Research

Simply Complex Lab is driven towards deciphering emergent, complex, far from equilibrium phenomena. We are determined to solve scientifically and technologically persistent problems by exploring solutions under far from equilibrium conditions. Such conditions dictate:

    
• sufficiently high nonlinearity to broaden the phase space of the studied system,
    
• strong stochasticity for the system to flexibly explore its phase space,
    
• intrinsic positive and negative feedback mechanisms to help control many degrees of freedom.

We deliberately design and exploit these conditions in our experiments and theoretical models to tackle difficult questions such as;

Can we fabricate confined-but-connected silicon quantum dots?

This was a >30-year old material challenge, which we addressed by demonstrating an anisotropic random network of Si QDs that operate on the microscale without detracting its nanoscale features. These properties were thought to be mutually exclusive because charge confinement goes hand-in-hand with localization. We have shown otherwise using diffusion-limited growth in a vacuum chamber. The thin film is aligned in the vertical direction to decrease the onset of QD percolation (a nonlinear, emergent phenomenon) while preventing further growth of QD diameters via local chemical interactions (negative feedback) (Nano Letters, 2016).

Can we design similar complex structures with any material or in different experimental settings?

This study is the offspring of the QD network study, which we are currently investigating. We have used different experimental settings and a theoretical model for understanding the importance of intrinsic feedback mechanisms on complex structure formation. We are collaborating with Prof. Oğuz Gülseren, Dr. C. Sibel Sayın, and Prof. Raşit Turan in this effort. Our plans involve fabricating the random network structure using different materials. The ultimate goal is to develop a universal methodology to atom-by-atom fabricating hierarchically complex structures and functionalities, similar to what we see in Nature, using any element. We are collaborating with Prof. F. Ömer İlday in this quest.

Where do we find millions of computer-generated hypothetical zeolite structures?

An incredibly tiny fraction of hypothetical zeolites have been experimentally synthesized. We believe that the underlying cause is that current synthesis techniques cannot produce different conformational transitions while operating near-equilibrium. We recently set-up an experimental system that explores these mythical creatures far from equilibrium. Currently, we are working towards reproducing our encouraging preliminary results. The next step will be to build a theoretical understanding of their formation and sustenance mechanisms.

Can we control zeolite nucleation and growth to achieve hierarchical, complex zeolite topologies?

This is a sister project to the hypothetical zeolite research. Here, we set out to device an experimental methodology, which will allow us to guide the growth and differentiation of the structure from smaller to the larger scales using critical physical and chemical “control nobs.” This study has received funding from TUBITAK (1001, basic science grant no. 118F115). We are collaborating with Prof. F. Ömer İlday and Prof. Parviz Elahi in this effort.

These four topics are oriented towards complex, hierarchical material design and engineering. We are also active in physics, specifically, statistical and condensed matter physics, and nonlinear dynamics. Five topics below describe our efforts on deciphering the fundamental principles of emergence and complexity for strongly stochastic and highly nonlinear systems.

Can we mimic the behavior of living organisms in nonliving systems?

This was a profoundly fundamental question at the interface between physics and biology, which we addressed by showing simple polystyrene nanospheres suspended in the water can form autocatalytic aggregates that exhibit a rich set of complex behaviors analogous to those commonly associated with living organisms (e.g., self-regulation, self-healing, self-replication, co-existence, competition, and motility) when driven far from equilibrium (Nature Communications, 2017). This study has received funding from TUBITAK (1001, basic science grant no. 115F110).

Can dissipative self-assembly methodologies transcend the specificity of the systems that are being studied?

This study has branched from our colloidal work. Here, we demonstrated the fundamental principles of a universal dissipative self-assembly process. We followed a reductionist approach, and judiciously exploited only the intrinsic physical mechanisms that drive and control the self-assembly processes. This allowed us to assemble and disassemble aggregates of materials with living and nonliving, simple and complex, passive and active, identical, and nonidentical constituents. We showcase complete control over the aggregates, which can take arbitrary geometrical shapes that can be dynamically moved within seconds. The physical universality of these dynamics is shown through scale-invariant autocatalytic growth curves and universal Tracy-Widom statistics of the interface fluctuations of the growing aggregates (Nature Physics, 2020). This work is also featured on the cover of Nature Physics October Issue (top right and bottom left; for full images see journal’s website banner). This issue has been dedicated to the journal’s 15th anniversary. The study has received funding from the European Research Council Starting Grant program (ERC-StG. Ph.D., grant no. 853387).

What drives dynamic adaptive pattern formation in simple systems? 

