arXiv subjects

Benjamin Allen

Publications and source records attributed to Benjamin Allen.

At least 19 recordsLinked to original sources

arXiv2026

Quantitative infrared nanoscopy: Probe-cavity eigenmodes and nano-gap polaritons for strongly coupled nanoscale optics

Optical nanoscopies including near-field optical microscopy and spectroscopy circumvent the diffraction limit of conventional optics thanks to the nanoscale light focus emerging at the apex of a sharp irradiated probe. However, while strong optical coupling between the apex and its dielectric environment affords both enhanced nanoscopic measurement sensitivity and potentially ultra-strong fields within a nano-gap cavity, the conditions for this coupling remain poorly quantified by prevailing analytic models. Here we present a robust formalism of probe-cavity eigenmodes that fully describes how mutual near-field interactions between probe and environment produce a composite response to external fields qualitatively distinct from that of its distinct components. This "EigenProbe" model identifies the fundamental excitations of realistic optical nanoscopies as nano-gap polaritons, which provide an elegant basis to accurately predict near-field microscopy and spectroscopy experiments especially when probe-sample interactions are non-perturbative. Through comparison to carefully controlled nanoscopies of polar phonons and molecular vibrations alike, we show how nano-gap polaritons are both realized and utilized for reliable and rapid "inversion" of local optical constants. This advance demands both a careful understanding of the probe response through quantitative calibration, and our efficient semi-analytic description of cavity eigenmode scattering at the probe apex. Our EigenProbe formalism sets the stage for maturing diverse and proliferating optical nanoscopies into precision metrologies of nano-scale optical environments, and guides future use of nano-gap cavities to manipulate local excitations of quantum materials and to achieve strong coupling over photonic emitters.

physics.optics↗

arXiv2025

Force chain dynamics in a quasi-static granular pile

In nature, granular materials fail in abrupt avalanches, earthquakes, and other hazardous events, and also creep over time. Proposed failure mechanisms for these systems are broadly framed as friction-limited. However, mechanical descriptions of friction in granular system vary, including those that consider the non-linear, heterogeneous dynamics of grain-contact forces. In order to study granular controls on failure and creep, we imaged contact forces between quasi-2D photoelastic discs at 15-minute intervals in experiments over weeks- to one-month-long observation periods. In the experiments, the particles are distributed in a slope below the angle of repose with a concomitant establishment of the force-chain network approximately along the principal static stress directions. The discrete force-chain shifts are initially described by an age-weakening Weibull distribution in frequency over time, with the most common clusters of events $<$1000 minutes apart, but there are long quiescent periods that are not well described by the distribution. The post-settling discrete events accompany a longer term strengthening of the localized stresses. We observe that some events may be related to 2$^o$C temperature change, but associated ground motions measured by a seismometer appear to have no correlation with particle displacements or force-chain changes. The results illustrate that local, grain-scale changes in force-chain networks can occur long after a granular pile reaches a mesoscale apparently stable state, sometimes without obvious external forcings or imposed state changes. Such force-chain dynamics may underlie transitions in natural granular systems between large-scale failures and creep events.

cond-mat.soft↗

arXiv2023

Symmetry in models of natural selection

Symmetry arguments are frequently used -- often implicitly -- in mathematical modeling of natural selection. Symmetry simplifies the analysis of models and reduces the number of distinct population states to be considered. Here, I introduce a formal definition of symmetry in mathematical models of natural selection. This definition applies to a broad class of models that satisfy a minimal set of assumptions, using a framework developed in previous works. In this framework, population structure is represented by a set of sites at which alleles can live, and transitions occur via replacement of some alleles by copies of others. A symmetry is defined as a permutation of sites that preserves probabilities of replacement and mutation. The symmetries of a given selection process form a group, which acts on population states in a way that preserves the Markov chain representing selection. Applying classical results on group actions, I formally characterize the use of symmetry to reduce the states of this Markov chain, and obtain bounds on the number of states in the reduced chain.

