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Source author record

Mohammad Reza Ejtehadi

Mohammad Reza Ejtehadi appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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cond-mat.softBiological Physicscond-mat.stat-mechcond-mat.mes-hallPopulations and EvolutionBiomoleculesphysics.flu-dyn

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Published work

15 published item(s)

preprint2026arXiv

Genotype specificity and spatial arrangement govern the direction and magnitude of selection in variable environments

Spatial environmental variation can either amplify or suppress the fixation of beneficial mutants in structured populations, yet the interplay of ecological factors and spatial structure in determining which outcome occurs remains theoretically unresolved. Here, we develop a unified framework for selection on lattice graphs with environmental heterogeneity, in which mutant and resident fitness depend on the local environmental state. Across three common classes of genotype-environment interactions and a wide range of spatial arrangements of environmental states, we identify two governing principles. Genotype specificity determines the direction of the effect: heterogeneity amplifies selection when it modulates resident fitness, but suppresses selection when it modulates mutant fitness, with genotype-symmetric modulation producing weaker amplification. Spatial arrangement determines the magnitude: intermixed versus clustered environments tune the strength of amplification or suppression without reversing the direction of the effect. Together, these principles reconcile disparate theoretical results and provide predictive criteria for adaptation in heterogeneous landscapes, from microbial communities to somatic evolution and cancer.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Counterintuitive properties of fixation probability and fixation time in population structures with spatially periodic resource distribution

Resource are often not uniformly distributed within a population. Spatial variations of concentration of a resource, change the fitness of competing strategies locally. The notion of fitness varying with respect to both genotype and environment is important in modeling cancer initiation, microbial evolution and evolution of drug resistance. Environmental interactions can be asymmetric, that is, they affect the fitness of one type more than the other. The question is how local environmental variations in network population structures change the selection dynamics in a finite population setting. We consider one-dimensional lattice population structures with spatial fitness distributions with a periodic pattern. Heterogeneity is determined by standard deviation of fitnesses and period. The model covers biologically relevant limits of two-habitat subdivided populations and randomly-distributed resources in high- and low-periods. We numerically calculate fixation probability and fixation times for a constant population birth-death process as fitness heterogeneity and period vary. We identify levels of heterogeneity for which a previously deleterious mutant, in a uniform environment, becomes beneficial. In other regimes of the problem we observe unexpected behavior where the fixation probability of both types are larger than their neutral value at the same time. This coincides with an exponential increase in time to fixation as a function of population size, which points to significant slow-down in selection process and the potential for coexistence between types in realistic time scales. We also discuss `fitness shift' model where the fitness function of one type is identical to the other up to a constant spatial shift. This leads to significant increase (or decrease) in the fixation probability of the mutant depending the value of the shift.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Structural and Dynamical Fingerprints of the Anomalous Dielectric Properties of Water Under Confinement

There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms which play a crucial role in electrochemistry and biology. In this study, the dielectric, structural and dynamical properties of confined water placed between two parallel graphene walls at different inter distances from the Angstrom scale to few tens of nanometer have been investigated using molecular dynamics. For dielectric properties of water, we show that the perpendicular component of water dielectric constant drastically decreases under sub $2\; nm$ spatial confinement. The achieved dielectric constant data through linear response and fluctuation-dissipation theory, are consistent with recent reported experimental results. By determining the charge density as well as fluctuations in the number of atoms, we provide a molecular rationale for the behavior of perpendicular dielectric response function. We also interpret the behavior of the dielectric response in terms of the presence of dangling O-H bonds of waters. By examining the residence time and lateral diffusion constant of water under confinement, we reveal that the water molecules tend to keep their hydrogen bond networks at the interface of water-graphene. We also found consistency between lateral diffusion and z-component of variance in the center of mass of the system as a function of confinement.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Active Brownian particles and run-and-tumble particles separate inside a maze

