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KONUŞMA VE BİLDİRİ ÖZETLERİ

ABSTRACT BOOK sivihal.pirireis.edu.tr

19 ARALIK 2015 İstanbul Üniversitesi, Baltalimanı Tesisleri, İstanbul

19. ULUSAL SIVI HAL SEMPOZYUMU MARIO TOSI ANISINA

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Sıvı Hal Sempozyumu Danışma Kurulu

Prof. Dr. Zehra Akdeniz zehra.akdeniz@pirireis.edu.tr

Prof. Dr. Nihat Berker nihatberker@sabanciuniv.edu

Prof. Dr. Bedia Erim Berker erim@itu.edu.tr

Prof. Dr. Can Fuat Delale delale@isikun.edu.tr

Prof. Dr. Levent Demirel LDEMIREL@ku.edu.tr

Prof. Dr. Gülay Dereli gudereli@ku.edu.tr

Prof. Dr. Sondan Durukanoğlu sondan@sabanciuniv.edu

Prof. Dr. Mustafa Keskin keskin erciyes.edu.tr

Prof. Dr. Ş. Erol Okan erolokan@trakya.edu.tr

Prof. Dr. Haluk Özbek hozbek@itu.edu.tr

Prof. Dr. Yani Skarlatos sakarlat@boun.edu.tr

Prof. Dr. Bilal Tanatar tanatar@fen.bilkent.edu.tr

Prof. Dr. Hasan Tatlıpınar htatli@yildiz.edu.tr

Prof. Dr. Mehmet Tomak tomak@metu.edu.tr

Prof. Dr. İskender Yılgör iyilgor@ku.edu.tr

Prof. Dr. Ersin Yurtsever eyurtsev@ku.edu.tr

Sıvı Hal Sempozyumu Düzenleme Kurulu

Prof. Dr. Zehra Akdeniz Pîrî Reis Üniversitesi

Prof. Dr. Haluk Özbek İstanbul Teknik Üniversitesi

Yrd. Doç. Dr. Gülşen Akın Evingür Pîrî Reis Üniversitesi

Dr. Ozan S. Sarıyer Pîrî Reis Üniversitesi

Hanifi Arslan Pîrî Reis Üniversitesi

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MARIO TOSI ANISINA

Mario TOSİ, İtalya'da Yoğun Madde Fiziği Teorisi'nin

kurucularından olup, sıvılar üzerinde önemli araştırmalar

yapmış saygın ve dünyaca tanınmış bir teorik fizikçidir.

Sıvıların yanı sıra iyonik katılar, sıvı metaller, elektron gazları,

Bose-Einstein yoğunlaşması ve fermiyonik-bozonik dejenere

gazlar gibi alanlarda istatistik mekaniğe önemli katkılar

sağlayan çok sayıda yayınları ve kitapları vardır.

Pavia'da eğitimini tamamlayan Mario TOSİ, ABD, Messina,

Roma ve Trieste'de Profesör olarak görevlerde bulunmuş olup

1977-1991 yılları arasında ICTP-Abdus Salam (Trieste-

Italya)'da "Condensed Matter Section"ın başkanlığını

yaptıktan sonra 'Scuola Normale Superiore-Pisa'ya geçerek

oradan ''Emeritus Profesörlük'' ünvanını almıştır.

Yorulmaz bir araştırmacı ve büyük bir eğitimci olan TOSİ, Ülkemiz de dahil olmak üzere dünya çapında tanınmış ve bugün önemli pozisyonlarda bulunan birçok bilim insanının eğitimlerinde ve kariyerlerinde katkılar sağlamıştır. Onlar, 1 Kasım 2015 Pazar günü vefat eden hocaları Mario TOSİ'yi asla unutmayacaklardır.

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19. ULUSAL SIVI HAL SEMPOZYUMU

MARIO TOSI ANISINA

19 Aralık 2015 İstanbul Üniversitesi, Baltalimanı Tesisleri

Baltalimanı-İSTANBUL

PROGRAM

19 ARALIK 2015 Cumartesi

10:00 - 10:30 Kayıt

10:30 - 11:00 Açılış Konuşması

11:00 – 11:30 Density-Wave Instability and Collective Modes in a

Bilayer System of Dipolar Bosons

Bilal Tanatar (Bilkent Üniversitesi)

11:30 – 12:00 İyonik Sıvılar: Genel Bakış Hasan Tatlıpınar (Yıldız Teknik Üniversitesi)

12:00 - 12:20 Generalized Reduced Order Gas Pressure Law for

Bubble Dynamics

Can Fuat Delale (MEF Üniversitesi)

12:30 - 13:30 ÖĞLE YEMEĞİ

13:40 - 14:00 Black Sea Modeling and Applications:

Etesians, Upwelling and Water Mass Formation

Emin Özsoy (İstanbul Teknik Üniversitesi)