q-bio.PE↗

arXiv2023

Nonlinear social evolution and the emergence of collective action

Organisms from microbes to humans engage in a variety of social behaviors, which affect fitness in complex, often nonlinear ways. The question of how these behaviors evolve has consequences ranging from antibiotic resistance to human origins. However, evolution with nonlinear social interactions is challenging to model mathematically, especially in combination with spatial, group, and/or kin assortment. We derive a mathematical condition for natural selection with synergistic interactions among any number of individuals. This result applies to populations with arbitrary (but fixed) spatial or network structure, group subdivision, and/or mating patterns. In this condition, nonlinear fitness effects are ascribed to collectives, and weighted by a new measure of collective relatedness. For weak selection, this condition can be systematically evaluated by computing branch lengths of ancestral trees. We apply this condition to pairwise games between diploid relatives, and to dilemmas of collective help or harm among siblings and on spatial networks. Our work provides a rigorous basis for extending the notion of ``actor", in the study of social evolution, from individuals to collectives.

q-bio.PE↗

arXiv2022

The coalescent in finite populations with arbitrary, fixed structure

The coalescent is a stochastic process representing ancestral lineages in a population undergoing neutral genetic drift. Originally defined for a well-mixed population, the coalescent has been adapted in various ways to accommodate spatial, age, and class structure, along with other features of real-world populations. To further extend the range of population structures to which coalescent theory applies, we formulate a coalescent process for a broad class of neutral drift models with arbitrary -- but fixed -- spatial, age, sex, and class structure, haploid or diploid genetics, and any fixed mating pattern. Here, the coalescent is represented as a random sequence of mappings $\mathcal{C} = \left(C_t\right)_{t=0}^\infty$ from a finite set $G$ to itself. The set $G$ represents the ``sites'' (in individuals, in particular locations and/or classes) at which these alleles can live. The state of the coalescent, $C_t:G \to G$, maps each site $g \in G$ to the site containing $g$'s ancestor, $t$ time-steps into the past. Using this representation, we define and analyze coalescence time, coalescence branch length, mutations prior to coalescence, and stationary probabilities of identity-by-descent and identity-by-state. For low mutation, we provide a recipe for computing identity-by-descent and identity-by-state probabilities via the coalescent. Applying our results to a diploid population with arbitrary sex ratio $r$, we find that measures of genetic dissimilarity, among any set of sites, are scaled by $4r(1-r)$ relative to the even sex ratio case.

q-bio.PE↗

arXiv2019

Social goods dilemmas in heterogeneous societies

Prosocial behaviors are encountered in the donation game, the prisoner's dilemma, relaxed social dilemmas, and public goods games. Many studies assume that the population structure is homogeneous, meaning all individuals have the same number of interaction partners, or that the social good is of one particular type. Here, we explore general evolutionary dynamics for arbitrary spatial structures and social goods. We find that heterogeneous networks, wherein some individuals have many more interaction partners than others, can enhance the evolution of prosocial behaviors. However, they often accumulate most of the benefits in the hands of a few highly-connected individuals, while many others receive low or negative payoff. Surprisingly, selection can favor producers of social goods even if the total costs exceed the total benefits. In summary, heterogeneous structures have the ability to strongly promote the emergence of prosocial behaviors, but they also create the possibility of generating large inequality.

q-bio.PE↗

arXiv2019

Fixation probabilities in evolutionary dynamics under weak selection

In evolutionary dynamics, a key measure of a mutant trait's success is the probability that it takes over the population given some initial mutant-appearance distribution. This "fixation probability" is difficult to compute in general, as it depends on the mutation's effect on the organism as well as the population's spatial structure, mating patterns, and other factors. In this study, we consider weak selection, which means that the mutation's effect on the organism is small. We obtain a weak-selection perturbation expansion of a mutant's fixation probability, from an arbitrary initial configuration of mutant and resident types. Our results apply to a broad class of stochastic evolutionary models, in which the size and spatial structure are arbitrary (but fixed). The problem of whether selection favors a given trait is thereby reduced from exponential to polynomial complexity in the population size, when selection is weak. We conclude by applying these methods to obtain new results for evolutionary dynamics on graphs.