A diverse range of natural and artificial self-propelled particles are known and are used nowadays. Among them, active Brownian particles (ABPs) and run-and-tumble particles (RTPs) are two important classes. We numerically study non-interacting ABPs and RTPs strongly confined to different maze geometries in two dimensions. We demonstrate that by means of geometrical confinement alone, ABPs are separable from RTPs. By investigating Matryoshka-like mazes with nested shells, we show that a circular maze has the best filtration efficiency. Results on the mean first-passage time reveal that ABPs escape faster from the center of the maze, while RTPs reach the center from the rim more easily. According to our simulations and a rate theory, which we developed, ABPs in steady state accumulate in the outermost region of the Matryoshka-like mazes, while RTPs occupy all locations within the maze with nearly equal probability. These results suggest a novel technique for separating different types of self-propelled particles by designing appropriate confining geometries without using chemical or biological agents.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Gaussian theory for spatially distributed self-propelled particles

Obtaining a reduced description with particle and momentum flux densities outgoing from the microscopic equations of motion of the particles requires approximations. The usual method, we refer to as truncation method, is to zero Fourier modes of the orientation distribution starting from a given number. Here we propose another method to derive continuum equations for interacting self-propelled particles. The derivation is based on a Gaussian approximation (GA) of the distribution of the direction of particles. First, by means of simulation of the microscopic model we justify that the distribution of individual directions fits well to a wrapped Gaussian distribution. Second, we numerically integrate the continuum equations derived in the GA in order to compare with results of simulations. We obtain that the global polarization in the GA exhibits a hysteresis in dependence on the noise intensity. It shows qualitatively the same behavior as we find in particles simulations. Moreover, both global polarizations agree perfectly for low noise intensities. The spatio-temporal structures of the GA are also in agreement with simulations. We conclude that the GA shows qualitative agreement for a wide range of noise intensities. In particular, for low noise intensities the agreement with simulations is better as other approximations, making the GA to an acceptable candidates of describing spatially distributed self-propelled particles.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals

A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rod-like shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rod-like particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

How effective is graphene nanopore geometry on DNA sequencing?

In this paper we investigate the effects of graphene nanopore geometry on homopolymer ssDNA pulling process through nanopore using steered molecular dynamic (SMD) simulations. Different graphene nanopores are examined including axially symmetric and asymmetric monolayer graphene nanopores as well as five layer graphene polyhedral crystals (GPC). The pulling force profile, moving fashion of ssDNA, work done in irreversible DNA pulling and orientations of DNA bases near the nanopore are assessed. Simulation results demonstrate the strong effect of the pore shape as well as geometrical symmetry on free energy barrier, orientations and dynamic of DNA translocation through graphene nanopore. Our study proposes that the symmetric circular geometry of monolayer graphene nanopore with high pulling velocity can be used for DNA sequencing.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Vortex with four-fold defect lines in a simple model of self-propelled particles

We studied formation of vortex with four-fold symmetry in a minimal model of self-propelled particles, confined inside a squared box, using computer simulations and also theoretical analysis. In addition to the vortex pattern, we observed five other phases in the system: homogeneous gaseous phase, band structures, moving clumps, moving clusters and vibrating rings. All six phases emerge from controlling strength of noise and contribution of repulsion and alignment interactions. We studied shape of the vortex and its symmetry in detail. The pattern shows exponential defect lines where incoming and outgoing flows of particles collide. We show that alignment and repulsion interactions between particles are necessary to form such patterns. Finally, we derived hydro-dynamical equations for our model and compared them with the results of both computer simulations and Quincke rotors. A good agreement between the three is observed.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

