erman
Sabanci University, Istanbul, Turkey
[email protected]
ABSTRACT
TALE(transcription activator-like effector) proteins are considered among the principal tools for targeted
genome editing. Crystal structure of PthXo1 TALE protein bound to its DNA target reveals specificity
of interactions between the two. TALE is coiled around DNA in a super-helix conformation, consisting
of 33-34 conserved amino acids repeated at each turn. Amino acids at positions 12-13 specifically bind
to DNA bases according to the code: HD→C, NG→T, NI→A, NN→G in most cases. To quantify
specific binding stability, we apply Perturbation-Response Scanning method that classifies four regions
of intrinsic stability. We further analyze point mutations introduced into select positions by free energy
perturbation calculations. Based on these findings, we make a model for DNA recognition by TALEs
that also explains the lower and upper bounds on the number of base-pairs recognized. We therefore
expand on current methods for computational design of TALEs for experimental tests of binding affinity
and off-target specificity.
İFG23-2
QUANTUM DOT OPTOFLUIDIC LASERS AND THEIR PROSPECTS FOR BIOCHEMICAL
SENSING
Alper Kiraz
Department of Physics, Koç University, Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey
ABSTRACT
We achieved three types of laser emissions with aqueous quantum dots (QDs) using the same high-Qfactor optofluidic ring resonator (OFRR) platform. In the first type, 2 µM QDs were in bulk buffer
solution that filled the entire OFRR cavity volume. The lasing threshold was 0.1 µJ/mm2 , over 3 orders
of magnitude lower than the state-of-the-art. In the second type, the QDs were immobilized as a single
layer on the interface between the OFRR inner wall and buffer solution with a surface density as low
as 3×109 -1010 cm−2 . The lasing threshold of 60 µJ/mm2 was achieved. In the third type, we achieved
optofluidic FRET lasing using QDs as FRET donors and Cy5 dye molecules as acceptors. We observed
lasing from Cy5 emission band in QD-Cy5 pair when excited at QD absorption band, far away from Cy5
absorption maximum. The demonstrated capability of QDs as donors in FRET lasers greatly improves
the versatility for optofluidic laser operation due to the broad and large absorption cross-section of QDs
in the blue and UV range.
I will also discuss the comprehensive theoretical analysis of optofluidic FRET lasers that we have performed based on a Fabry-Perot microcavity using a rate equation model. By comparing FRET lasingbased sensors with conventional sensors using FRET signals obtained by spontaneous fluorescence emission, we show that for optimal pump fluence and FRET pair concentration, FRET lasing can lead to more
than 100-fold enhancement in detection sensitivities of conformation changes for linker lengths in the
Förster radius range.
İFG23-3
CONTROLLING OPTICAL PROPERTIES OF THE RYDBERG-EIT MEDIUM
Sevilay Sevinçli
Izmir Institute of Technology, Gülbahçe Kampüsü, 35430 Urla, İzmir
ABSTRACT
Electromagnetically induced transparency (EIT) provides remarkable possibilities for nonlinear optics
by enabling ultra-slow group velocities and storage of light. The combination of EIT and interacting
Rydberg gases has recently attracted considerable theoretical and experimental interest, as it holds
promise for realizing extremely large nonlinearities by exploiting the exaggerated interactions between
Ryd- berg atoms. I present different many-body approaches to describe interaction effects on the propagation of classical light pulse in an Rydberg-EIT medium. Further analytical study on nonlinear response
of cold Rydberg gases shows that the nonlinear susceptibility is not only drastically enhanced but also
highly nonlocal in nature, corresponding to long-range photon-photon interactions. I also propose a microwave dressing scheme, that allows to modify the interactions between Rydberg atoms, and thereby
control the optical properties of the gas. It is demonstrated that microwave dressing provides a powerful
approach to control dipolar as well as van der Waals interactions and even permits us to turn them off
entirely. In addition, the proposed scheme opens up possibilities for engineering dominant three-body
interactions.
İFG23-4
MANYETİK NANOPARÇACIKLARDA DEĞİŞ-TOKUŞ ANİZOTROPİSİNİN DİNAMİK
MANYETİK ALANLAR VARLIĞINDAKİ DAVRANIŞI
Ümit Akıncı, Yusuf Yüksel
Dokuz Eylül Üniversitesi Tınaztepe Kampüsü Fen Fakültesi Fizik Bölümü TR-35160 Buca İZMİR
ABSTRACT
Ferromanyetik (FM) bir yapının antiferromanyetik (AFM) bir yapı ile manyetik olarak etkileşmesi sonucu
ortaya çıkan değiş-tokuş anizotropisi, manyetik-dirençli cihazlar, manyetik algılayıcılar, manyetik sabit
disklerde okuyucu başlıklar gibi birçok spintronik sistemin geliştirilmesinde yararlanılan temel bir fiziksel etkidir. Temel olarak manyetik nanoparçacıklar ve manyetik ince filmlerde gözlenen bu etki, mıknatıslanma - manyetik alan şiddeti düzleminde elde edilen histerezis halkalarındaki yatay ve dikey kaymalar
şeklinde kendisini gösterir. Sıcaklık, madde içi manyetik etkileşmeler, nanoparçacık çapı (benzer şekilde
film kalınlığı) ve yapısal kusurlar gibi parametreler, bu etkiyi doğrudan etkileyen temel fiziksel etmenlerdir.
Öte yandan, günümüzde üretilen sabit disk sürücülerinde hedef, konum uzayında az yer kaplayan, ama
depolama kapasitesi oldukça yüksek olan cihazlar imal etmektir. Ancak, bu amaçla kullanılan malzemenin yapısal boyutları belli bir kritik ölçeğin altına indirgendiğinde, ısısal dalgalanmalar malzemenin
kararlı yapısını bozarak teknolojik açıdan işlevselliğini yitirmesine neden olur. Teknolojik uygulamalar
açısından, süper paramanyetik etki yada süperparamanyetizma (SP) olarak bilinen bu olguyu yenmek
değiş-tokuş anizotropisi sayesinde mümkün olmakla beraber, SP etkisi bambaşka bir alanda; biyolojik
yapılarda organizma içersinde ilaç taşınımını mümkün kılmaktadır.
Değiş-tokuş anizotropisi ve SP fenomenlerinin yukarıda saydığımız (sıcaklık, madde içi manyetik etkileşmeler, vb) unsurlar ile değişimi literatürde çok sayıda kuramsal çalışmanın temel motivasyon kaynağı
olmuştur. Ancak deneysel olarak bu parametrelerin kontrolü genellikle pek kolay olmadığı için sözü
edilen fenomenlerden, gerçek sistemlerde faydalı ve kontrollü bir şekilde yararlanmak zorlu bir iştir.
Buna karşılık, laboratuar ortamında, genliği ve periyodu kontrol edilebilen salınımlı manyetik alanlar
üretmek ve malzeme üzerine etki ettirmek ise görece daha pratik ve etkili bir yöntem vaat etmekle
beraber, en iyi bilgimiz dahilinde, bu tür dinamik etkilerin söz konusu fenomenler üzerindeki etkisini
incelemek amacıyla ne kuramsal ne de deneysel anlamda bir girişim bugüne dek olmamıştır. Probleme kuramsal açıdan yaklaşılacak olan bu sunumda, kurgulanan nanoparçacık modeli için Monte Carlo
simülasyon yönteminin sonuçları ele alınacaktır.
[1] W. H. Meiklejohn and C. P. Bean, Phys. Rev. 102, 1413 (1956).
[2] J. Nogues and I. K. Schuller, J. Magn. Magn. Mater. 192, 203 (1999).
[3] O. Iglesias, Xavier Batlle, and A. Labarta, J. Nanosci. Nanotechno. 8, 2761 (2008).
[4] I. K. Schuller, Mrs Bull. 29, 642 (2004).
[5] M. Vasilakaki, E. Eftaxias, and K. N. Trohidou, Phys. Status Solidi A 205, 1865 (2008).
İFG23-5
ÇOK KATMANLI NANOTÜPLERİN MANYETİK HİSTEREZİS ÖZELLİKLERİ
Ümit Akıncı
Fizik Bölümü, Dokuz Eylül Üniversitesi Fen Fakültesi
ABSTRACT
Manyetik nanotüpler ilaç iletiminden biyoayrıştırmaya, çeşitli biyomedikal uygulamalardan sensör yapımına
kadar geniş uygulama alanlarına sahiptir [1,2,3]. Bu yapıların, sahip oldukları geometriden kaynaklı
olarak, uzunluk, çap veya katman sayılarının değiştirilmesi gibi yollarla manyetik özellikleri ayarlanabilir. Buna ek olarak, içlerine başka malzemelerin yerleştirilmesi ile çekirdek-kabuk (core-shell) nanoyapılar
oluşturulabilir. FePt ve Fe3O4 gibi nanotüpler, çekirdek kabuk modelleri ile ele alınıp, manyetik özellikleri
çeşitli teorik yöntemlerle hesaplanabilir [4]. Etkin alan yaklaşımı [5] ve Monte Carlo simülasyonları
[6] bu çözüm yöntemlerinin en sık kullanılanlarındandır. Bu yöntemler sıklıkla tek katmanlı nanotüp
geometrisine uygulanmıştır. Bu sunumda çok katmanlı ve farklı geometrilerdeki manyetik nanotüplerin
manyetik histerezis özellikleri incelenecektir. İlgili sistemler, model olarak çekirdek-kabuk geometrisinde
anizotropik Heisenberg modeli ile ele alınıp, yöntem olarak etkin alan yaklaşımı ile elde edilen sonuçlar
gözden geçirilecektir. Özellikle çoklu histerezis davranışı gibi farklı davranışlar gözden geçirilecek,
kalıcı manyetizasyon, koersif alan, histerezis döngü alanı gibi karakteristik niceliklerin değişimi için
elde edilen sonuçlar tartışılacaktır.
[1] H. B. Zeng, P. S. Liu, W. P. Cai, S. K. Yang, X. X. Xu, ” Controllable Pt/ZnO porous nanocages with
improved photocatalytic activity”, J. Phys. Chem. C, 49, 19620, (2008).
[2] K. Nielsch, F.J. Castano, C.A. Ross, R. Krishnan, ”Magnetic properties of template-synthesized
cobalt/polymer composite nanotubes”, Journal of Applied Physics 98, 034318, (2005).
