arXiv subjects

Dervis Can Vural

Publications and source records attributed to Dervis Can Vural.

25 records · Page 2Linked to original sources

arXiv2017

A Tissue Engineered Model of Aging: Interdependence and Cooperative Effects in Failing Tissues

Aging remains a fundamental open problem in modern biology. Although there exist a number of theories on aging on the cellular scale, nearly nothing is known about how microscopic failures cascade to macroscopic failures of tissues, organs and ultimately the organism. The goal of this work is to bridge microscopic cell failure to macroscopic manifestations of aging. We use tissue engineered constructs to control the cellular-level damage and cell-cell distance in individual tissues to establish the role of complex interdependence and interactions between cells in aging tissues. We found that while microscopic mechanisms drive aging, the interdependency between cells plays a major role in tissue death, providing evidence on how cellular aging is connected to its higher systemic consequences.

q-bio.TO↗

arXiv2017

Muscle-Cell-Based "Living Diodes"

A new type of diode that is made entirely of electrically excitable muscle cells and nonexcitable fibroblast cells is designed, fabricated, and characterized. These two cell types in a rectangular pattern allow the signal initiated on the excitable side to pass to the nonexcitable side, and not in the opposite direction.

q-bio.TO↗

arXiv2015

The Organization and Control of an Evolving Interdependent Population

Starting with Darwin, biologists have asked how populations evolve from a low fitness state that is evolutionarily stable to a high fitness state that is not. Specifically of interest is the emergence of cooperation and multicellularity where the fitness of individuals often appears in conflict with that of the population. Theories of social evolution and evolutionary game theory have produced a number of fruitful results employing two-state two-body frameworks. In this study we depart from this tradition and instead consider a multi-player, multi-state evolutionary game, in which the fitness of an agent is determined by its relationship to an arbitrary number of other agents. We show that populations organize themselves in one of four distinct phases of interdependence depending on one parameter, selection strength. Some of these phases involve the formation of specialized large-scale structures. We then describe how the evolution of independence can be manipulated through various external perturbations.

q-bio.PE↗

arXiv2013

The "Tunneling Two-Level Systems" Model of the Low-Temperature Properties of Glasses: Are "Smoking-Gun" Tests Possible?

Following a brief review of the "two-level (tunneling) systems" model of the low-temperature properties of amorphous solids ("glasses"), we ask whether it is in fact the unique explanation of these properties as is usually assumed, concluding that this is not necessarily the case. We point out that (a) one specific form of the model is already experimentally refuted, and (b) that a definitive test of the model in its most general form, while not yet carried out, would appear to be now experimentally feasible.

cond-mat.dis-nn↗

arXiv2013

Increased Network Interdependency Leads to Aging

Although species longevity is subject to a diverse range of selective forces, the mortality curves of a wide variety of organisms are rather similar. We argue that aging and its universal characteristics may have evolved by means of a gradual increase in the systemic interdependence between a large collection of biochemical or mechanical components. Modeling the organism as a dependency network which we create using a constructive evolutionary process, we age it by allowing nodes to be broken or repaired according to a probabilistic algorithm that accounts for random failures/repairs and dependencies. Our simulations show that the network slowly accumulates damage and then catastrophically collapses. We use our simulations to fit experimental data for the time dependent mortality rates of a variety of multicellular organisms and even complex machines such as automobiles. Our study suggests that aging is an emergent finite-size effect in networks with dynamical dependencies and that the qualitative and quantitative features of aging are not sensitively dependent on the details of system structure.

q-bio.PE↗

arXiv2012

Universal Sound Attenuation in Amorphous Solids at Low-Temperatures

Disordered solids are known to exhibit quantitative universalities at low temperatures, the most striking of which is the ultrasonic attenuation coefficient Q. The established theory of tunneling two state systems (TTLS) in its original form (i.e. without extra fitting functions and parameters), is unable to explain this universality. While the TTLS model can be modified, particularly by including long range phonon induced interactions to explain the universal value of Q, (a) it is not clear that the essential features of the original model that has been successful in explaining the experimental data is preserved, and (b) even if it is, it is not clear that the postulates of the original model remain necessary. The purpose of this study is to derive the universal acoustic absorption and related quantities observed in disordered solids by starting from a many-body quantum theory of unspecified amorphous blocks that mutually interact through the strain field. Based on very generic assumptions and having no adjustable fitting parameters, the frequency and initial state averaged macroscopic attenuation of a group of interacting disordered blocks is calculated in the low temperature regime by a novel "trace method", which then is iterated up-to experimental length scales through a real space renormalization group approach. Then using a heuristic second-order perturbation argument, the frequency dependence of Q is found, and combined with the previous result to yield the observed universal values in the MHz-Ghz range of frequencies. It is concluded that strong microscopic postulates are not necessary in order to explain the thermal conductivity, velocity shift and sound attenuation of disordered media in the low temperature regime.

cond-mat.dis-nn↗

arXiv2011

When Models Interact with their Subjects: The Dynamics of Model Aware Systems

A scientific model need not be a passive and static descriptor of its subject. If the subject is affected by the model, the model must be updated to explain its affected subject. In this study, two models regarding the dynamics of model aware systems are presented. The first explores the behavior of "prediction seeking" (PSP) and "prediction avoiding" (PAP) populations under the influence of a model that describes them. The second explores the publishing behavior of a group of experimentalists coupled to a model by means of confirmation bias. It is found that model aware systems can exhibit convergent random or oscillatory behavior and display universal 1/f noise. A numerical simulation of the physical experimentalists is compared with actual publications of neutron life time and Λ mass measurements and is in good quantitative agreement.

physics.data-an↗