arXiv subjects

Erkan Tuzel

Publications and source records attributed to Erkan Tuzel.

17 recordsLinked to original sources

arXiv2017

Enhanced flagellar transport in asymmetric periodic arrays

Active swimmers are ubiquitous in nature, found in many diverse biological systems ranging from bacteria to vertebrate fish. Of particular importance are sperm cells which are swimmers that are crucial for the survival of many species including humans. Despite decades of work, the fluid physics of sperm in complex micro-environments such as the cervical tract, or the microfluidic devices used in assistive reproductive technologies remains illusive. Recently, a novel microfluidic device featuring periodic post arrays has been developed, and shown to select sperm cells with better motility, morphology and DNA integrity, more efficiently than existing approaches. Motivated by this, here we present a multi-scale model that aims to provide insight physical insight into the motility behavior of sperm in such periodic geometries. Our model combines a fluctuating hydrodynamic model of sperm with a probabilistic discrete-time lattice approach, and we show how hydrodynamic and boundary interactions facilitate both the enhancement of speed and persistence length of sperm cells in this post array. We then discuss how this enhancement of flagellar transport is related to its propensity, and develop a phase diagram. Our findings not only shed light into the fluid physics of flagellar swimmers in periodic arrays, but also have direct implications in a broad range of areas beyond fertility, including bio-inspired robotics, disease detection and drug delivery.

physics.bio-ph↗

arXiv2007

Mesoscopic model for the fluctuating hydrodynamics of binary and ternary mixtures

A recently introduced particle-based model for fluid dynamics with continuous velocities is generalized to model immiscible binary mixtures. Excluded volume interactions between the two components are modeled by stochastic multiparticle collisions which depend on the local velocities and densities. Momentum and energy are conserved locally, and entropically driven phase separation occurs for high collision rates. An explicit expression for the equation of state is derived, and the concentration dependence of the bulk free energy is shown to be the same as that of the Widom-Rowlinson model. Analytic results for the phase diagram are in excellent agreement with simulation data. Results for the line tension obtained from the analysis of the capillary wave spectrum of a droplet agree with measurements based on the Laplace's equation. The introduction of "amphiphilic" dimers makes it possible to model the phase behavior and dynamics of ternary surfactant mixtures.

cond-mat.soft↗

arXiv2006

Static and dynamic properties of a particle-based algorithm for non-ideal fluids and binary mixtures

A recently introduced particle-based model for fluid dynamics with effective excluded volume interactions is analyzed in detail. The interactions are modeled by means of stochastic multiparticle collisions which are biased and depend on local velocities and densities. Momentum and energy are exactly conserved locally. The isotropy and relaxation to equilibrium are analyzed and measured. It is shown how a discrete-time projection operator technique can be used to obtain Green-Kubo relations for the transport coefficients. Because of a large viscosity no long-time tails in the velocity auto-correlation and stress correlation functions were seen. Strongly reduced self-diffusion due to caging and an order/disorder transition is found at high collision frequency, where clouds consisting of at least four particles form a cubic phase. These structures were analyzed by measuring the pair-correlation function above and below the transition. Finally, the algorithm is extended to binary mixtures which phase-separate above a critical collision rate.

cond-mat.soft↗

arXiv2006

Dynamic correlations in stochastic rotation dynamics

The dynamic structure factor, vorticity and entropy density dynamic correlation functions are measured for Stochastic Rotation Dynamics (SRD), a particle based algorithm for fluctuating fluids. This allows us to obtain unbiased values for the longitudinal transport coefficients such as thermal diffusivity and bulk viscosity. The results are in good agreement with earlier numerical and theoretical results, and it is shown for the first time that the bulk viscosity is indeed zero for this algorithm. In addition, corrections to the self-diffusion coefficient and shear viscosity arising from the breakdown of the molecular chaos approximation at small mean free paths are analyzed. In addition to deriving the form of the leading correlation corrections to these transport coefficients, the probabilities that two and three particles remain collision partners for consecutive time steps are derived analytically in the limit of small mean free path. The results of this paper verify that we have an excellent understanding of the SRD algorithm at the kinetic level and that analytic expressions for the transport coefficients derived elsewhere do indeed provide a very accurate description of the SRD fluid.