[3] S. J. Son, J. Reichel, B. He, M. Schuchman, S. B. Lee, ”Magnetic nanotubes for magnetic-fieldassisted bioseparation, biointeraction, and drug delivery”, J. Am. Chem. Soc., 127, 7316, (2005).
[4] Y. C. Su, R. Skomski, K. D. Sorge, D. J. Sellmyer, ”Nanotube magnetism”, Applied Physics Letters,
84, 1525 (2004).
[5] T. Kaneyoshi, ” Some characteristic properties of initial susceptibility in a Ising nanotube ” Journal
of Magnetism and Magnetic Materials 322, 3014 (2010).
[6] E. Konstantinova, ”Theoretical simulations of magnetic nanotubes using monte carlo method”, Journal of Magnetism and Magnetic Materials, 320, 2721, (2008).
İFG23-6
RASTGELE FERROMANYETİK-ANTİFERROMANYETİK BAĞ DAĞILIMLI İNCE FİLM
SİSTEMLERİN MANYETİK ÖZELLİKLERİ
Musa Atlıhan, Ümit Akıncı
Fizik Bölümü, Dokuz Eylül Üniversitesi, Tınazpete Kampüsü, İzmir Tr-35160, Türkiye
ABSTRACT
Hacimsel malzemelere göre oldukça farklı özellik sergileyen sonlu yapıdaki nano malzemelerden biri
olan ince filmler, bu türden malzemelerin yüzey etkilerinin araştırılması bakımından ideal yapılardır.
Bu çalışmada, farklı tabaka sayılarına sahip ince filmler, yüksek anizotropiye sahip sistemlerin modellenmesinde kullanılan spin-1/2 Heisenberg modeli ile etkin alan yaklaşımı kullanılarak incelendi ve
ferromanyetik-antiferromanyetik etkileşimlerin malzeme yüzeyinde rasgele dağılımlarının etkileri araştırıldı. Malzeme yüzeyinde rasgele dağıtılan ferromanyetik ve antiferromanyetik etkileşimlerin farklı
yüzdeleri için, farklı kalınlıktaki malzemelerin faz diyagramları elde edilerek; bu diyagramlar üzerinde,
literatürde bilinen adıyla özel noktanın değişimi farklı parametreler için elde edildi. Ek olarak yine
özel nokta civarındaki sıcaklık parametreleri için farklı kalınlık ve yüzey dağılımına sahip malzemelerin
sıcaklık-manyetizasyon eğrileri elde edildi.
[1] T. Kaneyoshi, Phys. A 293 (2001) 200.
[2] Ü. Akıncı, Thin Solid Films, 550,602-607 (2014)
İFG23-7
İKİLİ ALAŞIM MANYETİK MALZEMELERİN MANYETİK HİSTEREZİS
KARAKTERİSTİKLERİ
Gülşen Karakoyun, Ümit Akıncı
Fizik Yüksek Lisans, Fen Bilimleri Enstitüsü, Dokuz Eylül Üniversitesi
Fizik Bölümü, Fen Fakültesi, Dokuz Eylül Üniversitesi
ABSTRACT
İkili alaşım manyetik malzemeler teknolojide bir çok uygulama alanına sahiptir. İkili alaşım sistemler;
rasgele manyetik sistemlerin bir alt sınıfını oluşturmakta olup, spin camları, manyetik ve manyetik olmayan iyonların karışımından oluşan rasgele seyreltilmiş sistemler, rasgele manyetik sistemlerin diğer
kesimlerinden birkaçıdır. Yapılan deneysel çalışmalara örnek olarak, rare earth (RE) - 3d geçiş metalleri
(TM) ultraince filmler, Fe-Al alaşımları, Fe-Mn alaşımları gibi Fe,Gd, Tb iyonları için uygun spinli sistemler, ikili çok tabakalı ince filmler, Ni-Au alaşım nanotelleri, Co58.5Ga 41.5 alaşımları, Mn merkezli
ikili alaşım filmleri, MnxGa epitaksiyal ultraince filmler gibi çok geniş bir spektrumdaki çalışmalar verilebilir.
İkili alaşım manyetik malzemeleri Ising modeli dahilinde farklı yöntemler ile çözülerek kritik özellikleri
belirlenmiştir. Ortalama alan yaklaşımı [1], etkin alan yaklaşımı [2], Monte Carlo yöntemi[3], BethePeierls yaklaşımı[4] bu yöntemler arasındadır.
Bu malzemelerin kritik ve manyetik özellikleri literatürde yaygın bir şekilde çalışılmış olsa da histerezis
karakteristiklerini konu alan çalışmalar henüz yaygın bir şekilde gerçekleştirilmemiştir. Bu konuşmanın
içeriği spin-1/2 spin-1 ikili alaşım Ising modeli ile modellenebilen malzemelerin histeresis karakteristiklerine dair, etkin alan yaklaşımı ile elde edilen çözümlerdir. Özellikle histerezis döngü alanı, koersif
alan, kalıcı manyetizasyon gibi niceliklerin sistem parametreleri ile değişimi incelenmiş, ikili histerezis
gibi ilginç davranışlar gözlenmiştir.
[1] M.F. Thorpe and A.R. McGurn, Phys. Rev. B 20 (1979) 2142.
[2] T. Kaneyoshi, Phys. Rev. B 34 (1986) 7866.
[3] P.D. Scholten, Phys. Rev. B 32 (1985) 345.
[4] S. Katsura, Can. J. Phys. 52 (1974) 120.
İFG23-8
ARTIFICIAL MAGNETISM IN A CARBON DIAMOND NANOLATTICE WITH THE SPIN
ORIENTATION EFFECT
Numan Şarlı
Institute of Science, Erciyes University, 38039 Kayseri, Turkey
ABSTRACT
In this paper, we investigate the spin orientation effects on the magnetic properties of the Carbon diamond nanolattice (CDNL) by using Kaneyoshi approach (KA) within the effective field theory. In our
calculations, we use the normalized lattice constant (na = 3.566 = a/1 A0) which is obtained from the real
lattice constant (a = 3.566 A0) of the CDNL. The CDNL has three different magnetic atoms according
to nearest-neighbor, and they are defined as corner atoms (mc), face atoms (mf) and inner atoms (mi).
For mc, mf and mi, the CDNL has eight spin orientations as +++, -++, ++-, -+-, –+, —, +– and +-+, respectively. We find that the CDNL has two kinds of critical temperature behaviors, we call themas high
critical temperature behavior (HCTB) for the first four spin orientations and lowcritical temperature behavior (LCTB) for the second four spin orientations. However, the CDNL exhibits ferromagnetic (FM),
antiferromagnetic (AFM), superconductivity (SC), discontinuous diamagnetic (DM) and discontinuous
paramagnetic (PM) hysteresis behaviors according to the spin orientation of its atoms. Therefore, we
suggest that it is possible to obtain different magnetic behaviors and artificial magnetism from the Carbon and Carbon-based materials with the spin orientations of their atoms [1].
Our results published in journal of Diamond & Related Materials [1].
[1] N. Şarlı, “Artificial magnetism in a carbon diamond nanolattice with the spin orientation effect”,
Diamond & Related Materials, 64, (2016), 103–109.
İFG23-9
CELL CYCLE BASED GENE REGULATION DYNAMICS OF AN EUKARYOTE MODEL
ORGANISM
Emir Haliki, Nadide Kazancı, Nurşen Keskin
Physics Department, Ege University Faculty of Science
ABSTRACT
Inference of gene regulation and their regulatory networks are one of the most challenging research
problems of computational biophysics and complexity. Gene regulation is formed by indirect interaction
of DNA segments, which are protein- coding genes, for configuring the expression level of one another.
The expression of most genes in eukaryotes are regulated predominantly on the transcriptional level.
This work contains the aspect of gene regulatory dynamics within the cell cycle network of the eukaryote model organism called S. Cerevisiae (budding yeast). A Boolean network is used to model the time
evolution of the expression level of genes taking part in the gene regulation. Simulation shows the global
attractor of a more detailed cell cycle dynamics of the budding yeast. Biological pathway of the cell
cycle and mutational robustness are investigated. Computations made by the gene regulatory network of
the budding yeast are compared to random networks.
[1] Zenkin, N., Yuzenkova, Y. and Severinov, K., 2006, Transcript-assisted transcriptional proofreading,
Science, 313:518-520pp.
[2] Lahdesmaki, H., Shmulevich, I. and Ylı-Harja, O., On learning gene regulatory networks under the
boolean network model, Machine Learning, 52:147-167pp.
[3] Garg, A., Cara, A., Xenarios, I., Mendoza, L. and Micheli, G., 2008, Synchronous versus asynchronous modeling of gene regulatory networks, Bioinformatics, 24:1917-1925pp.
[4] Hidde, J., 2002, Modeling and simulation of genetic regulatory systems: a literature review, Journal
of Computational Biology, 9:67-103pp.
[5] Li, F., Long, T., Lu, Y., Ouyang, Qi. and Tang, C., 2004, The yeast cell-cycle network is robustly
designed, Proceedings of the National Academy of Sciences, 101:4781-4786pp.
[6] Watson, J. D., Baker, T. A., Bell, S. P., Gann, A., Levine, M. and Losick R., 2004, Molecular Biology
of the Gene, Pearson, New Jersey, 244p.
[7] Pauleau, A.-L. and Erhardt, S., 2011, Centromere regulation: New players, new rules, new questions,
European Journal of Cell Biology, 90:805-810.
[8] Alarcon, T. and Jensen, H. J., 2010, From gene regulatory networks to population dynamics: robustness, diversity and their role in progression to cancer, Arxiv:1003.2366.
[9] Krumsiek, J., Marr, C., Schroeder, T. and Theis, F. J., 2011, Hierarchical differentiation of myeloid
progenitors is encoded in the transcription factor network, PloS One, 6(8): e22649.
[10] Davidich, M. I. and Bornholdt, S., 2008, Boolean network model predicts cell cycle sequence of
fission yeast, PLoS One, 3(2): e1672.
[11] Lopes, F. M., Ray, S. S., Hashimoto, R. F. and Cesar, R. M., 2014, Entropic biological score: a cell
cycle investigation for GRNs inference, Gene, 541:129-137pp.