14:00 - 14:20 Investigation of Allosteric Coupling in Human

β2-adrenergic Receptor in the Presence of Intracellular

loop 3 (ICL3)

Demet Akten (Kadir Has Üniversitesi)

14:20 - 14:40 Infrared Spectroscopy in Cryogenic Matrices

Gülce Öğrüç Ildız (İstanbul Kültür Üniversitesi)

14:40 - 15:00 Modeling Common Vascular Diseases via Microfluidics

Ozan S. Sarıyer (Pîrî Reis Üniversitesi)

15:00 - 15:20 ARA

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15:20 - 15:40 Ab initio calculations of the potential of mean force for

dissociation of salts in water

Serdar Kuyucak (University of Sydney)

15:40 - 16:00 Hydrogen-Bonded Layer-by-Layer Films and pH-Annealing Levent Demirel (Koç Üniversitesi)

16:00 - 16:20 İki Boyutta Tuzaklanmış Aşırı Soğuk Bozonlarda

Etkileşmelerin Önemi

Ali İhsan Meşe (Trakya Üniversitesi)

KISA KONUŞMALAR

16:20 - 16:30 Elasticity of Polyacrylamide- Graphene Oxide composites

Gülşen Akın Evingür (Pîrî Reis Üniversitesi)

16:30 - 16:40 Aljinat-Kitosan Çoklu Tabaka Filmleri ve Özellikleri

Hakan Kaygusuz (İstanbul Teknik Üniversitesi)

16:40 - 16:50 Tight Binding Molecular Dynamics Simulations of

Vacancy Defected Single Walled Carbon Nanotubes

Can Ferman Gülmez (Yıldız Teknik Üniversitesi)

16:50 - 17:00 A Theoretical Approach to Heptamers of ZnCl2 :

A DFT Study

Cihan Özen (Pîrî Reis Üniversitesi)

17:00 KAPANIŞ

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Density-Wave Instability and Collective Modes in a Bilayer System of Dipolar

Bosons

B. Tanatar(a)*, E. Akaturk(a) and S. H. Abedinpour(b)

(a) Bilkent Üniversitesi, Ankara (b) Institute for Advanced Studies in Basic Sciences, Zanjan

* e-mail address: tanatar@fen.bilkent.edu.tr

Abstract: We consider a bilayer of dipolar bosons in which the polarization of dipoles are perpendicular to the planes, in both parallel and antiparallel configurations. Using accurate static structure factor S(q) data from hypernetted-chain calculation for single layer dipolar bosons we construct effective screened interactions for intralayer particles. We adopt the random-phase approximation for interlayer interactions, and study the instability of the homogeneous bilayer system against the formation of density waves by investigating the poles of the density-density response function. The dispersion of collective modes of this system also signals the density-wave instability. We also investigate the effect of counter flow on the collective mode dispersion and on the density-wave instability and discuss the dissipationless super fluid drag effect in the presence of a background velocity.

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İyonik Sıvılar: Genel Bakış

Hasan Tatlıpınar

Yıldız Teknik Üniversitesi, İstanbul. e-mail address: htatli@yildiz.edu.tr

Özet: İyonik sıvılar, sıvı hal fiziğinin günümüzdeki önemli çalışma konularından birisidir. İyonik sıvılar genel olarak suyun kaynama noktası göz önüne alındığında “düşük sıcaklıkta iyonik sıvılar” ve “yüksek sıcaklıkta iyonik sıvılar” olarak adlandırılabilir. Yüksek sıcaklıkta iyonik sıvılara örnek olarak ergimiş metal tuzları gösterilebilir. Yer kabuğu büyük oranda metal tuzları barındırır, fakat bu tuz karışımlarının katı fazda olması teknoloji ve endüstride kullanımlarını sınırlar. Bu nedenle metal tuzlarının eritilerek sıvı fazdaki özelliklerinin incelenmesi oldukça önemlidir. Oda sıcaklığındaki iyonik sıvılar ise günümüzde çevreye zararsız endüstrinin önemli bir girdisi olarak büyük önem kazanmışlardır. Genellikle moleküler yapıdaki bu daha karmaşık sistemlerin kuramsal olarak incelenmesinde de yüksek sıcaklık iyonik sıvılar için kullanılan yöntemlerle aynıdır. Bu konuşmada ergimiş metal tuzlarının fiziksel özelliklerinin incelenmesi ile ilgili kuramsal çalışmalar hakkında genel bilgiler verilerek Prof. M. P. TOSI ve çalışma gruplarının bu konulardaki katkıları üzerinde durulacaktır.

