Erdal Toprak

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Antibiotic resistance can evolve through the sequential accumulation of multiple mutations. To study such gradual evolution, we developed a selection device, the 'morbidostat', that continuously monitors bacterial growth and dynamically regulates drug concentrations, such that the evolving population is constantly challenged. We analyzed the evolution of(More)
The centroid of a fluorophore can be determined within approximately 1.5-nm accuracy from its focused image through fluorescence imaging with one-nanometer accuracy (FIONA). If, instead, the sample is moved away from the focus, the point-spread-function depends on both the position and 3D orientation of the fluorophore, which can be calculated by defocused(More)
Kinesin I can walk on a microtubule for distances as long as several micrometers. However, it is still unclear how this molecular motor can remain attached to the microtubule through the hundreds of mechanochemical cycles necessary to achieve this remarkable degree of processivity. We have addressed this issue by applying ensemble and single-molecule(More)
Predicting evolutionary paths to antibiotic resistance is key for understanding and controlling drug resistance. When considering a single final resistant genotype, epistatic contingencies among mutations restrict evolution to a small number of adaptive paths. Less attention has been given to multi-peak landscapes, and while specific peaks can be favoured,(More)
The technique of determining the position of individual fluorescent molecules with nanometer resolution, called FIONA, has become an important tool for several biophysical applications such as studying motility mechanisms of motor proteins. The position determination is usually done by fitting a 2-D Gaussian (x-y vs. photon number) to the emission intensity(More)
Molecular motors, which use energy from ATP hydrolysis to take nanometer-scale steps with run-lengths on the order of micrometers, have important roles in areas such as transport and mitosis in living organisms. New techniques have recently been developed to measure these small movements at the single-molecule level. In particular, fluorescence imaging has(More)
Single-molecule biophysics has been serving biology for more than two decades. Fluorescence microscopy is one of the most commonly used tools to identify molecules of interest and to visualize biological events. Here we describe some of the most commonly used fluorescence imaging tools to measure nanoscale movements and the rotational dynamics of(More)
In many research areas such as biology, biochemistry, and biophysics, measuring distances or identifying and counting objects can be of great importance. To do this, researchers often need complicated and expensive tools in order to have accurate measurements. In addition, these measurements are often done under nonphysiological settings. X-ray diffraction,(More)
In this paper we study the large Nc limit of SO(Nc) gauge theory coupled to a real scalar field following ideas of Rajeev[1]. We will see that the phase space of this resulting classical theory is Sp1(H)/U(H+) which is the analog of the Siegel disc in infinite dimensions. The linearized equations of motion give us a version of the well-known ’t Hooft(More)
We introduce a bifocal imaging method that enables three-dimensional (3D) tracking of both fluorescent and nonfluorescent particles. We accomplish this by simultaneously imaging a focused plane, for in-plane position (x,y), and a defocused plane, for out-of-plane position (z), of a molecule using a single CCD camera. We applied our method to several systems(More)