q-bio.PE↗

arXiv2019

Effective drag of a rod in fluid-saturated granular beds

We measure the drag encountered by a vertically oriented rod moving across a sedimented granular bed immersed in a fluid under steady-state conditions. At low rod speeds, the presence of the fluid leads to a lower drag because of buoyancy, whereas a significantly higher drag is observed with increasing speeds. The drag as a function of depth is observed to decrease from being quadratic at low speeds to appearing more linear at higher speeds. By scaling the drag with the average weight of the grains acting on the rod, we obtain the effective friction $\mu_e$ encountered over six orders of magnitude of speeds. While a constant $\mu_e$ is found when the grain size, rod depth and fluid viscosity are varied at low speeds, a systematic increase is observed as the speed is increased. We analyze $\mu_e$ in terms of the inertial number $I$ and viscous number $J$ to understand the relative importance of inertia and viscous forces, respectively. For sufficiently large fluid viscosities, we find that the effect of varying the speed, depth, and viscosity can be described by the empirical function $\mu_e = \mu_o + k J^n$, where $\mu_o$ is the effective friction measured in the quasi-static limit, and $k$ and $n$ are material constants. The drag is then analyzed in terms of the effective viscosity $\eta_e$ and found to decrease systematically as a function of $J$. We further show that $\eta_e$ as a function of $J$ is directly proportional to the fluid viscosity and the $\mu_e$ encountered by the rod.

cond-mat.soft↗

arXiv2019

Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs

The spatial structure of an evolving population affects which mutations become fixed. Some structures amplify selection, increasing the likelihood that beneficial mutations become fixed while deleterious mutations do not. Other structures suppress selection, reducing the effect of fitness differences and increasing the role of random chance. This phenomenon can be modeled by representing spatial structure as a graph, with individuals occupying vertices. Births and deaths occur stochastically, according to a specified update rule. We study death-Birth updating: An individual is chosen to die and then its neighbors compete to reproduce into the vacant spot. Previous numerical experiments suggested that amplifiers of selection for this process are either rare or nonexistent. We introduce a perturbative method for this problem for weak selection regime, meaning that mutations have small fitness effects. We show that fixation probability under weak selection can be calculated in terms of the coalescence times of random walks. This result leads naturally to a new definition of effective population size. Using this and other methods, we uncover the first known examples of transient amplifiers of selection (graphs that amplify selection for a particular range of fitness values) for the death-Birth process. We also exhibit new families of "reducers of fixation", which decrease the fixation probability of all mutations, whether beneficial or deleterious.

q-bio.PE↗

arXiv2019

Evolutionary Games on Isothermal Graphs

Population structure affects the outcome of natural selection. Static population structures can be described by graphs, where individuals occupy the nodes, and interactions occur along the edges. General conditions for evolutionary success on any weighted graph were recently derived, for weak selection, in terms of coalescence times of random walks. Here we show that for a special class of graphs, the conditions for success take a particularly simple form, in which all effects of graph structure are described by the graph's "effective degree"---a measure of the effective number of neighbors per individual. This result holds for all weighted graphs that are isothermal, meaning that the sum of edge weights is the same at each node. Isothermal graphs encompass a wide variety of underlying topologies, and arise naturally from supposing that each individual devotes the same amount of time to interaction. Cooperative behavior is favored on a large isothermal graph if the benefit-to-cost ratio exceeds the effective degree. We relate the effective degree of a graph to its spectral gap, thereby providing a link between evolutionary dynamics and the theory of expander graphs. As a surprising example, we report graphs of infinite average degree that are nonetheless highly conducive for promoting cooperation.

q-bio.PE↗

arXiv2018

Stationary frequencies and mixing times for neutral drift processes with spatial structure