Referanslar:

[1] M. Rovere and M. P. Tosi, “Structure and Dynamics of Molten Salts”, Rep. Prof. Phys. 49, 1001-1081 (1986). [2] Z. Akdeniz, and M. P. Tosi, Proc. R. Soc. London Ser. A 437, 85-96 (1992). [3] H. Tatlipinar, Z. Akdeniz, G. Postore, and M. P. Tosi, “Atomic Size Effects on Local Coordination and Medium-Range Order in Molten Trivalent Metal Halides”, J. Phys.: Condens. Matter 4 8933-8944 (1992). [4] H. Tatlipinar, M. Amoruso, M. P. Tosi, “Ionic charge transport in strongly structured molten salts” Physica B 275, 281-284 (2000).

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Generalized Reduced Order Gas Pressure Law for Bubble Dynamics

Can F. Delale(a)* and Şenay Pasinlioğlu(b)

(a) MEF University, Sarıyer (b) İstanbul Technical University, Sarıyer

* e-mail address: delalec@mef.edu.tr

Abstract: The thermal behaviour of a spherical gas bubble in a

liquid driven by an acoustic pressure is investigated in the uniform

pressure approximation by considering the energy balance between

the gas bubble and the surrounding liquid. An iterative method of

solution is constructed to solve the temporal evolution of the

coupled equations for the temperature distribution and the pressure

inside the bubble. It is shown that the first iterative solution leads to

the first order law of the gas pressure as a polytropic power law of

the bubble wall temperature and of the bubble radius, with the

polytropic index given as an explicit function of the isentropic

exponent of the gas. The resulting first order law of the gas pressure

reduces to the classical isothermal and adiabatic laws in the

appropriate limits. The bubble wall temperature is obtained from

the Plesset-Zwick solution of the energy equation from the liquid

side coupled to the equation of spherical bubble dynamics. The first

order gas pressure law is then applied to an acoustically driven

cavitation bubble coupled to the Rayleigh-Plesset equation of

spherical bubble dynamics. Results obtained for a typical acoustic

signal show that the bubble wall temperature pulses during collapse

and rebound can become an order of magnitude higher than the

bulk liquid temperature.

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Black Sea Modeling and Applications: Etesians, Upwelling and Water Mass Formation

Emin Özsoy(a)*, Robinson Hordoir(b), Nathalie Toque(a), Hazem Nagy(a), Adil Sözer(b), Sinan Çevik(c) ve

Ozan Mert Göktürk(d)*

(a) Middle East Technical University, Erdemli, Mersin (b) Swedish Meteorological And Hydrological Inst., Norrköping

(c)Turkish State Meteorology Service, İnebolu (d)İstanbul Technical University, İstanbul

* e-mail address: ozsoyem@itu.edu.tr (present address: İstanbul Technical University, İstanbul, Turkey)

Abstract: The Etesian wind regime in summer dominates the climate of the Aegean Sea as well as a larger area extending from the Balkans and the Black Sea to the Levantine Basin of the Eastern Mediterranean are able to create forest fires and upwelling in the Aegean Sea, upwelling on the southwestern Black Sea, and severe floods in the mountainous southeastern Black Sea regions all at the same time. The wind system and its regional effects are described, and the upwelling events in the southwestern Black Sea are investigated through observations as well as modeling studies of the Black Sea circulation.

Keywords: Etesian, upwelling, floods, forest fires, Aegean, Black Sea, modeling

The summer Etesian wind regime often develops to gale force winds in the Aegean Sea, strengthening especially near Crete (Tyrlis and Lelieveld, 2013; Tyrlis et al., 2014), while it is being fed by northerly winds from the Balkan gap and northeasterly winds from the Black Sea area (Fig 1a). Often the sustained wind pattern is suitable to create forest fires in the Aegean Sea region, as demonstrated in Fig 1a on August 20, 2012, declared a state of emergency near Athens. At the same time in the eastern Black Sea, moisture picked up by winds from the northern steppes trapped against the steep Anatolian and Caucasian mountain ranges (Fig. 1b) created extreme flooding event in the southeast (Fig. 1c), with precipitation of about 230 mm in two

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days. Several times in the summer of 2012 the pattern was repeated, and a similar flooding extreme event had occurred earlier on July 7, 2012, associated with a small-scale cyclone trapped in the mountainous eastern Black Sea region. The storm created the worst floods in 70 years in Krasnodar and Krymsk, Russia, with rainfall amounting to 270 mm/day and a death toll of more than hundred people.

(a) (b) (c)

Figure 1. Atmospheric model forecasts of (a) surface winds (km/h), (b) surface relative humidity (%) and wind (km/h) on 20 August 2012 and (c) total precipitation (mm) during 18-21 August 2012.

The mainly cyclonic circulation of the highly stratified Black Sea is buoyancy and wind driven (Özsoy and Ünlüata, 1998). A distinctive feature of the Black Sea thermal stratification is the subsurface Cold Intermediate Water (CIW) usually found above the pycnocline, upwelled in summer in the southwest as well as around Crimea (Fig. 2a). Also shown in the same figure are the surface winds (Fig. 2b), temperature (Fig. 2c) and salinity (Fig. 2d) produced by the NEMO model continuous hindcast for the years 2010-2014, confirming the observed features.