[12] Weaver, W., 1991, Science and Complexity, Facets of System Science, Springer-Verlag US, 449p.
[13] Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., Ploegh, H. and Matsudaria, P., 2008, Molecular Cell Biology, W. H. Freeman and Company, New York, 323p.
İFG23-10
[14] Wagner, A., 1994, Evolution of gene networks by gene duplications: a mathematical model and its
implications on genome organization, Proceedings of the National Academy of Sciences, 91:4387-4391
pp.
[15] Wagner, A., 2007, Robustness and Evolvability in Living Systems, Princeton University Press, New
Jersey, 91p.
[16] Bell, W. B. and Losick, G. L., 2004, Molecular Biology of the Genes, Pearson, 5th edition.
[17] Soto, C. E., Martin, O. C. and Wagner, A., 2011, Phenotypic Plasticity can Facilitate Adaptive
Evolution in Gene Regulatory Circuits, Evolutionary Biology, 11(5).
[18] Mayr, E., 1982, The Growth of Biological Thought, Harvard University Press.
İFG23-11
WHERE AGENTS SEEK DIVERSITY, THE SOCIETY BECOMES MORE COHESIVE
Burcu Güneş, Dicle Yağmur Özdemir, and Ali Rana Atılgan
Faculty of Natural Science and Engineering, Sabancı University, Istanbul
ABSTRACT
We assume that there is a population of individuals, whom we refer to as agents. In this work, each
agent is colored green or red. We think of the two types as representing some immutable characteristic,
for example, race or ethnicity. The agents are located in the cells of a lattice (and in general a complex
network), intended as a toy model to focus on the interactions between agents. The neighbors of a cell
on the lattice are those that touch it, including the diagonal contacts; thus, a cell has eight neighbors.
Each agent desires to have at least some other agents of its type as neighbors. Black cells denote empty
locations where unfulfilled agents may move.
Schelling assumed that there is a threshold t common to all agents: if an agent discovers that less than t
of its neighbors are of the same type as itself, then it has an interest in moving to a new cell [1]. First,
each agent moves to a cell where they will be satisfied. This may cause other agents to become unsatisfied; then, the second round of movements begins. After a finite number of rounds, representing a fixed
time period during which unsatisfied agents have changed where they live, we do not find any agent
who is unhappy. We then analyze what type of patterns emerge in the “equilibrated” community. For
very low values of the threshold t, for instance, t = 1, or 2, segragated patterns are not easily observed.
However, a t takes relatively higher values, for instance t = 3, we start observing islands of similar colors.
In figures 1(a) and 1(b), both the green and the red respondents feel satisfied if they live in a neighborhood where at least 25 and 35%, respectively, of the neighborhood population are like-colored. This
simple model of Schelling illustrates how the forces leading to segregation (phase separation) are remarkably robust. Even if people only have a mild preference for living with neighbors of the same color,
a significant level of segregation may occur.
Inspired from the fact that some respondents want to live in mixed neighborhoods rather than where
there are mostly populated by the same color, we included in the model an upper bound of like-colored
agents for each agent’s satisfaction function. In our model, therefore, the agents are not only tolerant to
opposite colors, but deliberately seek diversity. A real life counterpart of this diversity desire is that in
multiethnic communities where the agents reportedly said that they want their children to learn to get
along with others.
Figures 1(c) and (d) are the outcomes when both the green and the red respondents demand at least 5%
of their neighbors are opposite-colored. In other words, in Figure 1(c), the agents are happy only if their
like-colored neighborhood population is between 25% and 95%; similarly, in Figure 1(d) the agents are
happy if their like-colored neighborhood population is between 35% and 95%. It is observed that the segregation patterns in Figures 1(c) and (d) are neither topologically nor geometrically equivalent to those
in Figures 1(a) and (b). The segregated pattern of Figure 1(b) is converted to a more integrated mold in
Figure 1(d), wherein, the arrangement of empty regions displays a different phase. The importance of
these empty islands is discussed in detail since they may be interpreted as common social or public place
İFG23-12
for different groups.
In our work, we also introduce several measures to quantify different patterns emerging from both tolerant and diversity seeking agents. The conventional segregation measures cannot appreciate the differences, for instance, between the communities Figures 2(a) and (b). In Figure 2(a) both respondents
feel satisfied if they live in a place where at least 25% of the neighborhood population is like-colored.
In Figure 2(b), on the other hand, the agents are happy if their like-colored neighborhood population is
between 30% and 95%. In our work, we have defined new segregation indices that take into account
neighborhood distribution functions that represent well the distinction between the segregated and integrated regions that appear due to variety of happiness (utility) functions.
[1] Schelling, T., “Dynamic models of segregation,” Journal of Mathematical Sociology, Vol. 1, 1971,
pp. 143 – 186.
Figure 1: Simulation outcomes of networks with lower bounds 25% (a), 35% (b) and with lower and upper bounds 25% - 95% (c) and
35%-95% (d), respectively.
Figure 2: Two different networks which have same segregation indices with 25% lower bound (a) and %30 - %95 lower – upper bound (b)
İFG23-13
CONTROLLING AND IMAGING THE DYNAMICS OF COMPLEX NEURAL NETWORKS
Aşkın Kocabaş
Koç University, Istanbul, Turkey
ABSTRACT
The brain is the most complex organ in nature. Remarkably, the massive number of interactions between
its component neurons can orchestrate complex internal dynamics to generate precise and robust behavioral outputs. Understanding the detailed network dynamics leading specific behaviors is a challenging
task even in the simplest nervous system of nematode Caenorhabditis elegans (C. elegans), which has
only 302 neurons interconnected through 7000 synapses. To approach this challenge we asked whether
we could control the dynamics of neural network well enough to be able to evoke specific behaviors. To
make this approach possible, we combined optogenetics and novel imaging systems that could visualize,
identify and specifically illuminate the neuron(s) of interest to drive any pattern of electrical activity in
the nervous system of freely moving C. elegans. In this talk, I will start by describing the challenges and
our achievements to control neural activity patterns to evoke complex behaviors in virtual environments.
Next, I will describe our recent complementary tools and techniques for whole-brain imaging of neural
activity patterns in a freely moving C. elegans. Finally, I will argue that combination of these control and
imaging-based approaches will provide powerful avenues for studying the complex dynamics of entire
nervous systems.
İFG23-14
SEVERELY CONTRACTED CONFIGURATION SPACE AND Q-STATISTICS IN RANK
DISTRIBUTIONS
G. Çiğdem Yalçın
Istanbul University, Faculty of Science, Department of Physics, Vezneciler, Istanbul, 34134, Turkey
[email protected]
ABSTRACT
In this talk we shall focus on a theoretical framework with dual nonstandard entropy expressions that
apply naturally to statistical-mechanical systems that experience an exceptional contraction of their configuration space. We also present a working explanation for the existing duality between two Tsallis-type
entropy expressions that generalize the canonical expression in the study of ranked data. One expression
relates to the rank distribution’s power-law exponent whereas the other ensures entropy extensivity. We
argue that phase-space contraction is farthest for ranked data of the Zipf type, for which we provide a
solid bridge between experimental data and theory [1,2].
[1] G.Cigdem Yalcin, Alberto Robledo, Murray Gell-Mann (2014) “Incidence of q-statistics in rank distributions”, Proc.Natl.Acad.Sci. USA 111(39): 14082-14087.
[2] G.Cigdem Yalcin, Carlos Velarde, Alberto Robledo (2015) “Entropies for severely contracted configuration space” to be published in Heliyon (Elsevier).
İFG23-15
PROBABILITY DISTRIBUTIONS AND SCALING RELATIONS FOR LOW DIMENSIONAL
DYNAMICAL SYSTEMS IN THE VICINITY OF CHAOS
Özgür Afşar
Department of Physics, Faculty of Science, Ege University, 35100 Izmir - Turkey
ABSTRACT
The standard central limit theorem (CLT) asserts that, under appropriate conditions, the probability density of the sum of large number of independent identically distributed (iid) random variables will be
approximately Gaussian. When the dynamical system is strongly mixing i.e., ergodic, standard CLT
is expected to be valid, but at the edge of chaos where iterates have strong correlations, the standard
CLT is not valid anymore. We investigate the probability density of rescaled sum of iterates of low
dimensional systems within periodic and quasi-periodic route to chaos. We numerically verify that the
probability density appears to converge to a q-Gaussian as the chaos threshold which corresponds to a
transition point between different dynamical regimes is approached. It is also well-known that dynamical systems which go to chaos via period doublings show an equivalent behavior during their transitions
between different dynamical regimes that can be expressed by a critical exponent which comes from
the well known Universal Huberman-Rudnick scaling law. This universal law is well studied, e.g., with
respect to the Lyapunov exponents. Here, we show the relations among size of the q-Gaussians, correlation length, Lyapunov exponent, fractal dimension by numerically studying their scaling behavior as
the chaos threshold is approached. Moreover, we find out the scaling behavior of the measures coming
from a popular tool to investigate the regime transitions in dynamical systems, which is called recurrence
quantification analysis.
İFG23-16
CONTROLLING ENTROPIC UNCERTAINTY BOUND THROUGH MEMORY EFFECTS
Göktuğ Karpat
Universidade Estadual Paulista, São Paulo, Brazil
ABSTRACT
One of the defining traits of quantum mechanics is the uncertainty principle which was originally expressed in terms of the standard deviation of two observables. Alternatively, it can be formulated using
entropic measures, and can also be generalized by including a memory particle that is entangled with
the particle to be measured. Here we consider a realistic scenario where the memory particle is an open
system interacting with an external environment. We provide a link between memory effects and the
rate of change of conditional entropy controlling the lower bound of the entropic uncertainty relation.
Our treatment reveals that the memory effects stemming from the non-Markovian nature of quantum
dynamical maps directly control the lower bound of the entropic uncertainty relation in a general way,
independently of the specific type of interaction between the memory particle and its environment.