A Low Reynolds Predator

Here we introduce a two-dimensional (2D) low-Reynolds swimmer and discuss the motion of the swimmer both in noise-free and stochastic regimes. Three spheres, linked by extensible arms, in a plane form the triangle body of micro-swimmer. Expansion and contraction of two-stated linkers in appropriate order causes both translational and rotational movement of the swimmer. It is shown that the motion of the swimmer could be controlled from a rotor to a directed linear swimmer depend on the sequence of the linkers activities. A few amount of noise in the the rhythm of the cycles introduces an interesting "random arc", while in the case of completely stochastic activity of the linkers the swimmer goes to a regular diffusive regime. Moreover, we show that in response to an external source of disturbance, the swimmer may approach or escape the source and shows interesting chemotaxis behavior. It is also shown that the model swimmer can easily be generalized to three dimensions or more complicated geometries.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Confinement dynamics of a semiflexible chain inside nano-spheres

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the chain for two different sizes of the spheres are studied in both procedures. It is shown that for the confined chains in the sphere sizes of our study, they appear in spiral or tennis-ball structures, and the tennis-ball structure is more likely to be observed in more compact confinements. Our results also show that the dynamical procedure of confinement and the rate of the confinement are influential parameters of the structure of the chain inside spherical cavities.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Polyelectrolytes polarization in non-uniform electric fields

Stretching dynamics of polymers in microfluidics is of particular interest for polymer scientists. As a charged polymer, a polyelectrolyte can be deformed from its coiled equilibrium configuration to an extended chain by applying uniform or non-uniform electric fields. By means of hybrid lattice Boltzmann-molecular dynamics simulations, we investigate how the condensed counterions around the polyelectrolyte contribute to the polymer stretching in inhomogeneous fields. As an application, we discuss the translocation phenomena and entropic traps, when the driving force is an applied external electric field.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Chain deformation helps translocation

Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the electric field inside and outside of a narrow pore is obtained. With an analysis based on "electrohydrodynamic equivalence" we determine the possibility of extension of a charged polymer due to the presence of an electric field gradient in the vicinity of the pore entrance. With a multi-scale hybrid simulation (LB-MD), it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers. We also highlight the role of long range hydrodynamic interactions via comparison of the LB-MD results with those obtained using a Langevin thermostat instead of the LB solver.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Peristaltic pumps work in nano scales

A design for a pump is suggested which is based on well-known peristaltic pumps. In order to simply describe the operation of the proposed pump, an innovative interpretation of low Reynolds number swimmers is presented and thereafter a similar theoretical model would be suggested to quantify the behavior of the pumps. A coarse-grained molecular dynamic simulation is used to examine the theoretical predictions and measure the efficiency of the pump in nano scales. It is shown that this pump with a modest design is capable of being a good option for transport processes in nano scale.

0 citations0 reviewsNo code linkedOpen access
preprint2010arXiv

Interaction of Spherical Colloidal Particles in Nematic Media with Degenerate Planar Anchoring

The interaction between two spherical colloidal particles with degenerate planar anchoring in a nematic media is studied by numerically minimizing the bulk Landau-de Gennes and surface energy using a finite element method. We find that the energy achieves its global minimum when the particles are in close contact and making an angle $θ= 28^\circ \pm 2$ with respect to the bulk nematic director, in agreement with the experiments. Although the quadrupolar structure of the director field is preserved in the majority of configurations, we show that for smaller orientation angles and at smaller inter-particle separations, the axial symmetry of the topological defect-pairs is continuously broken, resulting in the emergence of an attractive interaction.

0 citations0 reviewsNo code linkedOpen access
preprint2009arXiv

Simulation of Droplet Trains in Microfluidic Networks

In this work we show that in a microfluidic network and in low Reynolds numbers a system can be irreversible because of hysteresis effects.The network, which is employed in our simulations, is taken from recent experiments. The network consists of one loop connected to input and output pipes. A train of droplets enter the system at a uniform rate, but they may leave it in different patterns, e.g. periodic or even chaotic. The out put pattern depends on the time interval among the incoming droplets as well as the network geometry and for some parameters the system is not reversible.

0 citations0 reviewsNo code linkedOpen access