(a) (b)

Figure 2. September 12, 2012 (a) surface winds and (b) ocean model hindcasts of surface currents and temperature on the same dates.

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Daily observations of SST at the İnebolu indicate very frequent and persistent upwellings during repeated episodes in the summer season (Fig. 3a), with temperature drops to as low as 11oC, as a result of the cold intermediate water (CIW) surfacing at the coast, which differ strongly from the regional average SST in the ECMWF reanalysis (black). Local people in İnebolu take advantage of this by collecting dizzied fish at the coast at night (Fig. 3b).

(a) (b)

Figure 3. (a) Along-shore and cross-shore components of wind velocity at 42.2°N, 32°E based on ERA-interim reanalysis (ECMWF)

rotated clockwise by 40° (upper two panels, red dots are original unfiltered data points), the SST based on the reanalysis (black) and

the İnebolu meteorological station time-series data (blue) (lower panel) (b) İnebolu people searching for fish near the coast at night

(photos: Sinan Çevik).

Reference:

[1] E. Özsoy and Ü. Ünlüata “The Black Sea” in: A. R. Robinson and K. Brink (editors), The Sea: The Global Coastal Ocean: Regional Studies and Syntheses 11, John Wiley and Sons, New York, pp. 889-914 (1998).

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Investigation of Allosteric Coupling in Human

β2-adrenergic Receptor in the Presence of

Intracellular loop 3 (ICL3)

Canan Özgür(a), Pemra Doruker(a), E. Demet Akten(b)

(a) Bogazici University, Istanbul (b) Kadir Has University, Istanbul

Abstract: The largest class of drug targets are G-protein coupled receptors (GPCRs), one of which is the beta2-adrenergic receptor (β2-AR). Although the active and inactive states of β2-AR were revealed by x-ray crystallography,1,2 the conformational transition between inactive and active states is still not fully resolved.3 In this study, we focus on the conformational dynamics of apo form of β2-AR using molecular dynamics (MD) simulations under various distance constraints. Several independent runs starting with an inactive structure of β2-AR were carried out. The intracellular loop ICL3, which has an important role in G-protein recognition but is missing in crystal structures, was incorporated as an unstructured loop in all simulations.4

In our previous MD study4 on apo β2-AR, the allosteric coupling between the intra- and extracellular parts of the receptor was revealed only in the presence of intact ICL3 during a 1000 ns run, named as the original run. Specifically, we observed that the closure of the G-protein binding site, as a result of a tightly packed ICL3 under the receptor, was paired with the expansion of the ligand-binding site. In this study, we aim to investigate further this allosteric effect due to loop opening/closure by imposing specific distance constraints on the ligand-binding site of the receptor. Principal component analysis was performed to reveal the biologically relevant motions of the receptor in all runs. The conformational dynamics and hydrogen bonding patterns of the transmembrane helices were also analyzed in order to observe their hinge sites. Initially, we performed two independent 500 ns runs using the final snapshot of the original run with a closed ICL3 loop without imposing any constraints. In both runs, ICL3 stayed almost in closed position indicating that the packing of ICL3 under the receptor is an energetically favorable position that blocks G-protein

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binding. Then, three constrained runs were performed, by keeping the ligand-binding site either in relatively open or closed position. In all these constrained runs, the allosteric coupling between the intra- and extra-cellular regions of the receptor was once more confirmed. As the binding site was kept open, the ICL3 was guided to a closed position, and vice versa. This coupling provides insight for further drug design studies.

Keywords: allosteric mechanism, GPCR, β2 adrenergic receptor, intracellular loop 3 (ICL3), transmembrane helices, G protein binding site, ligand-binding site.

References:

[1] S. G. F. Rasmussen, H. J. Choi, M. D. Rosenbaum, T. S. Kobilka, S. F. Thian, C. P. Edwards, M. Burghammer, R. P. V. Ratnala, R. Sanishvili, F. R. Fischetti, F. X. G. Schertler, I. W. Weis, B. K. Kobilka, Nature 450, 383 - 388 (2007). [2] S. G. Rasmussen, B. T. DeVree, Y. Zou, A. C. Kruse, K. Y. Chung, T. S. Kobilka, F. S. Thian, P. S. Chae, E. Pardon, D. Calinski, J. M. Mathiesen, S. T. Shah, J. A. Lyons, M. Caffrey, S. H. Gellman, J. Steyaert, G. Skiniotis, W. I. Weis, R. K. Sunahara, and B. K. Kobilka, “Crystal structure of the beta2 adrenergic receptor-Gs protein complex” Nature 477 549 - 555 (2011). [3] R. O. Dror, D. H. Arlow, P. Maragakis, T. J. Mildorf, A. C. Pan, H. Xu, D. W. Borhani, and D. E. Shaw, “Activation Mechanism of the Beta2-adrenergic Receptor” PNAS 108, 18684 - 18689 (2011). [4] O. Ozcan, A. Uyar, P. Doruker, and E.D. Akten, “Effect of Intracellular Loop 3 on Human β2-Adrenergic Receptor Dynamics: Another Inactive State Observed in Simulations”, BMC Structural Biology, 82013.