İFG23-17
STRUCTURAL-BASED PREDICTION OF NOVEL LINEAR B-CELL EPITOPES IN
PICORNAVIRUSES
Caroline Ross, Özlem Tastan Bishop, Canan Atilgan, Caroline Knox
Sabancı Üniversitesi, İstanbul
ABSTRACT
The Picornaviridae family includes numerous human and animal pathogens of economic and clinical
importance. At present no antiviral treatment against picornavirus infections has been developed and the
application of effective vaccines has only been susscessful for certain viruses. The recent emergence of
novel picornaviruses associated with gastrointestinal, neurological and respiratory diseases in humans
increases the incentive to develop vaccines which protect against such infections. The understanding
of virus antigenicity and the identifcation of epitopes which are conserved across multiple serotypes is
fundamental to the development of improved vaccines that may be more cross-reactive. Picornavirus
capsids are icosaherdal, comprising of 60 protomer structures which assemble through the interaction of
3 subunit proteins VP0, VP1 and VP3. The subsequent cleavage of VP0 reveals a mature virion with
external proteins VP1-VP3, and VP4 residing on the internal side of the capsid. Although it has been
hypothesized that the early steps of capsid assembly are dependent on the interactions with host cellular
proteins, the mechanism remains poorly understand. The VP1 protein is the most external and has been
reported as the major antigenic determinant. However neutralisation sites have also been identified in the
VP2 and VP3 proteins of numerous picornaviruses. Furthermore neutralisation sites within internal VP1
regions which are exposed during capsid breathing have been reported in Poliovirus and Parechovirus.
This study investigates the conservation of motifs which match predicted and experimentally determined
epitopes across the Picornaviridae family. A comprehensive motif discovery was performed across all
available VP1-VP3 protein sequences. A total of 22 cystral structures of various picornavirus species
were analysed in-silico for the structural-based prediction of linear B-cell epitopes. For comparison
to known neutralisation sites the predicted epitopes were matched against the peptide sequences corresponding to over 600 experiementally determined picornavirus epitopes. Subseqeuntly all predicted and
experimental epitope peptides were scanned for the presense of the motifs discovered in this study. We
respectively identified a total of 29, 13 and 23 motifs in the VP1, VP2 and VP3 proteins that matched
known experimental epitopes. The motifs were differentially conserved across serotypes of indivudal
viral species. We also characterise 17 VP1, 6 VP2 and 8 VP3 motifs which correspond to peptides of
novel epitope predictions. The surface exposure of these regions were determined through structural
mapping and visualisation, combined with normal mode analysis to examine exposure during capsid
breathing. The epitope motifs were also comparatively anlaysed to elucidate the conservation of individual residues according to viral species. The results presented in this study may be imperative for furture
research towards improved vaccine development. Moreover, the predictions of novel epitopes may serve
as guidelines for the generation of antibodies to further investigate the role of host-pathogen interactions
during the viral assembly and replication processes.
İFG23-18
CENTRALITY AND PATH LENGTH OF RESIDUES AND ALTERATIONS IN THEIR
COMMUNICATION NETWORK EXPLAIN THE MUTATIONS IN DHFR
T.F. Güçlü, C. Atılgan, and A. R. Atılgan
Molecular Biology, Genetics And Bioengineering, Sabanci University, İstanbul, Turkey
[email protected]
ABSTRACT
Antibiotic resistance is a significant challenge that threats humanity by leading to incurable infections.
The bacterial enzyme dihydrofolate reductase [1] (DHFR, pdb id: 1rx2) is an important model system
widely used to explain the origins of this problem. To investigate the effect of point mutations on the
communication within the residue network of DHFR, we have performed alanine mutation scan [2]. The
scheme is based on mutating each amino acid to alanine then minimizing the structure in water at physiological ionic strength. Our analysis of residue networks assigns a node per residue and treats it as a
graph [3], [4]. We focus on the changes in the shortest path length of residues (∆L) and betweenness
centrality (∆BC) of mutated nodes with respect to the wild-type averaged over all the mutations. We
relate the ∆L and ∆BC to conservation scores for DHFRs within the bacterial families as well as overall
known DHFRs. This method explains the evolutionary importance and the dynamical significance of
resistance invoking point mutations, particularly at positions P21, D26, L28, W30, I94 and F153 [5].
[1] C. T. Liu, P. Hanoian, J. B. French, T. H. Pringle, S. Hammes-Schiffer, and S. J. Benkovic, “Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans.,”
Proc. Natl. Acad. Sci. U. S. A., vol. 110, no. 25, pp. 10159–64, 2013.
[2] G. Ozbaykal, A. Rana Atilgan, and C. Atilgan, “In silico mutational studies of Hsp70 disclose sites
with distinct functional attributes,” Proteins Struct. Funct. Bioinforma., vol. 83, no. 11, pp. 2077–2090,
2015.
[3] A. R. Atilgan, P. Akan, and C. Baysal, “Small-World Communication of Residues and Significance
for Protein Dynamics,” vol. 86, no. January, pp. 85–91, 2004.
[4] A. R. Atilgan, D. Turgut, and C. Atilgan, “Screened Nonbonded Interactions in Native Proteins Manipulate Optimal Paths for Robust Residue Communication,” Biophys. J., vol. 92, no. 9, pp. 3052–3062,
2007.
[5] E. Toprak, A. Veres, J. Michel, R. Chait, D. L. Hartl, and R. Kishony, “Evolutionary paths to antibiotic
resistance under dynamically sustained drug selection,” Nat. Genet., vol. 44, no. 1, pp. 101–105, 2011.
İFG23-19
ÇOK-CİSİM YAKLAŞIMIYLA YATAY MANYETİK ALAN ALTINDA PARÇACIKLARIN
DAVRANIŞI
Erol Kurt1 , Bekir Dursun2 , H. Hilal Kurt3
1 Elektrik
2 Elektrik
Elektronik Mühendisliği Bölümü, Teknoloji Fakültesi, Gazi Üniversitesi, Ankara
ve Enerji Bölümü, Edirne Teknik Bilimler Meslek Yüksekokulu, Trakya Üniversitesi, Edirne
3 Fizik Bölümü, Fen Fakültesi, Gazi Üniversitesi, TR-06500, Teknikokullar, Ankara
ABSTRACT
Durağan Elektrostatik Hapsetme (DEH) cihazı deneysel füzyon çalışmaları için kullanılan bir cihazdır
[1,2]. Bu cihaz füzyon enerjisi yanında, kararlı x-ışını oluşturma, nötron litografi, materyal işleme
ve tahribatsız muayene gibi pek çok amaçla kullanılmaktadır [3,4,5]. Bu çalışmada, silindirik geometriye sahip bir DEH cihazı modellenerek, cihazın içersine düşük basınç altında tamamen iyonize
olmuş Döteryum gazı konulmuş; cihazın merkezinde yer alan katot çubuklarla cihazın dış yüzeyini
oluşturan metal duvar arasına negatif elektrostatik potansiyel uygulanmıştır (Figure 1). İlaveten yenilikçi
yön olarak, yatay yönde homojen manyetik bir etki de eklenmiştir. Cihaz hacminde etkileşen iyonlar ve
elektronlar için Coulomb kuvveti tanımlanmış, görüntü yük metoduyla sınır koşulları sağlanmış ve çok
cisim problemi ilk kez bir DEH sistemi için zamana bağlı olarak çözülmüştür. İyon ve elektronların
etkileşimleri incelendiğinde kütle farkından dolayı iyonların daha rijit hareket ettiği gözlenmiş, hem
elektronların, hem de iyonların konum ve hızlarında çeşitli düzensiz titreşimlerin varlığı tespit edilmiştir.
Faz uzayında gerçekleştirilen istatistiksel analizlerle 6 µs’de iyon sıcaklığının Ti= 7 keV mertebelerine
ulaştığı tespit edilmiştir. Hız dağılımlarından, parçacıkların büyük oranda 5x105 m/s’lik hızlarla hareket
ettiği, yüksek enerjili parçacıkların da ortamda bulunduğu tespit edilmiştir.
Figure 1: DEH ünitesi (solda) ve yatay düzlemde elektronların hareketi (sağda).
[1] B. Dursun, E. Kurt, “Many-body solution to the D2 gas filled inertial electrostatic confinement device”, Int. J. Hydrogen Energy, doi:10.1016/j.ijhydene.2015.12.135, (2016).
[2] E. Kurt, B. Dursun, “Particle Trajectories and Energy Distribution from a New IEC Fusion Device:
A Many-Body Approach”, J. Fusion Energy, 10.1007/s10894-015-0033-2,(2016).
[3] E. Kurt, “A stationary multi-component cathode modeling and ion trajectories for an inertial electrostatic confinement fusion device”, Int. J. Energy Res. 35, 89–95 (2011).
[4] Y. Akgun, A.S. Bolukdemir, A. Alacakir, “Preliminary results of experimental studies from low
pressure inertial electrostatic confinement device”, J. Fusion Energy, 32(5), 561–565 (2013).
İFG23-20
[5] T.A. Thorson, R.D. Durst, R.J. Fonck, L.P. Wainwright, “Convergence, electrostatic potential, and
density measurements in a spherically convergent ion focus”, Phys. Plasmas 4, 4–15 (1997).
İFG23-21
GROWTH OF BI-METALLIC NANO-PARTICLES
Efe İlker1 , Mine Konuk2,∗ , Mine Gökçen3 and Sondan Durukanoğlu4,5
1 Faculty
of Engineering and Natural Sciences,Sabancı University, Tuzla 34950 Istanbul, Turkey
2 Department of Physics, Istanbul Technical University, Istanbul, Turkey
3 Robert College, Arnavutköy 34345 Istanbul, Turkey
4 Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla 34950 Istanbul, Turkey
5 Nanotechnology Research and Application Center, Sabancı University, Tuzla 34950 Istanbul, Turkey
ABSTRACT
Controlling growth of metallic nano-structures has attracted considerable attention as these materials exhibit remarkable size and shape dependent properties that are relevant to many industrially and
technologically important phenomena such as catalysis, chemical reactivity, selectivity, and stability.
Clearly, morphology and structure at nano-scale play a crucial role in determining the behaviour of
nano-materials. To utilize such minuscule particles, with specific morphology and architecture requires
precise control of the growth and structure at the atomic scale. Recent developments in shape-controlled
synthesis of metallic nano-particles present a promising path for such precise tuning of the growth conditions. Although in recent studies of shape-controlled synthesis of metal nano-particles, surface diffusion
of atoms at the facets of a growing seed is also found to be critical in determining the growth front of
the seed thus controlling the final morphology of the end products. Identifying atomistic details involved
in a typical crystal growth process is not easy, in particular when the crystal growth occurs in solution.