We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types ("traits"), which can be discrete or continuous. Under minimal assumptions, we show that the marginal trait distributions of the evolutionary process, which specify the probability that any given individual has a certain trait, all converge to the stationary distribution of the mutation process. In particular, the stationary frequencies of traits in the population are independent of its size, spatial structure, and evolutionary update rule, and these frequencies can be calculated by evaluating a simple stochastic process describing a population of size one (i.e. the mutation process itself). We conclude by analyzing mixing times, which characterize rates of convergence of the mutation process along the lineages, in terms of demographic variables of the evolutionary process.

q-bio.PE↗

arXiv2018

Evolution of Cooperation on Stochastic Block Models

Cooperation is a major factor in the evolution of human societies. The structure of human social networks, which affects the dynamics of cooperation and other interpersonal phenomena, have common structural signatures. One of these signatures is the tendency to organize as groups. Among the generative models that network theorists use to emulate this feature is the Stochastic Block Model (SBM). In this paper, we study evolutionary game dynamics on SBM networks. Using a recently-discovered duality between evolutionary games and coalescing random walks, we obtain analytical conditions such that natural selection favors cooperation over defection. We calculate the transition point for each community to favor cooperation. We find that a critical inter-community link creation probability exists for given group density, such that the overall network supports cooperation even if individual communities inhibit it. As a byproduct, we present mean-field solutions for the critical benefit-to-cost ratio which perform with remarkable accuracy for diverse generative network models, including those with community structure and heavy-tailed degree distributions. We also demonstrate the generalizability of the results to arbitrary two-player games.

cs.SI↗

arXiv2018

A mathematical formalism for natural selection with arbitrary spatial and genetic structure

We define a general class of models representing natural selection between two alleles. The population size and spatial structure are arbitrary, but fixed. Genetics can be haploid, diploid, or otherwise; reproduction can be asexual or sexual. Biological events (e.g.~births, deaths, mating, dispersal) depend in arbitrary fashion on the current population state. Our formalism is based on the idea of genetic sites. Each genetic site resides at a particular locus and houses a single allele. Each individual contains a number of sites equal to its ploidy (one for haploids, two for diploids, etc.). Selection occurs via replacement events, in which alleles in some sites are replaced by copies of others. Replacement events depend stochastically on the population state, leading to a Markov chain representation of natural selection. Within this formalism, we define reproductive value, fitness, neutral drift, and fixation probability, and prove relationships among them. We identify four criteria for evaluating which allele is selected and show that these become equivalent in the limit of low mutation. We then formalize the method of weak selection. The power of our formalism is illustrated with applications to evolutionary games on graphs and to selection in a haplodiploid population.

q-bio.PE↗

arXiv2018

Conjoining uncooperative societies facilitates evolution of cooperation

Social structure affects the emergence and maintenance of cooperation. Here we study the evolutionary dynamics of cooperation in fragmented societies, and show that conjoining segregated cooperation-inhibiting groups, if done properly, rescues the fate of collective cooperation. We highlight the essential role of inter-group ties, that sew the patches of the social network together and facilitate cooperation. We point out several examples of this phenomenon in actual settings. We explore random and non-random graphs, as well as empirical networks. In many cases we find a marked reduction of the critical benefit-to-cost ratio needed for sustaining cooperation. Our finding gives hope that the increasing worldwide connectivity, if managed properly, can promote global cooperation.

cs.SI↗

arXiv2018

Granular bed consolidation, creep and armoring under subcritical fluid flow

We show that a freshly sedimented granular bed settles and creeps forward over extended periods of time under an applied hydrodynamic shear stress, which is below the critical value for bedload transport. The rearrangements are found to last over a time scale which is millions of times the sedimentation time scale of a grain in the fluid. Compaction occurs uniformly throughout the bed, but creep is observed to decay exponentially with depth, and decreases over time. The granular volume fraction in the bed is found to increase logarithmically, saturating at the random close packing value $\phi_{rcp} \approx 0.64$, while the surface roughness is observed to remain essentially unchanged. We demonstrate that an increasingly higher shear stress is required to erode the bed after a sub-critical shear is applied which results in an increase in its volume fraction. Thus, we find that bed armoring occurs due to a deep shear-induced relaxation of the bed towards the volume fraction associated with the glass transition.