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Infrared Spectroscopy in Cryogenic Matrices

Gülce Öğrüç Ildız

Istanbul Kültür Üniversitesi, Istanbul Coimbra University, Coimbra

e-mail address: g.ogruc@iku.edu.tr

Abstract: The matrix isolation technique is used for trapping and producing chemical species and preserving them in solidified inert gases at low temperatures (10–40K) achieved by cryostats with closed helium-cycles. These matrices are generally formed, by a non-reactive substance such as rare gases. This talk will stress the power of the matrix isolation technique, coupled with infrared spectroscopy, in particular for the molecular structure analysis and photochemistry involving UV-visible excitation. A series of case studies will be presented which illustrate the use of the method in the investigation of molecular structure of trapped species and chemical processes induced by both UV-visible and IR light. The infrared spectrum, and unimolecular UV induced photochemistry of the parent hydantoin monomer and 1-Methylhydantoin monomer are investigated experimentally by matrix isolation infrared spectroscopy, which was complemented by quantum chemical calculations performed at the DFT(B3LYP) and MP2 levels of theory. Upon irradiation at λ =230 nm, matrix-isolated hydantoin was found to photofragment into isocyanic acid, CO, and methylenimine while photolysis of 1-Methyhydantoin occured via two different pathways, which lead to fragmentation to OCNH + CO + H2C=NCH3 (preferred pathway) or to 2CO + 2H2C=NH. Thermal analysis study of 1-MH allowed observation of two polymorphs of the compound, a previously reported form (I) and a new form (II) which can be obtained by sublimation at T= 100 °C, p = 103 Pa, using the coldfinger technique.

Additionaly temperature dependence of host media and the trapped species were investigated for the first time in literature through a series of simple carboxylic acids such as Acetic acid, trichloroacetic acid, propionic acid, E-crotonic acid, and benzoic acid. We have shown that the O–H stretching band sitecomponents in the infrared spectra of these simple carboxylic acids in solid xenon matrices

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undergo reversible frequency blue-shifts with temperature, which are more pronounced for the lowest-frequency components. Such observation reveals that different type of H-bond like O–H · · · Xe specific interaction occur, depending on different trapping sites. MP2/aug-cc-pVDZ-PP Stuttgart ECP calculations were used to estimate the O–H · · · Xe interaction energies, which were also evaluated from them spectroscopic data in the light of the empirical correlation developed by Wendler et al [5]. The changes in the interaction energies upon temperature variation were also evaluated.

References:

[1] E.Whittle, D.A.Dows, and G.C.Pimentel, J.Chem.Phys. 22 (1954).

[2] Gulce Ogruc Ildiz, Cláudio M. Nunes, Nihal Kuş and Rui Fausto,

J. Chem. Phys. 137, 064309 (2012).

[3] Gulce Ogruc Ildiz, Claudio M. Nunes, and Rui Fausto, J. Phys.

Chem. A 117, 726 (2013).

[4] Bernardo A. Nogueira, Gulce O. Ildiz, Joao Canotilho,M.

Ermelinda S. Eusebio, and Rui Fausto, J. Phys. Chem. A 118, 5994

(2014).

[5] K.Wendler, J. Thar, S. Zahn, and B. Kirchner, J. Phys. Chem. A

114, 9529(2010).

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Modeling Common Vascular Diseases via Microfluidics

Ozan S. Sarıyer(a)*, Yang Li(b), Arun Ramachandran(b), Sergey Panyukov(c), Michael Rubinstein(d), and

Eugenia Kumacheva(b)

(a) Pîrî Reis University, Tuzla (b) University of Toronto, Toronto

(c) P. N. Lebedev Physics Institute, Moscow (d) University of North Carolina, Chapel Hill

* e-mail address: ossariyer@pirireis.edu.tr

Abstract: Flow of soft matter objects through one-dimensional environments is important in industrial, biological and biomedical systems. Establishing the underlying principles of the behavior of soft matter in confinement can shed light on many artificial and natural systems. We report an experimental and theoretical study of translocation of μm-size hydrogels (microgels) through microfluidic channels with a diameter smaller than an unperturbed microgel size (see Fig. 1). For microgels with different dimensions and mechanical properties, under a range of applied pressures, we established the universal principles of microgel entrance and passage through microchannels with different geometries. We also show a non-monotonic change in the flow rate of liquid through the constrained microgel, governed by its progressive confinement. Experimental results were in agreement with the theory for non-linear deformation of gels. Our work has implications for a broad range of phenomena, including occlusion of blood vessels by thrombi and needle-assisted hydrogel injection in tissue engineering. [1]

Figure 1: Microgels move along the direction indicated by the arrow, under the pressure drop applied along the microfluidic channel.