Atomistic simulations, on the other hand, are real alternative to examine the structure and dynamics of
growing particles at the atomic scale and thereby specify the important individual atomistic processes
taking place in the course. Through extensive energetic and molecular dynamic calculations on Cu
and Ni nano-particles we successfully determined the growth modes, identified the individual atomistic
mechanisms and corresponding energetics that influence the morphological evolution of growing particles. In this talk, we will not only explain homogenous and heterogenous growth modes of Cu and Ni
systems at atomistic scale, but also provide a quantitative atomistic view of how exactly growth characteristics change when bi-metallic growth is carried out.
∗ Current
Address: UNAM-National Nanotechnology Research Center, Bilkent University, Ankara
06800, Turkey
İFG23-22
LOOSE-KNIT COMMUNITIES DISSEMINATE INFORMATION EXTENSIVELY, BUT
CANNOT ACT COLLECTIVELY AS WELL
Murat Mustafa Tunç, Dicle Yağmur Özdemir, and Ali Rana Atılgan
Faculty of Natural Science and Engineering, Sabancı University, Istanbul
ABSTRACT
A collective action problem is where an activity produces benefits only if enough people participate.
In the lattices shown in Figure1 (a) and (b), each agent has four neighbors. Here “x”s are not willing to
attend an activity; “o”s are willing only if half of their friends do. There are (almost) equal number of
“x”s and “o”s in the figures.
First, in Figure 1(a) a single “o” (colored yellow) informs her neighbors to initiate the information
cascade. Sometime later, through diffusion, all are informed (colored green, in Figure 1b). Starting
from the boundaries, each “o” decides depending on the attitude of the majority of her friends. The red
“o”s cannot attend because not enough number of their friends participates to the activity. Finally (blues,
Figure 2a) only a few participate. A simple switch in the position of an “x” and “o” increases remarkably
the collective attendees (blues, Figure 2b).
In our work, the collective behavior has been thoroughly analyzed in different networks, including smallworld and power-law networks, by studying various initial and boundary conditions.
Figure 1: Initial propagator and the diffusion of information
İFG23-23
Figure 2: The set of collective attendees in two different, but almost identical, initial conditions
İFG23-24
REPRESENTING POTENTIAL ENERGY SURFACE OF LI-SI ALLOYS WITH ARTIFICIAL
NEURAL NETWORKS
Berk Onat, Ekin Doğuş Çubuk, Efthimios Kaxiras
Department of Physics and School of Engineering and Applied Sciences, Harvard University
ABSTRACT
There is an increasing demand to model the structural evolution of Li containing Si anodes, because
theoretically silicon absorbs high concentrations of lithium compared with graphite, which is the common anode material of Li-ion batteries (LIB). Investigation of the lithiation and delithiation of Si anode
using realistic simulations is important for designing new LIBs and requires large numbers of atoms
and long time scales, which is generally inaccessible with first-principle approaches. These simulations
can be carried out using interatomic potentials that can capture the dependence of structure on chemical
composition. Compared with the fixed functional form of empirical potentials, a promising approach
to construct the potential energy surface is using artificial neural networks (ANN) that extends the time
scales of simulations without sacrificing the accuracy. Using density functional theory data for training,
we develop an ANN potential for Li-Si alloys. Our calculations indicate that ANN potential has a high
accuracy for the predictions of total energies and structures at different concentrations of Li-Si alloys.
Based on molecular dynamics simulations with ANN potential, we also show that estimated diffusion
coefficients of Li and Si in Li-Si alloys are in very good agreement with the experimental findings.
This work was supported in part by TUBITAK under post-doctoral research grant no 2219. Berk ONAT’s
current address is UNAM-Bilkent University, Ankara, 06800.
İFG23-25
MOLECULAR MOTION ON METAL SURFACES: ATOMISTIC APPROACH
Melihat Madran, Alimet Özen, Zehra Akdeniz, Sondan Durukanoğlu
Sabanci University, Istanbul, Turkey
Piri Reis University, Istanbul Turkey
ABSTRACT
Today, molecular nanotechnology has reached such a level of sophistication that it seems possible to design and build artificial molecular machines like rotors, wheels, and motors. With the enhanced atomic
scale techniques in imaging and controlling, there is a remarkable increase in experimental studies devoted to manipulation of molecules on the surfaces. However, controlled-manipulation of molecules
and understanding the underlying molecular mechanisms in the process require atomic scale electronic
structure calculations, potential energy surface scanning and molecular dynamics calculations. Such
complementary calculations help not only fulfill the need in the area but also make significant contribution to the improvement of molecular nanotechnology.
In this talk, we will discuss results of various atomic-scale computational calculations for investigating
the observed translational and rotational motion of molecules, ranging from small ones like C2H2 to
large ones involving many atoms and varying functional groups like C44H24, on metal surfaces in great
detail.
İFG23-26
SYNTHESIS OF ONE- DIMENSIONAL NANOSTRUCTURES FOR PHOTOVOLTAIC
APPLICATIONS
Elif Peksu
İTÜ Fizik Mühendisliği Bölümü
ABSTRACT
In this study, silicon nanowires (NWs) were synthesized by a simple and cost-effective technique, electroless etching, using an n-type Si (100) wafer. In addition, Hydrothermal technique were employed
for the synthesis of well-aligned dense arrays of ZnO nanowires (NWs) on a wide range of substrates
including silicon, soda-lime glass (SLG), indium tin oxide (ITO) and polyethylene terephalate (PET).
Results showed that ZnO NWs can be successfully grown on any substrate that can withstand the growth
temperature ( 90oC) and precursor solution chemicals. Results also revealed that there was a strong impact of growth parameters on the orientation, density, diameter and uniformity of synthesized nanowires.
As a device application of synthesized ZnO and Si nanowires a third generation nanowire/chalcopyrite
thin film based solar cell was constructed, device characterization of which will be discussed in detail.
İFG23-27
THE PRICE OF INFORMATION:
THERMODYNAMICS AND THE LIMITS OF SIGNALING IN LIVING SYSTEMS
Michael Hinczewski
Case Western Reserve University, Cleveland, Ohio, USA
ABSTRACT
Biological cells have an elaborate machinery for probing their external environment. They gather information about the many small molecules diffusing around them, whether nutrients, or hormones, or
toxic agents. This information is conveyed from receptors on the surface of the cell to the interior by a
multitude of protein enzymes, catalyzing reactions that add or remove chemical tags from other proteins.
These tags are the basic units of biological signaling, analogous to the zeros and ones in which a digital
message is encoded in engineered communication systems. But biological circuits are extremely errorprone, distorting the signal through the stochastic nature of protein interactions under constant thermal
agitation. So the cell expends enormous amounts of energy on error-correction mechanisms, maintaining the fidelity of the signal. My talk shows how we can understand this energy consumption through
the language of thermodynamics, building on recent advances in nonequilibrium statistical physics and
information theory. Cellular signaling networks essentially act as “information engines”, converting energy from chemical potential reservoirs into useful “work” in the form of accurate information transfer.
And just like the second law of thermodynamics constrains the efficiency of mechanical engines, analogous relationships hold for biochemical signaling, putting bounds on the minimum error that can be
achieved. We look at the tradeoffs between efficiency and power, and the necessity of these biological
circuits operating in a highly dissipative, nonequilibrium regime.
İFG23-28
POLARIZED DIPOLAR FERMIONS IN A TWO-DIMENSIONAL HARMONIC TRAP
Hande Toffoli
Middle East Technical University, Ankara, Turkey
ABSTRACT
Since its proposition in 1964 by Hohenberg and Kohn, density functional theory has seen a tremendous
amount of development both in terms of its theoretical foundations and with recent advances in computational resources also in practical applications. The method, shifting the focus from a wavefunction-based
description of the many-particle problem to the particle density, has provided a much more affordable
treatment of numerous physical systems. A search in ISI Web of Knowledge reveals some 38000 publications on density functional theory between the years of 2005 and 2010.
Traditionally utilized heavily for atomistic problems such as those in quantum chemistry and solid state
physics, other many-particle applications in physics have recently been tackled with density functional
theory, uncovering new insight that has been absent in models previously developed.
In this talk, I will first give a brief description of the density functional theory and its foundations. I
will then present results from our recent study on the behavior of polarized dipolar fermions in a twodimensional harmonic trap in the framework of the density functional theory (DFT) formalism using the
local density approximation. In this work, we treat only a few particles interacting moderately. I will
present important results deduced concerning key characteristics of the system such as total energy and
particle density.
İFG23-29
NMR SUPPORTED STRUCTURAL BIOLOGY:
WITH A FOCUS ON FUNCTIONAL AMYLOIDS FROM BACTERIAL BIOFILMS
Ümit Akbey
Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus
Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus
[email protected]
ABSTRACT
Structural biology relies on established techniques like X-ray crystallography, electron microscopy, solution NMR, and ssNMR spectroscopy. ssNMR is a powerful technique for studying structure and
dynamics of large, non-crystalline, heterogeneous or insoluble biological systems. It does not require
long-range order and it does not have an intrinsic size limitation. Moreover, solid and solution NMR
can deliver valuable dynamics information in a site-specific manner at atomic resolution over a large
timescale.
My primary goal is to determine the atomic-resolution structures of biofilm forming functional fibrils
from Gram positive and negative bacteria, by using advanced ssNMR. Starting from these structural
insights, I aim to understand fibril formation in function and disease, the role of amyloids in biofilms,
ways of controlling or preventing biofilm formation in the associated chronic diseases, and finally, the
structural switch of proteins between soluble, oligomeric and fibrillar states. Moreover, the interactions
of major-biofilm forming fibrils will be studied with their minor partners (in the context of protein - protein interactions), polysaccharides or DNA; the molecular details of potential chaperone-aided control
of fibril formation will be investigated by studying the effect of the ClpC chaperone on isotope labeled
TasA for B. subtilis. As a novel method, with the recent development in the filed of ssNMR, it is now
possible to study functional amyloids in their complex, native and insoluble bacterial biofilms, without
the need of purification, even at their live conditions via ”In-vivo structural biology”. Preliminary results
will be shown on several protein systems from different bacteria.
