arXiv subjects

David R. Nelson

Publications and source records attributed to David R. Nelson.

At least 55 records · Page 3Linked to original sources

arXiv2017

Spatial gene drives and pushed genetic waves

Gene drives have the potential to rapidly replace a harmful wild-type allele with a gene drive allele engineered to have desired functionalities. However, an accidental or premature release of a gene drive construct to the natural environment could damage an ecosystem irreversibly. Thus, it is important to understand the spatiotemporal consequences of the super-Mendelian population genetics prior to potential applications. Here, we employ a reaction-diffusion model for sexually reproducing diploid organisms to study how a locally introduced gene drive allele spreads to replace the wild-type allele, even though it possesses a selective disadvantage $s>0$. Using methods developed by N. Barton and collaborators, we show that socially responsible gene drives require $0.5<s<0.697$, a rather narrow range. In this "pushed wave" regime, the spatial spreading of gene drives will be initiated only when the initial frequency distribution is above a threshold profile called "critical propagule", which acts as a safeguard against accidental release. We also study how the spatial spread of the pushed wave can be stopped by making gene drives uniquely vulnerable ("sensitizing drive") in a way that is harmless for a wild-type allele. Finally, we show that appropriately sensitized drives in two dimensions can be stopped even by imperfect barriers perforated by a series of gaps.

q-bio.PE↗

arXiv2017

Non-Hookean statistical mechanics of clamped graphene ribbons

Thermally fluctuating sheets and ribbons provide an intriguing forum in which to investigate strong violations of Hooke's Law: large distance elastic parameters are in fact not constant, but instead depend on the macroscopic dimensions. Inspired by recent experiments on free-standing graphene cantilevers, we combine the statistical mechanics of thin elastic plates and large-scale numerical simulations to investigate the thermal renormalization of the bending rigidity of graphene ribbons clamped at one end. For ribbons of dimensions $W\times L$ (with $L\geq W$), the macroscopic bending rigidity $κ_R$ determined from cantilever deformations is independent of the width when $W<\ell_\textrm{th}$, where $\ell_\textrm{th}$ is a thermal length scale, as expected. When $W>\ell_\textrm{th}$, however, this thermally renormalized bending rigidity begins to systematically increase, in agreement with the scaling theory, although in our simulations we were not quite able to reach the system sizes necessary to determine the fully developed power law dependence on $W$. When the ribbon length $L > \ell_p$, where $\ell_p$ is the $W$-dependent thermally renormalized ribbon persistence length, we observe a scaling collapse and the beginnings of large scale random walk behavior.

cond-mat.soft↗

arXiv2017

Thermal stiffening of clamped elastic ribbons

We use molecular dynamics to study the vibrations of a thermally fluctuating two-dimensional elastic membrane clamped at both ends. We directly extract the eigenmodes from resonant peaks in the frequency domain of the time-dependent height and measure the dependence of the corresponding eigenfrequencies on the microscopic bending rigidity of the membrane, taking care also of the subtle role of thermal contraction in generating a tension when the projected area is fixed. At finite temperatures we show that the effective (macroscopic) bending rigidity tends to a constant as the bare bending rigidity vanishes, consistent with theoretical arguments that the large-scale bending rigidity of the membrane arises from a strong thermal renormalization of the microscopic bending rigidity. Experimental realizations include covalently-bonded two-dimensional atomically thin membranes such as graphene and molybdenum disulfide or soft matter systems such as the spectrin skeleton of red blood cells or diblock copolymers.

cond-mat.soft↗

arXiv2016

Population Genetics with Fluctuating Population Sizes

Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges naturally and allows adiabatic elimination of a fast population size variable to deduce the fluctuations-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

q-bio.PE↗

arXiv2016

Evolutionary Dynamics with Fluctuating Population Sizes and Strong Mutualism

Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

q-bio.PE↗

arXiv2016

Statistical mechanics of thin spherical shells

We explore how thermal fluctuations affect the mechanics of thin amorphous spherical shells. In flat membranes with a shear modulus, thermal fluctuations increase the bending rigidity and reduce the in-plane elastic moduli in a scale-dependent fashion. This is still true for spherical shells. However, the additional coupling between the shell curvature, the local in-plane stretching modes and the local out-of-plane undulations, leads to novel phenomena. In spherical shells thermal fluctuations produce a radius-dependent negative effective surface tension, equivalent to applying an inward external pressure. By adapting renormalization group calculations to allow for a spherical background curvature, we show that while small spherical shells are stable, sufficiently large shells are crushed by this thermally generated "pressure". Such shells can be stabilized by an outward osmotic pressure, but the effective shell size grows non-linearly with increasing outward pressure, with the same universal power law exponent that characterizes the response of fluctuating flat membranes to a uniform tension.