Reference: [1] Y. Li et al., Scientific Reports 5, 17017 (2015).

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Ab initio calculations of the potential of mean force for dissociation of salts in water

Serdar Kuyucak

University of Sydney, Sydney e-mail address: serdar@physics.usyd.edu.u

Abstract: Dissociation of salts in water is a fundamental problem in physical chemistry with many applications in other branches of science from molecular biology to climate science. Because life started and evolved in seas, salt water forms the bulk of life forms and its properties play a critical role in understanding the structure and function of biomolecules. Since the inception of computational molecular biology as a distinct field, there has been a keen interest in the properties of salt water from this community. Correct description of ion-water interactions is a central theme in molecular dynamics (MD) simulations, which is accepted as the standard model of molecular biology. However, lack of polarization interaction in the current force fields (i.e., potential functions), is a major problem in current applications of MD simulations. Explicit inclusion of polarization in the force fields was not feasible in the eighties due to lack of computing power. This is no more a problem but, despite ongoing efforts of several groups for over a decade, a polarizable force field for simulation of biomolecules has not been developed yet. This is most likely due to use of simple models for polarization (e.g., Drude model), and can be overcome by using ab initio calculations as a guide in incorporating polarization in the force fields. To this end, we have performed several ab initio MD simulations to study the hydration of ions in water [1], dissociation of NaCl [2] and CaCl [3], and the polarization effects in the gramicidin channel [4, 5].

Here we focus on the ab initio study of the dissociation of NaCl, which is the first such study. The significance of this problem is that there are no experimental constraints to guide the force fields for construction of ion-ion interactions—they are determined ad hoc using some combination rules. We determine the potential of mean force (PMF) between the two ions using the constrained-force method. The average force between the Na and Cl ions is calculated by performing Car-Parrinello MD simulations for a pair of Na-Cl

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ions in a water box. The simulation windows corresponding to the contact and solvent-separated minima, and the transition state in between, are further analyzed to determine the changes in the properties of hydration waters such as coordination number, dipole moment, and orientation. The ab initio results are compared with those obtained from classical MD simulations of aqueous NaCl using several common force fields. The ab initio PMF is found to have a shallower contact minimum and a smaller transition barrier compared with the classical ones. Also the binding free energy calculated from the ab initio PMF almost vanishes whereas it is negative for all the classical PMFs. Water dipole moments are observed to exhibit little change during dissociation, indicating that description of NaCl with a non-polarizable force field may be feasible. However, over coordination of the ion pair at all distances remains as a serious shortcoming of the current classical models. The ab initio results provide useful guidance for alternative parametrizations of the non-polarizable force fields as well as the polarizable ones currently under construction.

References:

[1] D. Bucher and S. Kuyucak, Polarization of water in the first hydration shell of K+ and Ca2+ ions. J. Phys. Chem. B 112, 10786-10790 (2008). [2] J. Timko, D. Bucher, and S. Kuyucak, Disociation of NaCl in water from ab initio molecular dynamics simulations. J. Chem. Phys. 132 #114510 (2010). [3] J. Timko, A. De Castro, and S. Kuyucak, Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl. J. Chem. Phys. 134 #114510 (2011). [4] D. Bucher and S. Kuyucak, Importance of water polarization for ion permeation in narrow pores. Chem. Phys. Lett. 477, 207-210 (2009). [5] J. Timko and S. Kuyucak, Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations. J. Chem. Phys. 137 #205106 (2012).

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Hydrogen-Bonded Layer-by-Layer Films and pH-Annealing

A. Levent Demirel

Koç University, İstanbul

Abstract: The layer-by-layer (LbL) formation of ultrathin films through alternating deposition of interacting materials has become a versatile tool to prepare functional surfaces. In this talk, I will first present the growth characteristics and pH-stability of various hydrogen-bonded LbL films. I will then discuss the effect of polymer chain relaxations on the pH-stability of spin coated LbL films. Different pH-induced disintegration profiles were observed depending on how long the films were kept in the dry state between exposures to buffer solutions. To understand the effect of slow relaxations on pH-stability, films were prepared at different nonequilibrium states by varying the spinning rate and solution-film contact time. The critical disintegration pH of the films increased with increasing spinning rate and decreasing solutionfilm contact time. pH-treatment of multilayers just below the critical disintegration pH, a process we call pH-annealing, enhanced their pH-stability significantly. Multilayers annealed longer at pH 7.0 showed better pH-stability (up to 1 h) at pH 9.0 whereas non-annealed films disintegrated within 10 min. The introduced pH-annealing process is promising for practical applications of H-bonded systems such as controlled drug delivery.