This study is also branched from the colloidal work in which we reported the first dynamic adaptive colloidal crystals comprising up to thousands of particles of a multiplicity of patterns (hexagonal, square, oblique lattices, and Moiré patterns) that emerged and were sustained far from equilibrium. Recently, we confirmed that this system could readily be placed in conditions where it has access to multiple steady states (in this case, multiple patterns) that can co-exist, co-evolve, compete, and in some instances, interchange into one another. We are currently working towards replicating these behaviors in numerical simulations and developing a theoretical model that qualitatively describes the observed phenomena. We are collaborating with Prof. F. Ömer İlday and Prof. Luca Biancofiore in this effort.

When a dynamic adaptive system is faced with multiple choices, which one will it choose? And why?

This is the third branch of our colloidal work, which scrutinize the fundamental question at the heart of the condensed matter, statistical and nonlinear physics: When far from equilibrium, in the presence of fluctuations, and faced with multiple steady states with small energy differences, what are the relative probabilities that the system evolves to each accessible steady state? Our goal is to create a phase map of these colloidal crystals, similar to a phase diagram of thermodynamics, but where each phase (here, crystal pattern) is dynamic and of finite occupation probability. We will use a convenient tool, fitness landscapes, which originates from evolutionary biology to describe the stability of each phase in various conditions. We will further ask to what extent this control is extendable down to the few-nm scale, where fluctuations are much more substantial than 500-nm polystyrene colloids, and if and how these findings change when using nonidentical, in size or shape, but still passive particles? This project has received funding from the European Research Council Starting Grant program (ERC-StG. Ph.D., grant no. 853387).

How noise affects physical systems and how it can be characterized?

Noise has mostly been treated as a potential source of error, which is believed to be detrimental to the functionality of human-made systems. However, Nature shows us that noise can increase robustness, improve evolutionary fitness, enhance functionality, or is outright necessary for certain functions to emerge. We are very interested in studying the effect of noise in physical and biological systems. Currently, we are developing a computational toolbox to study thermal noise in our colloidal system. The goal is to develop a computational toolbox to accurately resolve instantaneous velocities of interacting Brownian nanoparticles in a driven many-body system with high spatial and temporal resolution. We plan to extend this effort to study the effect of intense thermal fluctuations in biological systems. This project has received funding from TÜBİTAK – European Commission Marie Skłodowska-Curie Actions Cofund program (PI: Michaël Barbier, grant no. 120C074). 

The following three topics are more biology oriented, spanning from microbiology to cancer and immune system research. They are conceptually intertwined with the above-described topics in materials science, chemistry, and physics. 

How do emergent dynamics at the cellular and population-level improve bacterial fitness?

In this ongoing research effort, we investigate how many cells are required to activate quorum sensing? Does this number change with the external stimuli? Why? How? What are the minimum requirements for quorum sensing and biofilm formation? How environmental and physical constraints, in the presence of intense thermal noise, affect communication between bacterial cells and populations? We are using the same experimental settings we used in our colloidal work. This method offers great flexibility over the movement of individual cells and their populations. For instance, we can collect any number of cells (from one to tens, hundreds, thousands of cells), transport these populations from one location to the other, arrange distances between bacterial colonies, and separate or mix populations of different types of bacteria. Some of these capabilities are demonstrated in our recent work (Nature Physics, 2020). We believe further investigation using our unique experimental system can open up unexplored territories to microbiology research, the realm of far from equilibrium. This study has received funding from TUBITAK (1001, basic science grant no. 117F352). We are collaborating with Prof. E. Doruk Engin and Prof. Yilin Wu in this effort.

How cancer cells adapt and survive circulation?

Cancer cells have to develop adaptive strategies to invade and metastasize. These strategies heavily depend on their environment. A vast body of work investigated these strategies in primary and secondary site tumors. However, in between these two, there is circulation. How harsh physical conditions of circulation effects these strategies is, to us, the missing link in cancer metastasis research. We are set out to investigate this missing link by mimicking the circulation and observing different cancerous cells while they are exhibiting and changing their adaptive strategies to a highly dynamic environment. Currently, we are modeling our experimental observations to quantify our quite interesting empirical findings. We are collaborating with Prof. Özgür Şahin and Prof. Tayfun Özçelik in this effort.

How our immune system is “physically” affected by the type of diet?

Endoplasmic reticulum (ER) stress in macrophages contributes to the development of chronic inflammatory and metabolic diseases such as obesity, insulin resistance, and atherosclerosis. Our collaborator Prof. Ebru Erbay and her research group discovered that diet plays a significant role in remodeling the ER stress of macrophages. Now, we teamed up with the Erbay group to see how ER stress affects the physical fitness of these macrophages and how it impairs their effectiveness for chronic inflammatory and metabolic diseases.