cond-mat.soft↗

arXiv2016

Plastic deformation of tubular crystals by dislocation glide

Tubular crystals, two-dimensional lattices wrapped into cylindrical topologies, arise in many contexts, including botany and biofilaments, and in physical systems such as carbon nanotubes. The geometrical principles of botanical phyllotaxis, describing the spiral packings on cylinders commonly found in nature, have found application in all these systems. Several recent studies have examined defects in tubular crystals associated with crystalline packings that must accommodate a fixed tube radius. Here, we study the mechanics of tubular crystals with variable tube radius, with dislocations interposed between regions of different phyllotactic packings. Unbinding and separation of dislocation pairs with equal and opposite Burgers vectors allow the growth of one phyllotactic domain at the expense of another. In particular, glide separation of dislocations offers a low-energy mode for plastic deformations of solid tubes in response to external stresses, reconfiguring the lattice step by step. Through theory and simulation, we examine how the tube's radius and helicity affects, and is in turn altered by, the mechanics of dislocation glide. We also discuss how a sufficiently strong bending rigidity can alter or arrest the deformations of tubes with small radii.

cond-mat.soft↗

arXiv2016

Striated Populations in Disordered Environments with Advection

Growth in static and controlled environments such as a Petri dish can be used to study the spatial population dynamics of microorganisms. However, natural populations such as marine microbes experience fluid advection and often grow up in heterogeneous environments. We investigate a generalized Fisher-Kolmogorov-Petrovsky-Piscounov (FKPP) equation describing single species population subject to a constant flow field and quenched random spatially inhomogeneous growth rates with a fertile overall growth condition. We analytically and numerically demonstrate that the non-equilibrium steady-state population density develops a flow-driven striation pattern. The striations are highly asymmetric with a longitudinal correlation length that diverges linearly with the flow speed and a transverse correlation length that approaches a finite velocity-independent value. Linear response theory is developed to study the statistics of the steady states. Theoretical predictions show excellent agreement with the numerical steady states of the generalized FKPP equation obtained from Lattice Boltzmann simulations. These findings suggest that, although the growth disorder can be spatially uncorrelated, correlated population structures with striations emerge naturally at sufficiently strong advection.

q-bio.PE↗

arXiv2016

Non-Hermitian Localization in Biological Networks

We explore the spectra and localization properties of the N-site banded one-dimensional non-Hermitian random matrices that arise naturally in sparse neural networks. Approximately equal numbers of random excitatory and inhibitory connections lead to spatially localized eigenfunctions, and an intricate eigenvalue spectrum in the complex plane that controls the spontaneous activity and induced response. A finite fraction of the eigenvalues condense onto the real or imaginary axes. For large N, the spectrum has remarkable symmetries not only with respect to reflections across the real and imaginary axes, but also with respect to 90 degree rotations, with an unusual anisotropic divergence in the localization length near the origin. When chains with periodic boundary conditions become directed, with a systematic directional bias superimposed on the randomness, a hole centered on the origin opens up in the density-of-states in the complex plane. All states are extended on the rim of this hole, while the localized eigenvalues outside the hole are unchanged. The bias dependent shape of this hole tracks the bias independent contours of constant localization length. We treat the large-N limit by a combination of direct numerical diagonalization and using transfer matrices, an approach that allows us to exploit an electrostatic analogy connecting the "charges" embodied in the eigenvalue distribution with the contours of constant localization length. We show that similar results are obtained for more realistic neural networks that obey "Dale's Law" (each site is purely excitatory or inhibitory), and conclude with perturbation theory results that describe the limit of large bias g, when all states are extended. Related problems arise in random ecological networks and in chains of artificial cells with randomly coupled gene expression patterns.

cond-mat.dis-nn↗

arXiv2015

Response of thermalized ribbons to pulling and bending

Motivated by recent free-standing graphene experiments, we show how thermal fluctuations affect the mechanical properties of microscopically thin solid ribbons. A renormalization group analysis of flexural phonons reveals that elongated ribbons behave like highly anisotropic polymers, where the two dimensional nature of ribbons is reflected in non-trivial power law scalings of the persistence length and effective bending and twisting rigidities with the ribbon width. With a coarse-grained transfer matrix approach, we then show how thermalized ribbons respond to pulling and bending forces over a wide spectrum of temperatures, forces and ribbon lengths.