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İki Boyutta Tuzaklanmış Aşırı Soğuk Bozonlarda Etkileşmelerin Önemi

A. I. Mese(a)*, P. Capuzzi(b), Z. Akdeniz(c), S. E. Okan(a) and

M. P. Tosi(d)

(a) Trakya Üniversitesi, Edirne (b) Universidad de Buenos Aires, Buenos Aires

(c) Pîrî Reis Üniversitesi, İstanbul (d) NEST-INFM and Scuola Normale Superiore, Pisa

* e-mail address: aliihsanmese@trakya.edu.tr

Özet: İki boyutlu bir manyetik tuzakta hapsedilmiş ve birbirleriyle güçlü etkileşme içerisinde olan aşırı soğuk bozonların lokalizasyonu, logaritmik ve Bessel fonksiyonları ile tanımlı iki farklı model kullanarak incelenmiştir. Bose-Einstein yoğuşmasında sonlu sayıdaki girdaplar ile Abrikosov örgülerini anlamaya yönelik, Hartree, Hartree-Fock ve varyasyonel yöntemleriyle ayrı hesaplamalar yapılmıştır. Sayısı 2 ile 6 arasında değişen bozonik Rubidyum atomlarından oluşmuş sistemin taban durum enerjileri ve yoğunluk profilleri elde edilmiştir.

İzotropik tuzak altında, yoğuşmanın fiziksel özellikleri parçacıklar arasındaki etkileşme şiddeti değiştirilerek incelenmiştir. Böylelikle atomlar arasındaki güçlü etkileşmelerin sebep olduğu simetri kırılmaları nedeniyle, Bose-Einstein yoğuşmasından, fermiyonik kristal fazına geçiş açık bir şekilde görülmektedir. Sonuçlar, varyasyonel yöntemlerin Wigner Molekülü lokalizasyona, Hartree-Fock yaklaşımının bir süper molekülün delokalizasyonuna izin verdiği görülmüştür. Ek olarak, logaritmik etkileşme potansiyeli kullanımı ile kristalleşen bozonlar Coulombik etkileşmelere göre farklı kristalizasyon oluşturmaktadır.

Referans:

[1] A. I. Meşe, P. Capuzzi, Z. Akdeniz, S. E. Okan, and M. P. Tosi, Journal Phys: Condens Matter 20, 335222 (2008).

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Elasticity of Polyacrylamide - Graphene Oxide Composites

Gülşen Akın Evingür (a)* and Önder Pekcan(b)

(a)* Pîrî Reis University, Istanbul (b)Kadir Has University, Istanbul

* e-mail address: gulsen.evingur@pirireis.edu.tr

Abstract: Graphene oxide (GO) is a two dimensional carbon material with similar on atom thickness but with a large number of hydrophilic oxygenated functional groups [1]. Graphene oxide is light and has extremely high strength, and thermal stability. Therefore, GO is an efficient filler for the enhancement of electrical, mechanical and thermal properties of composite materials [2]. Moreover, GO is also used in such applications as nanoelectronic devices, hygienic products, super capacitors, and drug delivery systems [3].

In this study, we prepare Polyacrylamide (PAAm)-GO composites and investigate the mechanical behavior of PAAm- GO composites before and after swelling. This behavior was determined by using compressive technique and modeled by the Flory-Erman theory. Elasticity increased by increasing GO content, until 8µl of GO and then decreased by increasing GO content at 30 0C.

References:

[1] Y. Huang, M. Zeng, J. Ren, J. Wang, L. Fan, and Q. Xu, Colloids and Surf. A, 401, 97 (2012). [2] L. Zhang, Z. Wang, C. Xu, Y. Li, J. Gao, W. Wang, and Y. Lui, J. Mat. Chem., 2, 10399 (2011). [3] J. Shen, B. Yan, Ti. Li, Y. Long, N. Li, and M. Ye, Composites: Part A, 43, 1476 (2012).

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Aljinat-Kitosan Çoklu Tabaka Filmleri ve Özellikleri

Hakan Kaygusuz(a,b) *, F. Bedia Erim(a) ve Regine von Klitzing(b)

(a) İstanbul Teknik Üniversitesi, İstanbul (b) Berlin Teknik Üniversitesi, Berlin

* e-mail address: kaygusuzh@itu.edu.tr

Özet: Aljinat ve kitosan oldukça iyi bilinen ve pek çok uygulama alanına sahip doğal polielektrolitlerdir. Bu maddelerden yola çıkarak pek çok uygulama alanı geliştirilmiş olsa da, tekli ve birlikte yapılarının ayrıntılı incelenmesine halen ihtiyaç vardır. Bu çalışmada adı geçen biyopolimerlerin ardışık daldırma yöntemiyle çoklu tabaka filmleri hazırlanmış ve bu filmlere çeşitli fiziksel ve kimyasal etkiler incelenmiştir. Bunlardan en dikkat çekici olan, eksi yüklü bir yüzey aktif madde olan sodyum dodesil sülfatın (SDS) etkisi olarak gözlemlenmiştir. Silisyum destek üzerine hazırlanan filmler; elipsometri, atomik kuvvet mikroskopu (AFM), X-ışını reflektometrisi (XRR) gibi yöntemlerle karakterize edilmiştir. SDS varlığı, filmtabaka sayıları, tuz derişimi ve nem oranı gibi pek çok parametrenin film kalınlığına olan etkisi tartışılmıştır.