cond-mat.soft↗

arXiv2018

Testing constitutive relations by running and walking on cornstarch and water suspensions

The ability of a person to run on the surface of a suspension of cornstarch and water has fascinated scientists and the public alike. However, the constitutive relation obtained from traditional steady-state rheology of cornstarch and water suspensions has failed to explain this behavior. In a previous paper, we presented an averaged constitutive relation for impact rheology consisting of an effective compressive modulus of a system-spanning dynamically jammed structure (arXiv:1407:0719). Here, we show that this constitutive model can be used to quantitatively predict, for example, the trajectory and penetration depth of the foot of a person walking or running on cornstarch and water. The ability of the constitutive relation to predict the material behavior in a case with different forcing conditions and flow geometry than it was obtained from suggests that the constitutive relation could be applied more generally. We also present a detailed calculation of the added mass effect to show that while it may be able to explain some cases of people running or walking on the surface of cornstarch and water for pool depths $H >1.2$ m and foot impact velocities $V_I> 1.7$ m/s, it cannot explain observations of people walking or running on the surface of cornstarch and water for smaller $H$ or $V_I$.

cond-mat.soft↗

arXiv2017

System-spanning dynamically jammed region in response to impact of cornstarch and water suspensions

We experimentally characterize the impact response of concentrated suspensions of cornstarch and water. We hypothesize that the dynamically jammed region that propagates ahead of the impactor is responsible for the strong stress response to impact when it spans between solid boundaries. Using surface imaging and particle tracking at the boundary opposite the impactor, we observed that a visible structure and particle flow at the boundary occur with a delay after impact. We show the delay time is about the same time as the the strong stress response, confirming that the strong stress response results from deformation of the dynamically jammed structure once it spans between the impactor and a solid boundary. A characterization of this strong stress response is reported in a companion paper (arXiv:1407.0719). We also elaborate on the structure of the dynamically jammed region once it spans from the impactor to a solid boundary. We observed particle flow in the outer part of the dynamically jammed region at the bottom boundary, with a net transverse displacement of up to about 5\% of the impactor displacement, indicating shear at the boundary. Direct imaging of the surface of the outer part of the dynamically jammed region reveals a change in surface structure that appears the same as the result of dilation in other cornstarch suspensions. Imaging also reveals cracks, like a brittle solid. These observations suggest the dynamically jammed structure can temporarily support stress according to an effective modulus, like a soil or dense granular material, along a network of frictional contacts between the impactor and solid boundary.

cond-mat.soft↗

arXiv2017

Programmable Molecular Composites of Tandem Proteins with Graphene-Oxide for Efficient Bimoprh Actuators

The rapid expansion in the spectrum of two-dimensional (2D) materials has driven the efforts of research on the fabrication of 2D composites and heterostructures. Highly ordered structure of 2D materials provides an excellent platform for controlling the ultimate structure and properties of the composite material with precision. However, limited control over the structure of the adherent material and its interactions with highly ordered 2D materials results in defective composites with inferior performance. Here, we demonstrate the successful synthesis, integration, and characterization of hybrid 2D material systems consisting of tandem repeat (TR) proteins inspired by squid ring teeth and graphene oxide (GO). The TR protein layer acts as a unique programmable molecular spacer between GO layers. As an application, we further demonstrate thermal actuation using bimorph molecular composite films. Bimorph actuators made of molecular composite films (GO/TR) can lead to energy efficiencies 18 times higher than regular bimorph actuators consisting of a GO layer and a TR protein layer (i.e., conventional bulk composite of GO and TR). Additionally, molecular composite bimorph actuators can reach curvature values as high as 1.2 cm-1 by using TR proteins with higher molecular weight, which is 3 times higher than conventional GO and TR composites.

cond-mat.soft↗