cond-mat.soft↗

arXiv2005

Constructing thermodynamically consistent models with a non-ideal equation of state

A recently introduced particle-based model for fluid dynamics with continuous velocities is generalized to model fluids with excluded volume effects. This is achieved through the use of biased stochastic multi-particle collisions which depend on local velocities and densities and conserve momentum and kinetic energy. The equation of state is derived and criteria for the correct choice of collision probabilities are discussed. In particular, it is shown how a naive implementation can lead to inconsistent density fluctuations.

cond-mat.soft↗

arXiv2005

Equilibrium calculation of transport coefficients for a fluid-particle model

A recently introduced particle-based model for fluid flow, called Stochastic Rotation Dynamics, can be made Galilean invariant by introducing a random shift of the computational grid before collisions. In this paper, it is shown how the Green-Kubo relations derived previously can be resummed to obtain exact expressions for the collisional contributions to the transport coefficients. It is also shown that the collisional contribution to the microscopic stress tensor is not symmetric, and that this leads to an additional viscosity. The resulting identification of the transport coefficients for the hydrodynamic modes is discussed in detail, and it is shown that this does not impose restrictions on the applicability of the model. The collisional contribution to the thermal conductivity, which becomes important for small mean free path and small average particle number per cell, is also derived.

cond-mat.soft↗

arXiv2005

Consistent particle-based algorithm with a non-ideal equation of state

A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle collisions which depend on the local velocities and densities. Momentum and energy are exactly conserved locally. The equation of state is derived and compared to independent measurements of the pressure. Results for the kinematic shear viscosity and self-diffusion constants are presented. A caging and order/disorder transition is observed at high densities and large collision frequency.

cond-mat.soft↗

arXiv2004

Resummed Green-Kubo relations for a fluctuating fluid-particle model

A recently introduced stochastic model for fluid flow can be made Galilean invariant by introducing a random shift of the computational grid before collisions. This grid shifting procedure accelerates momentum transfer between cells and leads to a collisional contribution to transport coefficients. By resumming the Green-Kubo relations derived in a previous paper, it is shown that this collisional contribution to the transport coefficients can be determined exactly. The resummed Green-Kubo relations also show that there are no mixed kinetic-collisional contributions to the transport coefficients. The leading correlation corrections to the transport coefficients are discussed, and explicit expressions for the transport coefficients are presented and compared with simulation data.

cond-mat.soft↗

arXiv2003

Monitoring Diffusion of Reptating Polymer Chains by Direct Energy Transfer Method: a Monte Carlo Simulation

A kinetic Monte Carlo method was used to simulate the diffusion of reptating polymer chains across the interface. A time-resolved fluorescence technique conjunction with direct energy transfer method was used to measure the extend of diffusion of dye labeled reptating polymer chains. The diffusion of donor and acceptor labeled polymer chains between adjacent compartments was randomly generated. The fluorescence decay profiles of donor molecules were simulated at several diffusion steps to produce mixing of the polymer chains. Mixing ratios of donor and acceptor labeled polymer chains in compartments were measured at various stages (snapshots) of diffusion. It was observed that for a given molecular weight, the average interpenetration contour length was found to be proportional to the mixing ratio. Monte Carlo analysis showed that curvilinear diffusion coefficient is inversely proportional to the weight of polymer chains during diffusion.

cond-mat.soft↗

arXiv2003

Simulation of Interdiffusion in Between Compartments Having Heterogenously Distributed Donors and Acceptors