cond-mat.soft↗

arXiv2015

Survival Probabilities at Spherical Frontiers

Motivated by tumor growth and spatial population genetics, we study the interplay between evolutionary and spatial dynamics at the surfaces of three-dimensional, spherical range expansions. We consider range expansion radii that grow with an arbitrary power-law in time: $R(t)=R_0(1+t/t^*)^Θ$, where $Θ$ is a growth exponent, $R_0$ is the initial radius, and $t^*$ is a characteristic time for the growth, to be affected by the inflating geometry. We vary the parameters $t^*$ and $Θ$ to capture a variety of possible growth regimes. Guided by recent results for two-dimensional inflating range expansions, we identify key dimensionless parameters that describe the survival probability of a mutant cell with a small selective advantage arising at the population frontier. Using analytical techniques, we calculate this probability for arbitrary $Θ$. We compare our results to simulations of linearly inflating expansions ($Θ=1$ spherical Fisher-Kolmogorov-Petrovsky-Piscunov waves) and treadmilling populations ($Θ=0$, with cells in the interior removed by apoptosis or a similar process). We find that mutations at linearly inflating fronts have survival probabilities enhanced by factors of 100 or more relative to mutations at treadmilling population frontiers. We also discuss the special properties of "marginally inflating" $(Θ=1/2)$ expansions.

q-bio.PE↗

arXiv2014

Bending forces plastically deform growing bacterial cell walls

Cell walls define a cell shape in bacteria. They are rigid to resist large internal pressures, but remarkably plastic to adapt to a wide range of external forces and geometric constraints. Currently, it is unknown how bacteria maintain their shape. In this work, we develop experimental and theoretical approaches and show that mechanical stresses regulate bacterial cell-wall growth. By applying a precisely controllable hydrodynamic force to growing rod-shaped Escherichia coli and Bacillus subtilis cells, we demonstrate that the cells can exhibit two fundamentally different modes of deformation. The cells behave like elastic rods when subjected to transient forces, but deform plastically when significant cell wall synthesis occurs while the force is applied. The deformed cells always recover their shape. The experimental results are in quantitative agreement with the predictions of the theory of dislocation-mediated growth. In particular, we find that a single dimensionless parameter, which depends on a combination of independently measured physical properties of the cell, can describe the cell's responses under various experimental conditions. These findings provide insight into how living cells robustly maintain their shape under varying physical environments.

cond-mat.soft↗

arXiv2014

Asymmetric Mutualism in Two- and Three-Dimensional Range Expansions

Genetic drift at the frontiers of two-dimensional range expansions of microorganisms can frustrate local cooperation between different genetic variants, demixing the population into distinct sectors. In a biological context, mutualistic or antagonistic interactions will typically be asymmetric between variants. By taking into account both the asymmetry and the interaction strength, we show that the much weaker demixing in three dimensions allows for a mutualistic phase over a much wider range of asymmetric cooperative benefits, with mutualism prevailing for any positive, symmetric benefit. We also demonstrate that expansions with undulating fronts roughen dramatically at the boundaries of the mutualistic phase, with severe consequences for the population genetics along the transition lines.

q-bio.PE↗

arXiv2014

Quantum hexatic order in two-dimensional dipolar and charged fluids

Recent advances in cold atom experimentation suggest that studies of quantum two-dimensional melting of dipolar molecules, with dipoles aligned perpendicular to ordering plane, may be on the horizon. An intriguing aspect of this problem is that two-dimensional \emph{classical} aligned dipoles (already studied in great detail in soft matter experiments on magnetic colloids) are known to melt via a two-stage process, with an intermediate hexatic phase separating the usual crystal and isotropic fluid phases. We estimate here the effect of quantum fluctuations on this hexatic phase, for both dipolar systems and charged Wigner crystals. Our approximate phase diagrams rely on a pair of Lindemann criteria, suitably adapted to deal with effects of thermal fluctuations in two dimensions. As part of our analysis, we determine the phonon spectra of quantum particles on a triangular lattice interacting with repulsive $1/r^3$ and $1/r$ potentials. A large softening of the transverse and longitudinal phonon frequencies, due to both lattice effects and quantum fluctuations, plays a significant role in our analysis. The hexatic phase is predicted to survive down to very low temperatures.