İFG23-30
SOLVATION-DEPENDENT LATENCY OF PHOTOACID DISSOCIATION AND TRANSIENT
IR SIGNATURES OF PROTONATION DYNAMICS
Gül Bekçioğlu-Neffa,b , Felix Hoffmannb , and Daniel Sebastianib
a Physics
Department, Freie Universitaet Berlin, Arnimallee 14, 14195 Berlin, Germany,
b Institut für Chemie, Martin-Luther-Universitaet Halle-Wittenberg,
Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
ABSTRACT
Aqueous physical chemistry is strongly influenced by ability of water to form extended network of hydrogen bonds. It is the fluctuations and rearrangements of the network that stabilize reaction products and
drive the transport of proton through a hydrogen bonded chain. In this regard, photosensitive acid/base
systems provide a method to control and study ultrafast proton transport via infrared spectroscopy. [1,2]
Since their acidity can be controlled in a very defined manner they are important model system for the
investigation of proton transport in aqueous media. However, many details of the proton transfer from
the photoacid to water remain elusive, for example, the structure and stability of the contact ion pair
between the photoacid and the hydrated proton, in particular re- garding the hydrogen bonding network
around a solvated photosensitive probe molecule. A particular drastic drop in pKa value is exhibited
by the super photoacid N-methyl-6-hydroxyquinolinium (HMQ). [3]
Here, we present a microscopic study of the role water plays in mediating excited state proton transfer of HMQ in aqueous solution. The central question addressed here is the determination of elementary
steps that lead to a full dissociation of the proton and the corresponding photoacid an- ion. These steps
occur in the time range of a few picoseconds depending on the conformation of the solute and the surrounding solvent molecules. In this regard, we computed IR spectra from Wannier center calculations to
elucidate spectroscopic fingerprints of specific intermediates during the acid dissociation. [3]
[1] G. Bekçioğlu, C. Allolio, M. Ekimova, E. T. J. Nibbering, and D. Sebastiani, Phys. Chem. Chem.
Phys., (2014), 16, 13047–13051.
[2] G. Bekçioğlu, C. Allolio, and D. Sebastiani, J. Phys. Chem. B, (2015), 119, 4053-4060.
[3] G. Bekçioğlu, F. Hoffmann, and D. Sebastiani, J. Phys. Chem. A, (2015) , 119, 9244-9251.
İFG23-31
STEPWISE POSITIONAL-ORIENTATIONAL ORDER AND THE
MULTICRITICAL-MULTISTRUCTURAL GLOBAL PHASE DIAGRAM OF THE S=3/2
ISING MODEL FROM RENORMALIZATION-GROUP THEORY
Çağın Yunus1 , Başak Renklioğlu2,3 , Mustafa Keskin4 , and A. Nihat Berker5,6
1 Department
of Physics, Boğaziçi University, Bebek 34342, Istanbul, Turkey
of Sciences, Koç University, Sarıyer 34450, Istanbul, Turkey
3 Department of Physics, Bilkent University, Bilkent 06533, Ankara, Turkey
4 Department of Physics, Erciyes University, Kayseri 38039, Turkey
5 Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla 34956,
Istanbul, Turkey
6 Department of Physics, Massachusetts Institute of Technology, Cambridge,
Massachusetts 02139, USA
2 College
ABSTRACT
The spin-3/2 Ising model, with nearest-neighbor interactions only, is the prototypical system with two
different ordering species, with concentrations regulated by a chemical potential. Its global phase diagram, obtained in d=3 by renormalization-group theory in the Migdal-Kadanoff approximation or equivalently as an exact solution of a d=3 hierarchical lattice, with flows subtended by 40 different fixed points,
presents a very rich structure containing eight different ordered and disordered phases, with more than
fourteen different types of phase diagrams in temperature and chemical potential. It exhibits phases with
orientational and/or positional order. It also exhibits quintuple phase transition reentrances. Universality
of critical exponents is conserved across different renormalization-group flow basins, via redundant fixed
points. One of the phase diagrams contains a plastic crystal sequence, with positional and orientational
ordering encountered consecutively as temperature is lowered. The global phase diagram also contains
double critical points, first-order and critical lines between two ordered phases, critical endpoints, usual
and unusual (inverted) bicritical points, tricritical points, multiple tetracritical points, zero-temperature
criticality and bicriticality, and phase boundary quintuple reentrance. The 4-state Potts permutationsymmetric subspace is contained in this model.[1]
[1] Ç. Yunus, B. Renklioğlu, M. Keskin, and A. N. Berker, Phys. Rev. E, in press (2016).
İFG23-32
CRITICAL BEHAVIOR OF SOUND ATTENUATION OF A BLUME CAPEL MODEL WITH
CRYSTAL FIELD DISORDER
Gül Gülpınar
Fizik Bölümü, Fen Fakültesi, Dokuz Eylül Üniversitesi
ABSTRACT
In this study, the sound attenuation coefficient of a mean-field Blume-Capel model with a random crystal
field is calculated by the method of thermodynamics of irreversible processes. The behavior of sound
attenuation near the phase transition temperatures is studied in detail. It is found that frequency dependent sound attenuation peaks occur below the critical temperature. In addition, the critical behavior of
the sound attenuation in the hydrodynamic regime is obtained analytically via the critical exponents.
Moreover, the behavior of the sound attenuation as a function of frequency is also investigated and ω 2
dependence is observed for the attenuation coefficient. These results are in a good agreement with ultrasonic investigations of magnetic systems.
İFG23-33
KİTOSAN FİLMLERİN BOYAR MADDE ADSORPSİYON KİNETİĞİNE İYONİK ÇAPRAZ
BAĞLAYICI TÜRÜ VE SEÇİLEN BİR KATKI MADDESİNİN ETKİLERİ
Nilay Kahya1 , Hakan Kaygusuz1 , Gülşen Akın Evingür2 , F. Bedia Erim Berker1
1 Kimya
2 Elektrik
Bölümü/Fen Edebiyat Fakültesi/İstanbul Teknik Üniversitesi
Elektronik Mühendisliği/Mühendislik Fakültesi/Piri Reis Üniversitesi
ABSTRACT
Çevreye ve canlı biyolojik sistemlere karşı toksik özelliği bulunmayan, biyouyumlu, biyobozunur karakterdeki kitosan biyopolimerinden kitosan filmler adsorban olarak hazırlanmıştır. Filmler hazırlanırken,
% 1 kitosan % 1 (v/v)’lik asetik asit içerisinde çözüldükten sonra bu kitosan çözeltileri petri kapları
içerisine dökülmüş ve çözeltiler film oluşturmaları için laboratuvar buzdolabında bekletilmiştir. Kitosan hidrojel filmler, çapraz bağlayıcı olarak seçilen % 1’lik sodyum sülfat, trisodyum sitrat ve sodyum
sülfat çözeltilerinde uygun sürede bekletilerek çapraz bağlanmıştır. Kitosan filmlere sulu ortamda piranin
tutma deneyleri tatbik edildikten sonra sodyum sülfat çapraz bağlı filmlerin hız kinetiğinin diğer çapraz
bağlı filmlere karşılaştırmayla önde olduğu görülmüştür. Grafen oksit suda disperse olabilen ve biyopolimerik malzemelerin mekanik özelliklerini değiştirilebilen özellikleriyle son yıllarda ilgi çekmektedir.
Çalışmanın devamında kitosan filmler grafen oksit ile katkılandırılmışır. % 1’lik kitosan çözeltilerine,
çözeltideki konsantrasyonu 40-60-80-100-120 µg/mL olacak şekilde grafen oksit katılmıştır. Elde edilen
grafen oksit-kitosan kompozit film serisine % 1’lik sodyum sülfat çözeltilerinde çapraz bağlama yapılmıştır.
Sodyum sülfat çapraz bağlı olan grafen oksit-kitosan filmlerin piranin tutmaları floresans spektrokopisiyle
izlenmiştir. Farklı iyonik çapraz bağlı kitosan filmlerin ve sodyum sülfat çapraz bağlı grafen oksitkitosan kompozit filmlerinin piranin çekme deneylerinin sonuçları adsorpsiyon kinetik modellemelerine
uygulanarak hesaplanan hız kinetiği parametreleri aracılığıyla; kitosan filmlerin sulu ortamdan boyar
madde çekmesinin hız kinetiği belirlenmiştir.
Anahtar kelimeler: kitosan, çapraz bağlanma, adsorpsiyon, piranin
İFG23-34
DISORDER-INDUCED TOPOLOGICAL TRANSITIONS
IN MULTICHANNEL MAJORANA WIRES
Barış Pekerten1,∗ , Aykut Teker1 , Özgür Bozat1 , Michael Wimmer2 and İnanç Adagideli1
1 QFaculty
of Engineering and Natural Sciences, Sabancı University, Orhanlı - Tuzla, 34956, Turkey
2 QuTech and Kavli Institute for Nanoscience,
Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
∗ [email protected]
ABSTRACT
In this work, we investigate the effect of disorder on the topological properties of multichannel superconductor nanowires. While the standard expectation is that the spectral gap is closed and opened at
transitions that change the topological index of the wire, we show that the closing and opening of a
transport gap can also cause topological transitions, even in the presence of nonzero density of states
across the transition. Such transport gaps, induced by disorder, can change the topological index, driving
a topologically trivial wire into a nontrivial state or vice versa. We focus on Rashba spin-orbit coupled semiconductor nanowires in proximity to a conventional superconductor and demonstrate that the
p-wave superconductor picture is inadequate in describing the topological phase diagram. We obtain
analytical formulas for topological transitions in these wires, valid for generic realizations of disorder,
generalizing earlier results. Full tight-binding simulations show excellent agreement with our analytical
results without any fitting parameters.
İFG23-35
GENERATION OF AN EXTERNAL MAGNETIC FIELD WITH THESPIN ORIENTATION
EFFECT IN A SINGLE LAYER ISING NANOGRAPHENE
Numan Şarlı
Institute of Science, Erciyes University, 38039 Kayseri, Turkey
ABSTRACT
In this work,the magnetic properties of the single layer Ising nanogaphene (SLING) are investigated by
using Kaneyoshi approach (KA) within the effective field theory for different spin orientations of its
magnetic atoms.We find that the magnetizations of the SLING has no phase transition, certain Curie
temperature and distinct peak of susceptibility at Tc for the some spin orientations at the zero external
magnetic field (H=0). Because these behaviors occurat H6=0, we suggest that the SLING generates an
external magnetic field and behaves as an external magnetic field generator for these spin orientations.