The final stage of latex film formation was simulated by introducing donors and acceptors into the adjacent compartments of a cube. Homogenous and/or heterogeneous donor-acceptor distributions were chosen for different types of simulations. The interdiffusion of the donors and the acceptors within these cubes was generated using the Monte-Carlo technique. The decay of the donor intensity I(t) by direct energy transfer (DET) was simulated for several interdiffusion steps. Gaussian noise was added to the I(t) curves to obtain more realistic decay profiles. I(t) decay curves were fitted to the phenomenological equation to calculate the fractional mixing at each interdiffusion step. The reliability of the Fickian diffusion model in the case of heterogenous and homogeneous donor-acceptor distributions are discussed for latex film formation.

cond-mat.soft↗

arXiv2003

A Thermodynamic Model for Prebiotic Protein Function

We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can function as a heat pump. Rock surfaces can facilitate the folding of amino acid chains having polar and hydrophobic residues, with an accompanying heat loss to the surrounding rock. These chains then absorb heat from the soup as they unfold. This opens the way to the enhancement of RNA replication rates, by the enzymatic action of folded proteins present in greater numbers at reduced temperatures. This gives an evolutionary advantage to those RNA coding amino acid sequences with non-degenerate folded states which would provide the most efficient refrigeration.

cond-mat.soft↗

arXiv2003

Transport Coefficients for Stochastic Rotation Dynamics in Three Dimensions

Explicit expressions for the transport coefficients of a recently introduced stochastic model for simulating fluctuating fluid dynamics are derived in three dimensions by means of Green-Kubo relations and simple kinetic arguments. The results are shown to be in excellent agreement with simulation data. Two collision rules are considered and their computational efficiency is compared.

cond-mat.stat-mech↗

arXiv2001

Evolutionary route to diploidy and sex

Using a bit-string model of evolution, we find a successful route to diploidy and sex in simple organisms. Allowing the sexually reproducing diploid individuals to also perform mitosis, as they do in a haploid-diploid cycle, leads to the complete takeover of the population by sexual diploids. This mechanism is so robust, that even the accidental conversion and pairing of only two diploids give rise to a sexual population.

cond-mat.soft↗

arXiv2001

Strategies for the evolution of sex

We find that the hypothesis made by Jan, Stauffer and Moseley [Theory in Biosc., 119, 166 (2000)] for the evolution of sex, namely a strategy devised to escape extinction due to too many deleterious mutations, is sufficient but not necessary for the successful evolution of a steady state population of sexual individuals within a finite population. Simply allowing for a finite probability for conversion to sex in each generation also gives rise to a stable sexual population, in the presence of an upper limit on the number of deleterious mutations per individual. For large values of this probability, we find a phase transition to an intermittent, multi-stable regime. On the other hand, in the limit of extremely slow drive, another transition takes place to a different steady state distribution, with fewer deleterious mutations within the asexual population.

cond-mat.soft↗

arXiv2000

Testing a hypothesis for the evolution of sex

An asexual set of primitive bacteria is simulated with a bit-string Penna model with a Fermi function for survival. A recent hypothesis by Jan, Stauffer and Moseley on the evolution of sex from asexual cells as a strategy for trying to escape the effects of deleterious mutations is checked. This strategy is found to provide a successful scenario for the evolution of a stable macroscopic sexual population.

cond-mat.soft↗

arXiv1999

Dissipative Dynamics and the Statistics of Energy States of a Hookean Model for Protein Folding

A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range of energies. We show that this system with harmonic interactions, under dissipative dynamics driven by random noise, leads to a distribution of energy states obeying a modified one-dimensional Ornstein-Uhlenbeck process and giving rise to the so called Wigner distribution. A tunably fine- or coarse-grained sampling of the energy landscape yields a family of distributions for the energies and energy spacings.

cond-mat.soft↗

arXiv1999

Glassy Dynamics of Protein Folding

A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis dynamics at low temperatures with the exponent $β\simeq 1/4$, in agreement with the best experimental results. The time dependent correlation functions for fluctuations about the native state, computed in the Gaussian approximation for real proteins, have also been found to have the same functional form. Our results indicate that the energy landscape exhibits universal features over a very large range of energies and is relatively independent of the specific dynamics.

cond-mat.soft↗