cond-mat.quant-gas↗

arXiv2013

Thermal Excitations of Warped Membranes

We explore thermal fluctuations of thin planar membranes with a frozen spatially-varying background metric and a shear modulus. We focus on a special class of $D$-dimensional ``warped membranes'' embedded in a $d-$dimensional space with $d\ge D+1$ and a preferred height profile characterized by quenched random Gaussian variables $\{h_α({\bf q})\}$, $α=D+1,\ldots, d$, in Fourier space with zero mean and a power law variance $\overline{ h_α({\bf q}_1) h_β({\bf q}_2) } \sim δ_{α, β} \, δ_{{\bf q}_1, -{\bf q}_2} \, q_1^{-d_h}$. The case $D=2$, $d=3$ with $d_h = 4$ could be realized by flash polymerizing lyotropic smectic liquid crystals. For $D < \max\{4, d_h\}$ the elastic constants are non-trivially renormalized and become scale dependent. Via a self consistent screening approximation we find that the renormalized bending rigidity increases for small wavevectors ${\bf q}$ as $κ_R \sim q^{-η_f}$, while the in-hyperplane elastic constants decrease according to $λ_R,\ μ_R \sim q^{+η_u}$. The quenched background metric is relevant (irelevant) for warped membranes characterized by exponent $d_h > 4 - η_f^{(F)}$ ($d_h < 4 - η_f^{(F)}$), where $η_f^{(F)}$ is the scaling exponent for tethered surfaces with a flat background metric, and the scaling exponents are related through $η_u + η_f = d_h - D$ ($η_u + 2 η_f=4-D$).

cond-mat.soft↗

arXiv2013

Spinodal decomposition in homogeneous and isotropic turbulence

We study the competition between domain coarsening in a symmetric binary mixtures below the critical temperature and turbulent fluctuations. We find that the coarsening process is arrested in presence of turbulence. The physics of the process shares remarkable similarities with the behaviour of diluted turbulent emulsions and the arrest length scale can be estimated with an argument similar to the one proposed by Kolmogorov and Hinze for the maximal stability diameter of droplets in turbulence. Although in the absence of flow the microscopic diffusion constant is negative, turbulence does effectively arrest the inverse cascade of concentration fluctuations by making the low wavelength diffusion constant positive for scales above the Hinze length.

physics.flu-dyn↗

arXiv2013

Mechanical Properties of Warped Membranes

We explore how a frozen background metric affects the mechanical properties of planar membranes with a shear modulus. We focus on a special class of "warped membranes" with a preferred random height profile characterized by random Gaussian variables $h({\bf q})$ in Fourier space with zero mean and variance $<|h({\bf q})|^2> \sim q^{-d_h}$ and show that in the linear response regime the mechanical properties depend dramatically on the system size $L$ for $d_h \ge 2$. Membranes with $d_h=4$ could be produced by flash polymerization of lyotropic smectic liquid crystals. Via a self consistent screening approximation we find that the renormalized bending rigidity increases as $κ_R \sim L^{(d_h-2)/2}$ for membranes of size $L$, while the Young and shear modulii decrease according to $Y_R,\ μ_R \sim L^{-(d_h-2)/2}$ resulting in a universal Poisson ratio. Numerical results show good agreement with analytically determined exponents.

cond-mat.soft↗

arXiv2013

Nutrient Shielding in Clusters of Cells

Cellular nutrient consumption is influenced by both the nutrient uptake kinetics of an individual cell and the cells' spatial arrangement. Large cell clusters or colonies have inhibited growth at the cluster's center due to the shielding of nutrients by the cells closer to the surface. We develop an effective medium theory that predicts a thickness $\ell$ of the outer shell of cells in the cluster that receives enough nutrient to grow. The cells are treated as partially absorbing identical spherical nutrient sinks, and we identify a dimensionless parameter $ν$ that characterizes the absorption strength of each cell. The parameter $ν$ can vary over many orders of magnitude between different cell types, ranging from bacteria and yeast to human tissue. The thickness $\ell$ decreases with increasing $ν$, increasing cell volume fraction $ϕ$, and decreasing ambient nutrient concentration $ψ_{\infty}$. The theoretical results are compared with numerical simulations and experiments. In the latter studies, colonies of budding yeast, \textit{Saccharomyces cerevisiae}, are grown on glucose media and imaged under a confocal microscope. We measure the growth inside the colonies via a fluorescent protein reporter and compare the experimental and theoretical results for the thickness $\ell$.

physics.bio-ph↗