However, the SLING exhibits ferromagnetic behaviors for only one spin orientations. But, it exhibits
antiferromagnetic behaviors for the others. For the AFM cases, diamagnetic susceptibility behaviors and
type II superconductivity hysteresis behaviors are obtained. We hope that these results can open a door
to obtain new class of single layer graphene and graphene-based magnetic field generator devices with
the spin orientation effect [1].
Our results published in journal of Physica E [1].
[1] N. Şarlı, “Generation of an external magnetic field with thespin orientation effect in a single layer
Ising nanographene ”, Physica E, 83, (2016), 22–29.
İFG23-36
CURRENT-INDUCED SPIN ACCUMULATION IN 3D TOPOLOGICAL INSULATOR
Ali Asgharpour, İnanç Adagideli
Faculty of Engineering and Natural Sciences, Sabanci University
ABSTRACT
Spin-momentum locking in surface states of 3D topological insulators (TIs) provides a new avenue for
spintronics applications. In this work, we explore how to extract such spins induced in TIs to topologically trivial materials that are commonly used in conventional electronics devices; Paving the way to TI
based spintronics. In this work, we focus on 3D Bernevig Hughes Zhang (BHZ)[1] effective Hamiltonian and numerically explore spin accumulation caused by a flowing current on a TI surface. We focus
on a particular geometry, a side-pocket (SP) attached to various faces of a 3D TI quantum wire with a
rectangular cross section, and explore spin extraction into topologically non-trivial materials. We find
that it is possible to extract current induced spin accumulations from 3D TIs into trivial materials. We
further study how spin extraction depends on geometry, materials and material parameters and show that
electron-hole degrees of freedom can be utilized among other things to control the polarization of the
extracted spins.
[1] H. Zhang, et al., Nature Phys. 5, 438 (2009)
İFG23-37
ANALYSIS OF STRUCTURAL CHANGES OF PROTEINS BY FLUORESCENCE LIFETIME
DISTRIBUTIONS
İbrahim Ethem Özyiğit, E. Demet Akten, Önder Pekcan
Department of Chemistry, Yıldız Technical University
Department of Bioinformatics and Genetics, Kadir Has University
ABSTRACT
Spectrophotometric methods are widely used in examinations of protein structure and functions.
The differences in the degrees of interactions between the fluorophores localized in discrete regions of
proteins and solvent molecules may cause variations in fluorescence lifetimes, and these variations may
obtained as fluorescence lifetime distributions by the chi-square analysis of fluorescence decay data described mathematically as exponential series. Fluorescence lifetime distributions which are highly sensitive to the structural changes in proteins may provide comprehensive informations about modifications,
hydrolyses and denaturations of proteins. These informations may be useful to improve thermostable
enzymes for medical, medicinal and industrial applications and to distinguish the activities of proteases
from each others.
[1] Lakowicz, J.R. (2006).Principles of Fluorescence Spectroscopy, third edition, Springer Science +
Business Media, LLC, New York.
[2] Stubbs, C.D., Williams, B.W., (1992). “Fluorescence in Membranes”, Topics in Fluorescence Spectroscopy: Biochemical Applications, 3: 231-271; Editor: Lakowicz, J.R., (1992), Plenum Press, New
York.
[3] Kaneko, H., Minagawa, H., Shimada J. (2005). “Rational design of thermostable lactate oxidase by
analyzing quaternary structure and prevention of deamidation”, Biotechnology Letters, 27: 1777-1784.
İFG23-38
STRUCTURAL EFFECTS OF DIHYDROFOLATE AND TRIMETHOPRIM BINDING TO
E.COLI DIHYDROFOLATE REDUCTASE
Haleh Abdizadeh, Ömer Acar, Ali Rana Atılgan, Canan Atılgan
Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
ABSTRACT
We characterize structural and dynamical changes induced on E.coli dihydrofolate reductase (DHFR).We
investigate the structural features of the wild type protein in the presence of the antibiotic trimethoprim
(TMP), a competitive inhibitor of dihydrofolate. Within the all atom classical molecular dynamics (MD)
scheme, we study the detailed mechanistic characterization for conformational changes, and the catalytic
relevance of loop motions in DHF and TMP binding to E. coli DHFR as common mutants that confer
resistance to TMP are introduced into the three dimensional structure. We identify two characteristics of
DHFR conformational dynamics that differ in its binding to DHF versus TMP that might be responsible
for the major discrepancies between the two systems: (i) we show fluctuation differences in loop motions
despite the identical initial enzyme structures. MD simulations indicate that the increased magnitude of
equilibrium fluctuations of the two systems is common to the loop regions while they differ in the way
they communicate with the other parts of the enzyme. (ii) The equilibrium conformational motions of
DHFR in the presence of TMP facilitate the deformation of the active site shape. We conclude that after
amino acid substitutions that confer resistance, DHFR retains its dynamical features for the DHF bound
form, but displays suppressed dynamics in the presence of TMP.
İFG23-39
INVESTIGATION OF PHYSICAL PROPERTIES OF AII-BVI QUANTUM DOTS:
SYNTHESIS TECHNIQUES, OPTICAL PROPERTIES AND APPLICATIONS
Çağdaş Allahverdi and Selma ERAT
Nanomaterial Production Laboratory, Department of Electrical and Electronics Engineering,
Toros University, 45 Evler Campus, 33140 Yenişehir, Mersin/Turkey
ABSTRACT
Since early 1980s, semiconducting nanocrystals in the form of quantum dots of AII-BVI binary groups
such as cadmium chalcogenides (CdE; E= S, Se, Te) have attracted great attention because of their novel
physical properties and promising commercial applications in optoelectronic devices. [1, 2]
In the present work, the physical and chemical methods used to produce such nanocrystals are compared from the view of their advantages and disadvantages. Besides, the investigated crystallographic
structure, morphology and optical properties of the aforementioned nanocrystals produced by injection
into hot matrix method in our laboratory will be discussed in detail. The physical process upon synthesizing will be examined in the framework of classical nucleation and growth theory and quantum
confinement effect. X-ray powder diffraction (XRD), transmission electron microscopy (TEM), optical
absorption (ABS) and photoluminescence (PL) techniques are used to investigate these nanocrystals’
properties. Future promising applications of the nanocrystals in optoelectronics as well as medical sectors will be discussed.
[1] C. Mello Donegá, P. Liljeroth and D. Vanmaekelbergh, ”Physicochemical Evaluation of the HotInjection Method, a Synthesis Route for Monodisperse Nanocrystals”, Small 12, 1152-1162 (2005).
[2] H. V. Demir, S. Nizamoglu, T. Erdem, E. Mutlugun, N. Gaponik and A. Eychmüller, ”Quantum
Dot Integrated LEDs using Photonic and Excitonic Color Conversion”, Nano Today 6, 632-647 (2011).
Acknowledgement
We would like to thank to Prof. Dr. Hikmet YÜKSELİCİ from Physics Department at Yıldız Technical
University and Assoc. Prof. Dr. Ali GELİR from Physics Department at Istanbul Technical University
for their valuable contributions to this research.
İFG23-40
CONTEMPORARY COSMOLOGY AND POWER-LAW INFLATION WITHOUT A SCALAR
FIELD
Özgür Akarsu
Physics Department, Faculty of Science and Letters,
Istanbul Technical University, 34469, Sarıyer, Istanbul, Turkey
ABSTRACT
In this talk we will first introduce the main theoretical and observational constituents of the contemporary
cosmology, such as the inflation in the very early universe and the current acceleration of the universe
that lead the presence of inflaton and dark energy sources in the universe. These two sources are mostly
described as scalar fields with a potential. We will discuss generating a successful power-law inflation
without using a scalar field.
İFG23-41
POST NEWTONIAN APPROXIMATION OF BLACK HOLE ENTROPY
Levent Akant, Birses Debir
Physics Department, Boğaziçi University, Bebek, Istanbul, Turkey
ABSTRACT
A useful way to express thermodynamic quantities is to use trace of the heat kernel, which includes the
finite size effects due to the boundaries of the system. While the heat kernel is applied on the quantities,
the resulting expression involves harmonic sums and the Mellin transformation is required to study the
asymptotic of the sum. We study the non-relativistic limit in ultra-static background to describe the
free energy and the entropy by systemically applying the mentioned techniques. We then show that,
under a conformal transformation, the static background reduces to the ultra-static background. To
address the non-relativistic limit, we apply the saddle point approximation to the free energy with saddle
point identity. Then to determine the high temperature expansion of entropy, we use the heat kernel
approximation. We use the ultra-static description of the heat kernel coefficients (on the Schwarzschild,
the Dilaton and the Reissner-Nordström metrics) to construct each term. Additionally, we use both the
brick wall and the cut-off methods via specific values such as the Hawking temperature and the proper
cut-off. Finally these off-shell methods render our results predictable in terms of the area of the black
hole and the mass of the test particle.
İFG23-42
SPIN-ORBIT COUPLED FERMI GAS UNDER ADIABATIC ROTATION
E. Doko1 , A. L. Subaşı2 , and M. Işkın1
1 Department
of Physics, Koc University, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkey.
of Physics, Istanbul Technical University, Maslak, Istanbul, Turkey.
2 Department
ABSTRACT
We study trap profiles of a Rashba spin-momentum coupled two-dimensional atomic Fermi gas subject
to an adiabatic rotation. The characteristic ring shaped density profile for the rotating normal Fermi gas
with spin-orbit coupling in the harmonic trap is predicted to survive at experimentally accessible finite
temperatures. We calculate the critical rotation frequencies for pair breaking in the superfluid phase and
destruction of superfluidity due to Coriolis effects. Comparing full quantum mechanical Bogoliubov-de
Gennes calculations with local density approximation results, we establish that under extreme situations
the simultaneous presence of spin-momentum coupling and rotation may favor a ring-shaped normal
phase separated from the superfluid core by vacuum. We present extensive phase diagrams and find that
a gapless superfluid phase may occupy a considerable region in the trap profile.