22

Tight Binding Molecular Dynamics Simulations of Vacancy Defected Single

Walled Carbon Nanotubes

Gülay Dereli(a), Can Ferman Gülmez(b)*, and Banu Süngü Mısırlıoğlu(b)

(a) Koç University, Istanbul (b) Yildiz Technical University, Istanbul

* e-mail address: can.ferman.gulmez.@std.yildiz.edu.tr

Abstract: Single Wall Carbon Nanotubes (SWCNTs) are among the most promising one dimensional materials in nanotechnology applications due to their unique thermal, electronic and mechanical properties [1-6]. However a large amount of experiments have demonstrated that it is very difficult to synthesize defect-free carbon nanotubes under present conditions. On the other hand, both theoretical and experimental studies have also demonstrated that these defects such as vacancy induced ones have crucial importance for the characteristics of the SWCNTs. So it is important to study with the defected carbon nanotubes.

In this work, we have studied the variation of the structural stability, physical characteristics and the energetics of the vacancy defected Single-Walled Carbon Nanotubes (SWCNTs) by using real space, Order(N) Tight Binding Molecular Dynamic (O(N) TBMD) simulation method [7-9]. In our simulations, first we have optimized pristine (undeformed) tubes and than multi-vacancies are introduced in the horizontal direction, along the equator of the SWCNTs. According to our results, structural stability, physical characteristics such as bond angle distribution functions, bond length distribution functions, radial distribution functions and the energetics of the tubes are discussed with increasing number of vacancies. The simulations are performed for different types of SWCNTs so the effects of the tube diameter and chirality are also examined.

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References:

[1] G. Dereli, B. Süngü, Physical Review B 75, 184104 (2007). [2] G. Dereli, B. Süngü, C. Özdoğan, Nanotechnology 18, 245704 (2007). [3] B. Onat, M. Konuk, S. Durukanoğlu, G. Dereli, Nanotechnology 20, 075707 (2009). [4] G. Dereli, B. Süngü, Ö. Eyecioğlu, Balkan Physics Letters 18, 181023 (2010). [5] G. Dereli, B. Süngü Mısırlıoğlu, Ö. Eyecioğlu, N. Vardar, Comput. Mater.Sci. 69, 234 – 242 (2013). [6] G. Dereli, Ö. Eyecioğlu, B. Süngü Mısırlıoğlu, Journal of Optoelectronics and Advanced Materials 17, 918-924 (2015). [7] C. Özdoğan, G. Dereli, T. Çağın, Comp. Phys. Commun. 148, 188 (2002). [8] G. Dereli, C. Özdoğan, Physical Review B 67, 0354415 (2003). [9] G. Dereli, C. Özdoğan, Physical Review B 67, 0354416 (2003).

24

A Theoretical Approach to Heptamers of ZnCl2 : A DFT Study

Cihan Özen(a), Alimet Sema Özen(a)*, Zehra Akdeniz(a), Giorgio Pastore(b), Mario Tosi(c)

(a) Piri Reis University, Istanbul (b) University of Trieste, Trieste

(c) Scuola Normale Superiore, Pisa * e-mail address: cihan.ozen@pru.edu.tr

Abstract: Molten salts are the important class of compounds which have versatile properties and are used in many areas of industry such as high temperature heat transfer medium, pyroprocessing, coal gasification and fuel cells. Among the molten salts, ZnCl2 has received much attention in the literature over a number years. Recently, various ZnCl2 structures have been studied by us [1,2]. In this study, heptamers of ZnCl2 have been studied by DFT method with a level of theory M06-2x/6-311+g(d). In a conclusion, nine conformers have been optimized and it is found out that clumped structure (Figure 1) has the lowest energy. Our results are consist with experimental findings.

Figure 1: 3D representation of the conformer with the lowest energy.

References:

[1] A. S. Özen, Z. Akdeniz, R. Ruberto, G. Pastore, M.P. Tosi, Phys. Chem. Liq. 53, 1 (2014). [2] A. S. Özen, Z. Akdeniz, R. Ruberto, G. Pastore, M. P. Tosi, Physics Letter A 378, 431 (2014).

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NOTES

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