İFG23-43
ENERGY TRANSFER RATE BETWEEN BILAYER DIPOLAR GASES
B. Tanatar, B. Renklioğlu, and M. Ö. Oktel
Department of Physics, Bilkent University, Bilkent, 06800 Ankara, Turkey
ABSTRACT
We consider two parallel layers of dipolar ultracold Fermi gases at different temperatures and calculate
the heat transfer between them. The effective interactions describing screening and correlation effects
between the dipoles in a single layer are modelled within the Euler-Lagrange Fermi-hypernetted chain
approximation. The random-phase approximation is employed for the interactions across the layers.
We investigate the amount of transferred power between the layers as a function of the temperature
difference. Energy transfer proceed via the long-range dipole-dipole interactions. A simple thermal
model is established to investigate the feasibility of using the contactless sympathetic cooling of the
ultracold polar atoms/molecules. Our calculations indicate that dipolar heat transfer is effective for
typical polar molecule experiments and may be utilized as a cooling process.
İFG23-44
SUPERFLUID TRANSITION IN THE ATTRACTIVE HOFSTADTER-HUBBARD MODEL
R. O. Umucalılar, M. Işkın
Koç University, İstanbul, Sarıyer 34450, Turkey
http://arxiv.org/abs/1605.07426
ABSTRACT
We consider a Fermi gas that is loaded onto a square optical lattice and subjected to a perpendicular
artificial magnetic field, and determine its superfluid transition boundary by adopting a BCS-like meanfield approach in momentum space. The multi-band structure of the single-particle Hofstadter spectrum
is taken explicitly into account while deriving a generalized pairing equation. We present the numerical
solutions as functions of the artificial magnetic flux, interaction strength, Zeeman field, chemical potential, and temperature, with a special emphasis on the roles played by the density of single-particle states
and center-of-mass momentum of Cooper pairs.
İFG23-45
CHEMICAL REACTIVITY APPROACH TO THE GROUP 2B METALS HALIDES: STERIC
EFFECTS
Alimet Sema Özen, Zehra Akdeniz
Piri Reis Üniversitesi, Faculty of Science and Letters
ABSTRACT
Chemical reactivity descriptors within the Conceptual DFT can be used to understand the nature of the
interactions between two monomers of the Group 2B metal halides. In this study, MX2 monomers and
dimers, where M=Zn, Cd, Hg and X=F, Cl, Br, I, were investigated in terms of chemical reactivity descriptors (Figure 1). Relativistic effects were taken into account using the effective core potential (ECP)
approach. Correlations were produced between global and local reactivity descriptors and dimerization
energies. Steric effects were found to be responsible for the deviation from the chemical reactivity principles. They were introduced into the chemical reactivity descriptors such as local softness.
[1] Ozen, A. S.; Akdeniz, Z. Chemical Reactivity Perspective into the Group 2B Metals Halides, J. Phys.
Chem A (accepted)
[2] Ruberto, R.; Pastore, G.; Özen, A.S.; Akdeniz, Z.; Tosi, M.P. Static and Dynamic Structure of
Monomers, Dimers and Trimers of HgCl2 from Density-functional Calculations Eur. Phys. J. D 2012,
66, 229-236
[3] Özen, A.S.; Akdeniz, Z.; Ruberto, R.; Pastore, G.; Tosi, M.P. The Origins of Tetrahedral Coordination
in Molten and Glassy ZnCl2 and Other Group-2B Metal Dihalides Phys. Lett. A 2014, 431-433.
Figure 1: Main geometries of the dimers (X=Y for homodimers; X6=Y for heterodimers).
İFG23-46
PATLAYICI (EXPLOSIVE) PERKOLASYON ÖRGÜLERİNDE EŞEVRELİ AKTARIM
İ. Yalçınkaya, Z. Gedik
Mühendislik ve Doğa Bilimleri Fakültesi, Sabancı Üniversitesi, Tuzla 34956, İstanbul
ABSTRACT
Bağ perkolasyonu problemi, ayrık noktalardan oluşan bir ağa rastgele olarak bağların eklenmesi sonucunda oluşan bağ topaklarının yapıları ve büyümeleri ile ilgidir [1]. Bu durumda ayrık topaklar rastgele
olarak büyüyecektir. Bu tip problemler, en büyük topağın tüm ağı kaplama hızı bakımından ikinci derece
faz gelişleri ile ilişkilendirilir. Öte yandan, ağın gelişimi sırasında bir bağın eklenip eklenmeyeceği, farklı
rastgele bağlar arasından yapılan bir seçim ile belirlenebilir. Öyle ki bu seçim, bağ adaylarının eklenmeleri halinde meydana gelecek topakların büyüklükleri kıyaslanarak yapılır. Aclioptas ve arkadaşları
göstermiştir ki [2] eğer bu seçim kuralı sürekli olarak en büyük topağın büyümesini baskılayacak nitelikte ise, bir bağ yüzdesine kadar perkolasyon eşiği baskılanır. Fakat daha sonra en büyük topak aniden
büyüyerek ya da başka bir deyişle, Aclioptas ve arkadaşlarının da adlandırdığı üzere patlayarak tüm ağı
sarar. Bu tip bir perkolasyon birinci derece faz geçişlerine bir model olabilmesi bakımından önem taşır.
Bu çalışmamızda topak gelişiminin yukarıda bahsettiğimiz anlamda patlayıcı nitelikte olduğu sonlu kare
örgüler üzerinde eşevreli taşınımın özelliklerini inceledik. Belirli bir bağ yüzdesi için, patlayıcı perkolasyon (PP) örgülerinde taşınımın standart perkolasyon (SP) örgülerine göre daha verimli gerçekleşebildiğini gösterdik. Ayrıca bağ yüzdesine karşı verim artışının, taşınım eşiği yakınlarında bir kuvvet
fonksiyonu şeklinde olduğunu ve farklı örgü boyutları için üstellerin PP’da SP’a göre en az iki kat
daha fazla olduğunu gösterdik. Aslında söz konusu seçim kuralı nedeniyle oluşan topak yapısı çoğu
durumda SP ile kıyaslandığında daha fazla yerelleşmeye sebep olmakta ve eşevreli aktarım için biraz
daha elverişsiz kalmaktadır. Buna rağmen, PP’da en büyük topağın çok hızlı büyümesi bu etkiyi geride
bırakmakta ve daha verimli bir aktarıma olanak tanımaktadır.
[1] N. Bastas, P. Giazitzidis, M. Maragakis, K. Kosmidis, Phys. A 407, pp. 54-65 (2014).
[2] D. Aclioptas, R. M. D’Souza, J. Spencer, Science 323, 5920, pp. 1453-1455 (2009).
İFG23-47
BİRBİRİNE PARALEL MERDİVENLERDE TIRMANAN “ENTROPİ MAKINALARININ”
KAYNAKLAR ADALETSİZ DAĞITILDIĞINDA OLUŞTURDUKLARI HIYERARŞİNİN
İNCELENMESİ
Ayşe Ferhan Yeşil, M. Cemal Yalabık
Fizik Bölümü, Bilkent Üniversitesi
ABSTRACT
Beslendiği kaynağın entropisi düşükken ilerleyebilen nesnelerden oluşan bir sistem kurguladık. Bu nesnelere tırmanıcı adını verdik. Tırmanıcıları yaratırken Jarzynski’nin entropi makinalarından esinlendik
[1]. Bir sırada (sıra bir merdiven gibi düşünülebilir) tırmanan tırmanıcıların entropi artıklarını kaynak olarak bir yanındaki sıradaki tırmanıcılara besledik, onların artıklarını da onların yanındaki sıraya,
bu şekilde sınırlı sayıda sırayı birbirlerine entropi ilişkisiyle bağladık. Birinci sıraya en düşük entropili
dolayısıyla en avantajlı kaynağı sunduk. Sonuçta merdivenler arasında kaynağa bağlı bir hiyerarşi oluştu.
Sistem oldukça ilginç değişmez durumlar oluşturdu. Bu durumları merdivenin halka şeklinde olduğu ve
bir ucunun sonsuza gittiği koşullarda inceledik. Tek tırmanıcı ile oluşturduğumuz problemi analitik
olarak çözdük. Çok tırmanıcı ile oluşturduğumuz durumu ise Monte Carlo metoduyla inceledik.
[1] Mandal, Dibyendu, H. T. Quan, and Christopher Jarzynski. ”Maxwell’s refrigerator: An exactly
solvable model.” Physical review letters 111.3 (2013): 030602.
İFG23-48
ENHANCEMENT OF NON-MARKOVIANITY IN A COLLISION MODEL
B. Çakmak, Ö. E. Müstecaplıoğlu
Department of Physics, Koç University, İstanbul, Sarıyer 34450, Turkey
ABSTRACT
We have investigated the dynamics of a collision model in which both the system and environmental
states are considered to be spin-1/2 particles. In order to include non-Markovian features in our model
we have introduced interactions between environmental qubits and investigated the effect of different
models of this interaction on the degree of non-Markovianity in the system. We have seen that extending
the interaction between the environment qubits beyond nearest neighbor coupling enhances the nonMarkovianity in the system. A further significant increase can be observed if a collective interaction with
the forthcoming environmental qubits is considered, however, contrary to the case of separate interaction
case, it is non-monotonic with increasing number of interacting qubits. Another important result is that
it is also possible to increase the number of collisions needed for the degree of non-Markovianity to
saturate to a finite value in the collective interaction case. This implies that the system receives the
information from its past states for a longer time before completely decohering into the state of the
environment. We have observed a correlation between the degree of non-Markovianity and the prolonged
of the oscillations in the coherence contained in the system.
İFG23-49
KUANTUM SÜRTÜNME
Ferdi Altıntaş
Fizik Bölümü, Abant İzzet Baysal Üniversitesi, Bolu, Türkiye
Fizik Bölümü, Koç Üniversitesi, Sarıyer, Türkiye
ABSTRACT
Kısa sunumumda üniter zaman gelişmelerinin termodinamiksel yorumlanmalarını ele alacağım. İdeal
olmayan üniter zaman gelişimlerinde entropi artımı ve tersinmezlik gibi durumlar ortaya çıkmakta ve bu
etkiler içsel (kuantum) sürtünme olarak ifade edilmektedir.
İFG23-50

23. ifg program kitapçığı - İFG 23

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